new_module_template()
#> $mc
#> $mc$source
-#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/ZZ_module_components.R"
+#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/Rtmp3aSrsm/temp_libpath34c0767d3be3/formods/templates/ZZ_module_components.R"
#>
#> $mc$dest
#> [1] "NM_module_components.R"
#>
#> $mc$dest_full
-#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/NM_module_components.R"
+#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpR2lepg/NM_module_components.R"
#>
#>
#> $server
#> $server$source
-#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/ZZ_Server.R"
+#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/Rtmp3aSrsm/temp_libpath34c0767d3be3/formods/templates/ZZ_Server.R"
#>
#> $server$dest
#> [1] "NM_Server.R"
#>
#> $server$dest_full
-#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/NM_Server.R"
+#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpR2lepg/NM_Server.R"
#>
#>
#> $yaml
#> $yaml$source
-#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/ZZ.yaml"
+#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/Rtmp3aSrsm/temp_libpath34c0767d3be3/formods/templates/ZZ.yaml"
#>
#> $yaml$dest
#> [1] "NM.yaml"
#>
#> $yaml$dest_full
-#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/NM.yaml"
+#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpR2lepg/NM.yaml"
#>
#>
#> $funcs
#> $funcs$source
-#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/ZZ_funcs.R"
+#> [1] "/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/Rtmp3aSrsm/temp_libpath34c0767d3be3/formods/templates/ZZ_funcs.R"
#>
#> $funcs$dest
#> [1] "NM_funcs.R"
#>
#> $funcs$dest_full
-#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/NM_funcs.R"
+#> [1] "/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpR2lepg/NM_funcs.R"
#>
#>
diff --git a/docs/search.json b/docs/search.json
index b661576..b9c1e55 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"/articles/included_modules.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Included Modules","text":"ever make Shiny app think: Didn’t just stuff last week? creating data upload forms generating UI building ggplot figures certain components use apps. purpose formods create customizable Shiny modules allow many components created quickly can focus part app unique interesting. modules formods generates code dynamically produce underlying outputs. allows modules combined framework generate code allows state apps reproduced single script.","code":""},{"path":"/articles/included_modules.html","id":"implementation","dir":"Articles","previous_headings":"Introduction","what":"Implementation","title":"Included Modules","text":"module short name used functions namespaces. example upload data module use UD. use module need create appropriate UI elements well call module server. high level formods components individual modules configured YAML configuration files.","code":""},{"path":"/articles/included_modules.html","id":"avialable-modules","dir":"Articles","previous_headings":"","what":"Avialable modules","title":"Included Modules","text":"currently available modules listed table . SN column contains short name used identify module. individual HTML UI elements listed well UI outputs. Module SN htmlOutput Outputs App State Mangement ASM ui_asm_save_name, ui_asm_save_button, ui_asm_load_state ui_asm_msg, ui_asm_ace_code Upload Data UD ui_ud_load_data, ui_ud_select_sheets, ui_ud_text_load_result, ui_ud_data_preview ui_ud_ace_code Data Wrangling DW ui_dw_views, ui_dw_key, ui_dw_new_view, ui_dw_save_view, ui_dw_del_view, ui_dw_copy_view, ui_dw_add_element_button, ui_dw_select, ui_dw_new_element_row hot_dw_elements, hot_data_preview, ui_dw_msg, ui_dw_code Figure Generation FG ui_fg_curr_views, ui_fg_curr_figs, ui_fg_new_fig, ui_fg_save_fig, ui_fg_del_fig, ui_fg_copy_fig, ui_fg_fig_name, ui_fg_fig_notes, ui_fg_add_element_button, ui_fg_select, ui_fg_new_element_row, ui_fg_msg, ui_fg_slider_page hot_fg_elements, ui_fg_preview_ggplot, ui_fg_msg, ui_fg_code","code":""},{"path":"/articles/included_modules.html","id":"using-a-module","dir":"Articles","previous_headings":"Avialable modules","what":"Using a module","title":"Included Modules","text":"Using module requires two components: need add UI elements module, need add server component well. Take care use id UI server components. UI elements listed table . Also module formods contains example App file isolates UI component allow see ’s used. called XX_module_components.R, XX module short name. example see example upload data module run following copy file locally: want run App within package can just following:","code":"copy.file(system.file(package=\"formods\", \"templates\", \"UD_module_components.R\"), \"UD_module_components.R\") runApp(system.file(package=\"formods\", \"templates\", \"UD_module_components.R\"))"},{"path":"/articles/included_modules.html","id":"compact-ui-elements","dir":"Articles","previous_headings":"Avialable modules > Using a module","what":"Compact UI elements","title":"Included Modules","text":"Using module components script , can see whate UI element looks like behaves. allows granular control UI elements placement. module, formods provides single ui output place module UI components together. upload data module looks like : copy FM_compact.R file locally, can see used module: can run example see modules interact well:","code":"htmlOutput(NS(\"UD\", \"ui_ud_compact\")) copy.file(system.file(package=\"formods\", \"templates\", \"FM_compact.R\"), \"FM_compact.R\") runApp(system.file(package=\"formods\", \"templates\", \"FM_compact.R\"))"},{"path":"/articles/included_modules.html","id":"deployment","dir":"Articles","previous_headings":"Avialable modules > Using a module","what":"Deployment","title":"Included Modules","text":"deploy App need create App file appropriate ui server functions called App.R. create one : certain aspects app behave differently deployed. need indicate app deployed. can two ways. done setting deployed argument server functions TRUE.","code":"file.copy(from = system.file(package=\"formods\", \"templates\", \"FM_compact.R\"), to = \"App.R\")"},{"path":"/articles/included_modules.html","id":"server-functions","dir":"Articles","previous_headings":"Avialable modules > Using a module","what":"Server functions","title":"Included Modules","text":"module server function uses shortname followed underscore prefix. example server function named using convention: XX_Server(). XX module short name. example server function upload data module UD_Server(). minimum server take module ID, configuration file formods package, module configuration file, reactive object called react_state. react_state object used link reactions modules. different XX_module_components.R files shows use server functions module. Briefly, using UD module example following app server function:","code":"server <- function(input, output, session) { react_FM = reactiveValues() # Module server UD_Server(id=\"UD\", react_state=react_FM) }"},{"path":"/articles/included_modules.html","id":"yaml-configuration-files","dir":"Articles","previous_headings":"Avialable modules > Using a module","what":"YAML configuration files","title":"Included Modules","text":"formods individual modules configured YAML files. default, modules use included template YAML files. However, may want alter default formatting text. simply need make local copies files like : can modify files. use need point server functions instead default templates. following sections describe current modules use .","code":"copy.file(system.file(package=\"formods\", \"templates\", \"formods.yaml\"), \"formods.yaml\") copy.file(system.file(package=\"formods\", \"templates\", \"UD.yaml\"), \"UD.yaml\")"},{"path":"/articles/included_modules.html","id":"app-state-management-asm","dir":"Articles","previous_headings":"Avialable modules","what":"App State Management (ASM)","title":"Included Modules","text":"ASM module used manage app state. allows user save current app state load later time.","code":""},{"path":"/articles/included_modules.html","id":"upload-data-ud","dir":"Articles","previous_headings":"Avialable modules","what":"Upload Data (UD)","title":"Included Modules","text":"UD module allows users upload data files App. allow specify file types Excel files sheet used. Provides Data sets via: FM_fetch_ds()","code":""},{"path":"/articles/included_modules.html","id":"data-wrangling-dw","dir":"Articles","previous_headings":"Avialable modules","what":"Data Wrangling (DW)","title":"Included Modules","text":"DW module provides interface dplyr tidyr.used create chains data wrangling commands user can build transform data creating data views. DW module can use data UD module, can take list dataset. Provides Data views via: FM_fetch_ds() Reporting data views (Excel)","code":""},{"path":"/articles/included_modules.html","id":"figure-generation-fg","dir":"Articles","previous_headings":"Avialable modules","what":"Figure Generation (FG)","title":"Included Modules","text":"FG module provides interface ggplot allows user select original data set UD module well data views created DW module. user can create multiple figures. Provides Reporting figures (PowerPoint Word)","code":""},{"path":[]},{"path":"/articles/included_modules.html","id":"request-entity-too-large-","dir":"Articles","previous_headings":"Known Issues","what":"413 Request Entity too large.","title":"Included Modules","text":"running RStudio server (web browser) receive following message: 413 Request Entity large. problem lies NGINX server. proxy server used RStudio. issue limit maximum upload size NGINX server. solution edit configuration file (something like /etc/nginx/nginx.conf) set option client_mx_body_size something reasonable.","code":""},{"path":[]},{"path":"/articles/making_modules.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Making Modules","text":"vignette provide overview formods framework creating reproducable modules interact . module namespace mantained using module short name prefix functions. example figure generation module uses FG. want create module, please submit issue formods github repository following information: short name intend use brief description module list modules depends ","code":""},{"path":"/articles/making_modules.html","id":"current-modules","dir":"Articles","previous_headings":"Introduction","what":"Current modules","title":"Making Modules","text":"ASM - App State Management DW - Data Wrangling FG - Figure Generation FM - Formods UD - Upload Data MC - reserved word current modules development: NCA - Non-Compartmental Analysis MB - Model Builder","code":""},{"path":"/articles/making_modules.html","id":"formods-framework","dir":"Articles","previous_headings":"","what":"formods framework","title":"Making Modules","text":"get started need create template files. example assumes creating module package called mypackage running command git repository. Say module used produce widgets, short name MM stands Module: MM_module_components.R - app can used testing module highlighting different UI elements used within module (found inst/templates). MM_Server.R: bare bones file containing expected functions minimal inputs. (found R). MM.yaml: module configuration file contains minimal elements expected, can add fields suit modules needs (found inst/templates). MM_funcs.R: script contains example code different elements module can used function examples also quickly test different module functions develop (found inst/test_apps).","code":"use_formods(SN = \"MM\", Module_Name = \"My Module\", element = \"widgets\", package = \"mypackage\")"},{"path":"/articles/making_modules.html","id":"expected-functions","dir":"Articles","previous_headings":"","what":"Expected functions","title":"Making Modules","text":"module template create standard set functions . MM replaced whatever short name choose create templates. functions can customized specific module. optional can deleted. example MM_fetch_ds function needed module creates datasets provides modules use (like DW module exports data views used modules). modules designed create elements. example DW module creates data view elements, FG module used create figure elements, etc. MM_Server Shiny server function. MM_init_state Creates empty formods state module. MM_fetch_state module function fetch state. Within function interactivity. access elements Shiny input isolated. Based differences input elements (current state app) stored app state can used trigger different things. MM_fetch_code takes ’s first argument module state. called argument return character object containing code needed generate elements module represented app. can assume modules one depends defined previously. example FG module return code associated generating figures. appended code UD DW modules define loading dataset creation data views. modules code generated (e.g. ASM) just return NULL. MM_append_report module generates reportable outputs, function used append outputs overall reports generated formods. hasds Boolean variable indicating modules currently exportable datasets. isgood General return status funciton. Set FALSE errors encoutered. msgs character vector messages pass back user. label Text label dataset MOD_TYPE Short name type module. id module ID. DS Dataframe containing actual dataset. DSMETA Metadata describing DS. code Complete code build dataset. checksum Module checksum. DSchecksum Dataset checksum. hasmdl Boolean variable indicating modules currently exportable models. isgood General return status funciton. Set FALSE errors encountered. msgs character vector messages pass back user. label Text label model. MOD_TYPE Short name type module. id module ID. rx_obj rxode2 object holds model. rx_obj_name rxode2 object name generated code. fcn_def Text define model DSMETA Verbose metadata describing model. code Complete code build model. checksum Checksum module model came . DSchecksum Checksum model. isgood Boolean indicating exit status function. session value Shiny session variable (app) list (outside app) initialization. input value shiny input end session initialization. state App state. rsc react_state components. MM_new_element Creates new module element. MM_fetch_current_element Extracts current element state object. MM_set_current_element Sets current element provided value. MM_del_element Deletes current active element.","code":""},{"path":"/articles/making_modules.html","id":"expected-ui-components","dir":"Articles","previous_headings":"","what":"Expected UI components","title":"Making Modules","text":"ui_mm_compact UI output contains compact view module can called main ui functions App. composed individual UI elements shown MM_module_components.R file. allows user quick way utilize model (using ui_mm_compact), ability customize module UI manually arranging pieces found MM_module_components.R.","code":""},{"path":"/articles/making_modules.html","id":"module-interaction","dir":"Articles","previous_headings":"","what":"Module interaction","title":"Making Modules","text":"Say using UD module feed data DW module user goes back upload form uploads different data set. need trigger reset Data Wrangling module well tell larger app something changed.","code":""},{"path":"/articles/making_modules.html","id":"module-state-and-reacting-to-changes","dir":"Articles","previous_headings":"Module interaction","what":"Module state and reacting to changes","title":"Making Modules","text":"Changes module states detected react_state object. given module type \"MM\" module id \"ID\" detect changes reacting react_state[[\"ID\"]] looking changes checksum element : react_state[[\"ID\"]][[\"MM\"]][[\"checksum\"]] checksum checksum can used detect changes module. example UD module change uploaded file sheet selected currently uplo:waded file changes.","code":""},{"path":"/articles/making_modules.html","id":"helper-functions-in-formods","dir":"Articles","previous_headings":"","what":"Helper functions in formods","title":"Making Modules","text":"FM_le() - Creates log entries (le) displayed console. FM_tc() - can used evaluate code, trap errors, process results. has_changed() set_hold() - Used set hold one UI elements. prevents internal updating UI element based current value App. fetch_hold() - retrieve hold status UI element. remove_hold() - remove holds set UI element. ‘FM_build_comment()’ - creates comments strings form sections viewed RStudio. FM_add_ui_tooltip() - Attaches tooltip UI element. FM_init_state() - Called top module state initialization function create skeleton module state can build upon. FM_set_notification() - Within code can create notifications attach module state. FM_notify() - Used observeEvent() show notifications yet displayed. FM_set_mod_state() FM_fetch_mod_state() FM_set_ui_msg() FM_pretty_sort() - Used general sorting function try make sorted results prettier. FM_pause_screen() - Pauses screen something server side takes . FM_resume_screen() - Resumes activity (unpauses screen) ’re done pause. FM_fetch_data_format() - Creates formatting information display given data frame. examples require Shiny session variable formods state object. create examples objects needed demonstrate functions .","code":"library(formods) # This creates the state and session objects sess_res = UD_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 state = sess_res$state session = sess_res$session # Here we load an example dataset into the df object. data_file_local = system.file(package=\"formods\", \"test_data\", \"TEST_DATA.xlsx\") sheet = \"DATA\" df = readxl::read_excel(path=data_file_local, sheet=sheet)"},{"path":"/articles/making_modules.html","id":"setting-holds-on-ui-elements","dir":"Articles","previous_headings":"Helper functions in formods","what":"Setting holds on UI elements","title":"Making Modules","text":"mechanics fetch state functions mean time fetch state called, UI elements App pulled placed app state. generally works well exceptions. main exception want UI element changes another UI element. Say example selection box UI id my_selection. want selection alter text input id my_text. However just poll ui elements may update my_text based changes my_selection overwritten current value my_text. prevent , need two things: processing my_selection need set hold my_text (done set_hold()). processing my_text need hold set. checked fetch_hold() Lastly need remove hold. done UI refreshed new text value populated my_text (appropriate reactions set). done observeEvent triggered everything else (priority -100 ): remove_hold_listen object contain inputs create holds.","code":"remove_hold_listen <- reactive({ list(input$my_selection) }) observeEvent(remove_hold_listen(), { # Once the UI has been regenerated we # remove any holds for this module state = MM_fetch_state(id = id, input = input, session = session, FM_yaml_file = FM_yaml_file, MOD_yaml_file = MOD_yaml_file, react_state = react_state) FM_le(state, \"removing holds\") # Removing all holds for(hname in names(state[[\"MM\"]][[\"ui_hold\"]])){ remove_hold(state, session, hname) } }, priority = -100)"},{"path":"/articles/making_modules.html","id":"dataframe-formatting-information","dir":"Articles","previous_headings":"Helper functions in formods","what":"Dataframe formatting information","title":"Making Modules","text":"want tables pulldown menues based types data column can use FM_fetch_data_format() function. custom headers can used rhandsontable package. add subtext selection widget Shiny need use shinyWidgets package. alter formats shown need edit formods.yaml configuration file look FM\\(\\rightarrow\\)data_meta section.","code":"hfmt = FM_fetch_data_format(df, state) # Descriptive headers head(as.vector(unlist( hfmt[[\"col_heads\"]]))) #> [1] \"ID<\/b>
num<\/font><\/span>\" #> [2] \"TIME_DY<\/b>
num<\/font><\/span>\" #> [3] \"TIME_HR<\/b>
num<\/font><\/span>\" #> [4] \"NTIME_DY<\/b>
num<\/font><\/span>\" #> [5] \"NTIME_HR<\/b>
num<\/font><\/span>\" #> [6] \"TIME<\/b>
num<\/font><\/span>\" # Subtext head(as.vector(unlist( hfmt[[\"col_subtext\"]]))) #> [1] \"num: 1,⋅⋅⋅,360\" \"num: 0,⋅⋅⋅,84\" \"num: 0,⋅⋅⋅,2016\" \"num: 0,⋅⋅⋅,42\" #> [5] \"num: 0,⋅⋅⋅,1008\" \"num: 0,⋅⋅⋅,2016\" hot = rhandsontable::rhandsontable( head(df), width = \"100%\", height = \"100%\", colHeaders = as.vector(unlist(hfmt[[\"col_heads\"]])), rowHeaders = NULL ) sel_subtext = as.vector(unlist( hfmt[[\"col_subtext\"]])) library(shinyWidgets) shinyWidgets::pickerInput( inputId = \"select_example\", choices = names(df), label = \"Select with subtext\", choicesOpt = list(subtext = sel_subtext))"},{"path":"/articles/making_modules.html","id":"notifications","dir":"Articles","previous_headings":"Helper functions in formods","what":"Notifications","title":"Making Modules","text":"Notifications created using shinybusy package produced two different functions: FM_set_notification() FM_notify(). done centralized fashion notifications added state object user information processed. set notification called Example Notification. Along timestamp set: timestamp used track prevent notification shown multiple times. Next need setup reactions display notifications. can create reactive expression inputs lead notification: Next use observeEvent() reactive expression trigger notifications. need use fetch state function molecule get state object notifications. FM_notify() called unprocessed notifications displayed:","code":"state = FM_set_notification(state, \"Something happened\", \"Example Notification\") toNotify <- reactive({ list(input$input1, input$input2) }) observeEvent(toNotify(), { state = MM_fetch_state(id = id, input = input, session = session, FM_yaml_file = FM_yaml_file, MOD_yaml_file = MOD_yaml_file, react_state = react_state) # Triggering optional notifications notify_res = FM_notify(state = state, session = session) })"},{"path":"/articles/making_modules.html","id":"adding-tooltips","dir":"Articles","previous_headings":"Helper functions in formods","what":"Adding tooltips","title":"Making Modules","text":"Tooltips created interally using suggested prompter package. add tool tip ui element use FM_add_ui_tooltip() function. example add tool tip, need type harder! text input following:","code":"uiele = shiny::textInput( inputId = \"some_text\", label = \"You need to type harder!\") uiele = FM_add_ui_tooltip(state, uiele, tooltip = \"This is a tooltip\", position = \"left\")"},{"path":"/articles/making_modules.html","id":"pausing-the-screen","dir":"Articles","previous_headings":"Helper functions in formods","what":"Pausing the screen","title":"Making Modules","text":"pause screen shinybusy package also used. controlled two functions: FM_pause_screen() used pause screen /update pause message, FM_resume_screen() used end pause resume interaction user.","code":"FM_pause_screen(state, session) FM_resume_screen(state, session)"},{"path":"/articles/making_modules.html","id":"formods-state-objects","dir":"Articles","previous_headings":"","what":"formods state objects","title":"Making Modules","text":"create formods state object can following fields: yaml- Contents formods configuration file. MC - Contents module configuration file. MM - MM short name current module. MOD_TYPE ), store app information. (see ). MOD_TYPE - Short name module. id - ID module. FM_yaml_file - formods configuration file. MOD_yaml_file - Module configuration file. notifications - Contains notifications set user FM_set_notification().","code":""},{"path":"/articles/making_modules.html","id":"app-information-in-mm","dir":"Articles","previous_headings":"formods state objects","what":"App information in MM","title":"Making Modules","text":"field state$MM relatively free form reserved elements. reserved keyword : button_counters - Counter tracks button clicks ui_hold - List hold elements populated set_hold() isgood - Boolean variable indicating state module. ui_msg - Messaages returned UI captured errors populated FM_set_ui_msg() fields can store whatever else need module.","code":""},{"path":[]},{"path":"/articles/making_modules.html","id":"yaml-configuration-files","dir":"Articles","previous_headings":"","what":"YAML configuration files","title":"Making Modules","text":"","code":"# https://www.glyphicons.com/sets/basic/ #General formods (FM) configuration across modules FM: include: files: - file: source: 'file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\")' dest: 'file.path(\"config\",\"report.docx\")' - file: source: 'file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\")' dest: 'file.path(\"config\",\"report.pptx\")' - file: source: 'file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\")' dest: 'file.path(\"config\",\"report.yaml\")' # Some features (e.g. copy to clipboard) don't work when deployed deployed: FALSE #General code options for the modules code: theme: \"vibrant_ink\" showLineNumbers: TRUE # File name of the R script to contain generation code gen_file: run_analysis.R # This is the preamble used in script generation. It goes on the # top. Feel free to add to it if you need to. Note that packages should be # listed in the packages section at the same level. gen_preamble: |- # formods automated output ------------------------------------------------ # https://formods.ubiquity.tools/ rm(list=ls()) # Each module should have a packages section that lists the packages # needed for code genereated for that module. packages: [\"onbrand\", \"writexl\"] notifications: config: # You can put any arguments here that would be arguments for # config_notify(). See ?shinybusy::config_notify() for more information success: useFontAwesome: FALSE useIcon: FALSE background: \"#5bb85b\" failure: useFontAwesome: FALSE useIcon: FALSE background: \"#d9534f\" info: useFontAwesome: FALSE useIcon: FALSE background: \"#5bc0de\" warning: useFontAwesome: FALSE useIcon: FALSE background: \"#f0ac4d\" reporting: # enabled here controls reporting for the app. Individual modules can be # controlled in their respective configuration files enabled: TRUE # The content_init section is used to initialize reports. You shouldn't # change the xlsx rpt but the docx and pptx rpt can be altered to # use custom onbrand templates. The main thing is that you create an # object called rpt with the appropriate template type in it. You can # also do any preprocessing here as well such as adding default content or # doing any placeholder assignments you might want to use. The paths can # be absolute paths. If relative paths are used they will be relative to # the user directory (either the temp formods directory running in shiny # or the top level of the zip file structure when saving the app state). content_init: xlsx: |- rpt = list(summary = NULL, sheets = list()) docx: |- rpt = onbrand::read_template( template = file.path(\"config\", \"report.docx\"), mapping = file.path(\"config\", \"report.yaml\")) pptx: |- rpt = onbrand::read_template( template = file.path(\"config\", \"report.pptx\"), mapping = file.path(\"config\", \"report.yaml\")) ui: # See ?actionBttn for styles button_style: \"fill\" # Max size for picker inputs select_size: 10 color_green: \"#00BB8A\" color_red: \"#FF475E\" color_blue: \"#0088FF\" color_purple: \"#bd2cf4\" data_meta: # This controls the overall format of headers and the select subtext for # data frames with the following placeholders surrouned by ===: # COLOR - font color # NAME - colum name # LABEL - type label # RANGE - this depends on the nature of the data in the column: # - If there are between 1 and 3 values then those values are shown. # - If there are more than 3 values then the min and max are show. data_header: \"===NAME===<\/b>
===LABEL===<\/font><\/span>\" subtext: \"===LABEL===: ===RANGE===\" # Separator when showing more than three in a column. For exmaple if you # had a dataset with 1,2,3,4,5,6 and many_sep was \",...,\" then it would # appear as \"1,...,6\" many_sep: \",⋅⋅⋅,\" # This controls the differences for different data types. Take the output # of typeof(df$colname) and put an entry for that output here. data_types: character: color: \"#DD4B39\" label: \"text\" double: color: \"#3C8DBC\" label: \"num\" integer: color: \"#3C8DBC\" label: \"num\" other: color: \"black\" label: \"other\" labels: # JMH remove this once the datset stuff has been moved over default_ds: \"Original data set\" user_files: use_tmpdir: TRUE logging: enabled: TRUE timestamp: TRUE timestamp_fmt: \"%Y-%m-%d %H:%M:%S\" log_file: \"formods_log.txt\" console: TRUE"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Harrold. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Harrold J (2024). formods: 'Shiny' Modules General Tasks. R package version 0.1.4, https://formods.ubiquity.tools/.","code":"@Manual{, title = {formods: 'Shiny' Modules for General Tasks}, author = {John Harrold}, year = {2024}, note = {R package version 0.1.4}, url = {https://formods.ubiquity.tools/}, }"},{"path":"/index.html","id":"formods-","dir":"","previous_headings":"","what":"Shiny Modules for General Tasks","title":"Shiny Modules for General Tasks","text":"Shiny apps can often make use key elements, formods provides modules common tasks (data upload, wragling data, figure genration saving app state). modules can react interact well generate code create reproducable analyses. formods also defines framework creating reactive modules. vignettes outline use modules well create modules within framework.","code":""},{"path":[]},{"path":"/index.html","id":"from-cran","dir":"","previous_headings":"","what":"From CRAN","title":"Shiny Modules for General Tasks","text":"can install released version formods CRAN :","code":"install.packages(\"formods\")"},{"path":"/index.html","id":"development-version","dir":"","previous_headings":"","what":"Development version","title":"Shiny Modules for General Tasks","text":"can install development version GitHub : Note formods depends onbrand need first install development version onbrand.","code":"# Installing devtools if it's not already installed if(system.file(package=\"devtools\") == \"\"){ install.packages(\"devtools\") } devtools::install_github(\"john-harrold/onbrand\", dependencies=TRUE) devtools::install_github(\"john-harrold/formods\", dependencies=TRUE)"},{"path":"/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Shiny Modules for General Tasks","text":"","code":"library(shiny) library(formods) runApp(system.file(package=\"formods\", \"templates\",\"FM_compact.R\"))"},{"path":"/reference/ASM_Server.html","id":null,"dir":"Reference","previous_headings":"","what":"Save State Server — ASM_Server","title":"Save State Server — ASM_Server","text":"Server function Save State Shiny Module","code":""},{"path":"/reference/ASM_Server.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Save State Server — ASM_Server","text":"","code":"ASM_Server( id, FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"ASM.yaml\"), deployed = FALSE, react_state = NULL, mod_ids )"},{"path":"/reference/ASM_Server.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Save State Server — ASM_Server","text":"id ID string corresponds ID used call modules UI elements FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. deployed Boolean variable indicating whether app deployed . react_state Variable passed server allow reaction outside module (NULL) mod_ids Vector module IDs order needed (used code generation).","code":""},{"path":"/reference/ASM_Server.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Save State Server — ASM_Server","text":"UD Server object","code":""},{"path":"/reference/ASM_Server.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Save State Server — ASM_Server","text":"","code":"if(interactive()){ # These are suggested packages library(shinydashboard) library(ggpubr) library(plotly) library(shinybusy) library(prompter) library(utils) library(clipr) library(formods) CSS <- \" .wrapfig { float: right; shape-margin: 20px; margin-right: 20px; margin-bottom: 20px; } \" # Default to not deployed if(!exists(\"deployed\")){ deployed = FALSE } #https://fontawesome.com/icons?from=io data_url = \"https://github.com/john-harrold/formods/raw/master/inst/test_data/TEST_DATA.xlsx\" ui <- dashboardPage( skin=\"black\", dashboardHeader(title=\"formods\"), dashboardSidebar( sidebarMenu( menuItem(\"Source Data\", tabName=\"upload\", icon=icon(\"table\")) , menuItem(\"Wrangle\", tabName=\"wrangle\", icon=icon(\"hat-cowboy\")), menuItem(\"Plot\", tabName=\"plot\", icon=icon(\"chart-line\")), menuItem(\"App State\", tabName=\"app_state\", icon=icon(\"archive\")), menuItem(\"App Info\", tabName=\"sysinfo\", icon=icon(\"book-medical\")) ) ), dashboardBody( tags$head( tags$style(HTML(CSS)) ), tabItems( tabItem(tabName=\"app_state\", box(title=\"Manage App State\", htmlOutput(NS(\"ASM\", \"ui_asm_compact\")))), tabItem(tabName=\"upload\", box(title=\"Load Data\", width=12, fluidRow( prompter::use_prompt(), column(width=6, htmlOutput(NS(\"UD\", \"UD_ui_compact\"))), column(width=6, tags$p( tags$img( class = \"wrapfig\", src = \"https://github.com/john-harrold/formods/raw/master/man/figures/logo.png\", width = 100, alt = \"formods logo\" ), 'Formods is a set of modules and an framework for developing modules which interact and create code to replicate analyses performed within an app. To experiment download this', tags$a(\"test dataset\", href=data_url), 'and upload it into the App using the form on the left.')) ) ) ), tabItem(tabName=\"wrangle\", box(title=\"Transform and Create Views of Your Data\", width=12, htmlOutput(NS(\"DW\", \"DW_ui_compact\")))), tabItem(tabName=\"plot\", box(title=\"Visualize Data\", width=12, htmlOutput(NS(\"FG\", \"FG_ui_compact\")))), tabItem(tabName=\"sysinfo\", box(title=\"System Details\", width=12, shinydashboard::tabBox( width = 12, title = NULL, shiny::tabPanel(id=\"sys_modules\", title=tagList(shiny::icon(\"ghost\"), \"Modules\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_modules\")) ), shiny::tabPanel(id=\"sys_packages\", title=tagList(shiny::icon(\"ghost\"), \"Packages\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_packages\")) ), shiny::tabPanel(id=\"sys_log\", title=tagList(shiny::icon(\"clipboard-list\"), \"App Log\"), verbatimTextOutput(NS(\"ASM\", \"ui_asm_sys_log\")) ), shiny::tabPanel(id=\"sys_options\", title=tagList(shiny::icon(\"sliders\"), \"R Options\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_options\")) ) ) )) ) ) ) # Main app server server <- function(input, output, session) { # Empty reactive object to track and react to # changes in the module state outside of the module react_FM = reactiveValues() # This is the list of module ids used for reproducible script generation. The # order here is important. mod_ids = c(\"UD\", \"DW\", \"FG\") #Populating with test data FG_test_mksession(session) # Module servers formods::ASM_Server(id=\"ASM\", deployed = deployed, react_state = react_FM, mod_ids = mod_ids) formods::UD_Server( id=\"UD\", id_ASM = \"ASM\", deployed = deployed, react_state = react_FM) formods::DW_Server( id=\"DW\", id_ASM = \"ASM\",id_UD = \"UD\", deployed = deployed, react_state = react_FM) formods::FG_Server( id=\"FG\", id_ASM = \"ASM\",id_UD = \"UD\", id_DW = \"DW\", deployed = deployed, react_state = react_FM) } shinyApp(ui, server) }"},{"path":"/reference/ASM_fetch_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Module Code — ASM_fetch_code","title":"Fetch Module Code — ASM_fetch_code","text":"Fetches code generate results seen app","code":""},{"path":"/reference/ASM_fetch_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Module Code — ASM_fetch_code","text":"","code":"ASM_fetch_code(state)"},{"path":"/reference/ASM_fetch_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Module Code — ASM_fetch_code","text":"state ASM state ASM_fetch_state()","code":""},{"path":"/reference/ASM_fetch_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Module Code — ASM_fetch_code","text":"ASM module generate code","code":""},{"path":"/reference/ASM_fetch_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Module Code — ASM_fetch_code","text":"","code":"# Creating a state object for testing sess_res = ASM_test_mksession(session=list(), full_session=FALSE) #> Error in session$userData: object of type 'builtin' is not subsettable state = sess_res$state #> Error in eval(expr, envir, enclos): object 'sess_res' not found code = ASM_fetch_code(state)"},{"path":"/reference/ASM_fetch_dlfn.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Download File Name — ASM_fetch_dlfn","title":"Fetch Download File Name — ASM_fetch_dlfn","text":"Gets either file name specified user default value null","code":""},{"path":"/reference/ASM_fetch_dlfn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Download File Name — ASM_fetch_dlfn","text":"","code":"ASM_fetch_dlfn(state, extension = \".zip\")"},{"path":"/reference/ASM_fetch_dlfn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Download File Name — ASM_fetch_dlfn","text":"state ASM state ASM_fetch_state() extension File extension download (default: \".zip\")","code":""},{"path":"/reference/ASM_fetch_dlfn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Download File Name — ASM_fetch_dlfn","text":"character object download file name","code":""},{"path":"/reference/ASM_fetch_dlfn.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Download File Name — ASM_fetch_dlfn","text":"","code":"# Creating a state object for testing sess_res = ASM_test_mksession(session=list(), full_session=FALSE) #> Error in session$userData: object of type 'builtin' is not subsettable state = sess_res$state #> Error in eval(expr, envir, enclos): object 'sess_res' not found dlfn = ASM_fetch_dlfn(state) #> Error in ASM_fetch_dlfn(state): object 'state' not found dlfn #> Error in eval(expr, envir, enclos): object 'dlfn' not found"},{"path":"/reference/ASM_fetch_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch State Manager State — ASM_fetch_state","title":"Fetch State Manager State — ASM_fetch_state","text":"Merges default app options changes made UI","code":""},{"path":"/reference/ASM_fetch_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch State Manager State — ASM_fetch_state","text":"","code":"ASM_fetch_state(id, input, session, FM_yaml_file, MOD_yaml_file)"},{"path":"/reference/ASM_fetch_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch State Manager State — ASM_fetch_state","text":"id Shiny module ID input Shiny input variable session Shiny session variable FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section.","code":""},{"path":"/reference/ASM_fetch_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch State Manager State — ASM_fetch_state","text":"list containing current state app including default values yaml file well changes made user. list following structure: yaml: Full contents supplied yaml file. MC: Module components yaml file. ASM: isgood: Boolean object indicating file successfully loaded. checksum: MD5 sum loaded state file MOD_TYPE: Character data containing type module \"ASM\" id: Character data containing module id module session variable. FM_yaml_file: App configuration file FM main section. MOD_yaml_file: Module configuration file MC main section.","code":""},{"path":"/reference/ASM_fetch_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch State Manager State — ASM_fetch_state","text":"","code":"# Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = ASM_test_mksession(session=list(), full_session=FALSE) #> Error in session$userData: object of type 'builtin' is not subsettable session = sess_res$session #> Error in eval(expr, envir, enclos): object 'sess_res' not found input = sess_res$input #> Error in eval(expr, envir, enclos): object 'sess_res' not found # Configuration files FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\") MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"ASM.yaml\") # We need to specify the ID of the ASM module id = \"ASM\" state = ASM_fetch_state(id = id, input = input, session = session, FM_yaml_file = FM_yaml_file, MOD_yaml_file = MOD_yaml_file) #> Error in FM_fetch_mod_state(session, id): object 'session' not found state #> Error in eval(expr, envir, enclos): object 'state' not found"},{"path":"/reference/ASM_init_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize ASM Module State — ASM_init_state","title":"Initialize ASM Module State — ASM_init_state","text":"Creates list initialized module state","code":""},{"path":"/reference/ASM_init_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize ASM Module State — ASM_init_state","text":"","code":"ASM_init_state(FM_yaml_file, MOD_yaml_file, id, session)"},{"path":"/reference/ASM_init_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize ASM Module State — ASM_init_state","text":"FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. id ID string module. session Shiny session variable","code":""},{"path":"/reference/ASM_init_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize ASM Module State — ASM_init_state","text":"list containing empty ASM state","code":""},{"path":"/reference/ASM_init_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize ASM Module State — ASM_init_state","text":"","code":"# Within shiny the session variable will exist, # this creates an example here for testing purposes: sess_res = ASM_test_mksession(session=list(), full_session=FALSE) #> Error in session$userData: object of type 'builtin' is not subsettable session = sess_res$session #> Error in eval(expr, envir, enclos): object 'sess_res' not found state = ASM_init_state( FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"ASM.yaml\"), id = \"ASM\", session = session) #> Error in FM_init_state(FM_yaml_file = FM_yaml_file, MOD_yaml_file = MOD_yaml_file, id = id, MT = \"ASM\", button_counters = button_counters, ui_ids = ui_ids, ui_hold = ui_hold, session = session): object 'session' not found state #> Error in eval(expr, envir, enclos): object 'state' not found"},{"path":"/reference/ASM_test_mksession.html","id":null,"dir":"Reference","previous_headings":"","what":"Populate Session Data for Module Testing — ASM_test_mksession","title":"Populate Session Data for Module Testing — ASM_test_mksession","text":"Populates supplied session variable testing.","code":""},{"path":"/reference/ASM_test_mksession.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Populate Session Data for Module Testing — ASM_test_mksession","text":"","code":"ASM_test_mksession( session, id = \"ASM\", id_UD = \"UD\", id_DW = \"DW\", full_session = TRUE )"},{"path":"/reference/ASM_test_mksession.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Populate Session Data for Module Testing — ASM_test_mksession","text":"session Shiny session variable (app) list (outside app) id ID string corresponds ID used call modules UI elements id_UD ID string corresponds ID used call UD modules UI elements id_DW ID string corresponds ID used call DW modules UI elements full_session Boolean indicate full test session created (default TRUE).","code":""},{"path":"/reference/ASM_test_mksession.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Populate Session Data for Module Testing — ASM_test_mksession","text":"list following elements isgood: Boolean indicating exit status function. session: value Shiny session variable (app) list (outside app) initialization. input: value shiny input end session initialization. state: App state. rsc: react_state components.","code":""},{"path":"/reference/ASM_test_mksession.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Populate Session Data for Module Testing — ASM_test_mksession","text":"","code":"sess_res = ASM_test_mksession(session=list(), full_session=FALSE) #> Error in session$userData: object of type 'builtin' is not subsettable"},{"path":"/reference/ASM_write_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Write State to File for Saving — ASM_write_state","title":"Write State to File for Saving — ASM_write_state","text":"Called download handler used write saved state value null","code":""},{"path":"/reference/ASM_write_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write State to File for Saving — ASM_write_state","text":"","code":"ASM_write_state(state, session, file, mod_ids)"},{"path":"/reference/ASM_write_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write State to File for Saving — ASM_write_state","text":"state ASM state ASM_fetch_state() session Shiny session variable file File name write zipped state. mod_ids Vector module IDs order needed (used code generation).","code":""},{"path":"/reference/ASM_write_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write State to File for Saving — ASM_write_state","text":"function writes state return value.","code":""},{"path":"/reference/ASM_write_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Write State to File for Saving — ASM_write_state","text":"","code":"# \\donttest{ # Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = ASM_test_mksession(session=list(), full_session=FALSE) #> Error in session$userData: object of type 'builtin' is not subsettable session = sess_res$session #> Error in eval(expr, envir, enclos): object 'sess_res' not found input = sess_res$input #> Error in eval(expr, envir, enclos): object 'sess_res' not found # Configuration files FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\") MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"ASM.yaml\") # We need to specify the ID of the ASM module id = \"ASM\" state = ASM_fetch_state(id = id, input = input, session = session, FM_yaml_file = FM_yaml_file, MOD_yaml_file = MOD_yaml_file) #> Error in FM_fetch_mod_state(session, id): object 'session' not found ASM_write_state(state, session, file = tempfile(fileext=\".zip\"), mod_ids = c(\"UD\")) #> Error in c(\"ShinySession\", \"session_proxy\") %in% class(session): object 'session' not found # }"},{"path":"/reference/DW_Server.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Wrangling Server — DW_Server","title":"Data Wrangling Server — DW_Server","text":"Server function data wrangling module","code":""},{"path":"/reference/DW_Server.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Wrangling Server — DW_Server","text":"","code":"DW_Server( id, id_ASM = \"ASM\", id_UD = \"UD\", FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"DW.yaml\"), deployed = FALSE, react_state = NULL )"},{"path":"/reference/DW_Server.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data Wrangling Server — DW_Server","text":"id ID string corresponds ID used call modules UI elements id_ASM ID string app state managment module used save load app states id_UD ID string upload data module used handle uploads name list element react_state data set stored. FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file DW main section. deployed Boolean variable indicating whether app deployed . react_state Variable passed server allow reaction outside module (NULL)","code":""},{"path":"/reference/DW_Server.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data Wrangling Server — DW_Server","text":"DW Server object","code":""},{"path":"/reference/DW_Server.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Wrangling Server — DW_Server","text":"","code":"if(interactive()){ # These are suggested packages library(shinydashboard) library(ggpubr) library(plotly) library(shinybusy) library(prompter) library(utils) library(clipr) library(formods) CSS <- \" .wrapfig { float: right; shape-margin: 20px; margin-right: 20px; margin-bottom: 20px; } \" # Default to not deployed if(!exists(\"deployed\")){ deployed = FALSE } #https://fontawesome.com/icons?from=io data_url = \"https://github.com/john-harrold/formods/raw/master/inst/test_data/TEST_DATA.xlsx\" ui <- dashboardPage( skin=\"black\", dashboardHeader(title=\"formods\"), dashboardSidebar( sidebarMenu( menuItem(\"Source Data\", tabName=\"upload\", icon=icon(\"table\")) , menuItem(\"Wrangle\", tabName=\"wrangle\", icon=icon(\"hat-cowboy\")), menuItem(\"Plot\", tabName=\"plot\", icon=icon(\"chart-line\")), menuItem(\"App State\", tabName=\"app_state\", icon=icon(\"archive\")), menuItem(\"App Info\", tabName=\"sysinfo\", icon=icon(\"book-medical\")) ) ), dashboardBody( tags$head( tags$style(HTML(CSS)) ), tabItems( tabItem(tabName=\"app_state\", box(title=\"Manage App State\", htmlOutput(NS(\"ASM\", \"ui_asm_compact\")))), tabItem(tabName=\"upload\", box(title=\"Load Data\", width=12, fluidRow( prompter::use_prompt(), column(width=6, htmlOutput(NS(\"UD\", \"UD_ui_compact\"))), column(width=6, tags$p( tags$img( class = \"wrapfig\", src = \"https://github.com/john-harrold/formods/raw/master/man/figures/logo.png\", width = 100, alt = \"formods logo\" ), 'Formods is a set of modules and an framework for developing modules which interact and create code to replicate analyses performed within an app. To experiment download this', tags$a(\"test dataset\", href=data_url), 'and upload it into the App using the form on the left.')) ) ) ), tabItem(tabName=\"wrangle\", box(title=\"Transform and Create Views of Your Data\", width=12, htmlOutput(NS(\"DW\", \"DW_ui_compact\")))), tabItem(tabName=\"plot\", box(title=\"Visualize Data\", width=12, htmlOutput(NS(\"FG\", \"FG_ui_compact\")))), tabItem(tabName=\"sysinfo\", box(title=\"System Details\", width=12, shinydashboard::tabBox( width = 12, title = NULL, shiny::tabPanel(id=\"sys_modules\", title=tagList(shiny::icon(\"ghost\"), \"Modules\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_modules\")) ), shiny::tabPanel(id=\"sys_packages\", title=tagList(shiny::icon(\"ghost\"), \"Packages\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_packages\")) ), shiny::tabPanel(id=\"sys_log\", title=tagList(shiny::icon(\"clipboard-list\"), \"App Log\"), verbatimTextOutput(NS(\"ASM\", \"ui_asm_sys_log\")) ), shiny::tabPanel(id=\"sys_options\", title=tagList(shiny::icon(\"sliders\"), \"R Options\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_options\")) ) ) )) ) ) ) # Main app server server <- function(input, output, session) { # Empty reactive object to track and react to # changes in the module state outside of the module react_FM = reactiveValues() # This is the list of module ids used for reproducible script generation. The # order here is important. mod_ids = c(\"UD\", \"DW\", \"FG\") #Populating with test data FG_test_mksession(session) # Module servers formods::ASM_Server(id=\"ASM\", deployed = deployed, react_state = react_FM, mod_ids = mod_ids) formods::UD_Server( id=\"UD\", id_ASM = \"ASM\", deployed = deployed, react_state = react_FM) formods::DW_Server( id=\"DW\", id_ASM = \"ASM\",id_UD = \"UD\", deployed = deployed, react_state = react_FM) formods::FG_Server( id=\"FG\", id_ASM = \"ASM\",id_UD = \"UD\", id_DW = \"DW\", deployed = deployed, react_state = react_FM) } shinyApp(ui, server) }"},{"path":"/reference/DW_add_wrangling_element.html","id":null,"dir":"Reference","previous_headings":"","what":"Adding Wrangling Element to Current Data View — DW_add_wrangling_element","title":"Adding Wrangling Element to Current Data View — DW_add_wrangling_element","text":"Adds wrangling element current data view.","code":""},{"path":"/reference/DW_add_wrangling_element.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adding Wrangling Element to Current Data View — DW_add_wrangling_element","text":"","code":"DW_add_wrangling_element(state, dwb_res, dwee_res)"},{"path":"/reference/DW_add_wrangling_element.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adding Wrangling Element to Current Data View — DW_add_wrangling_element","text":"state DW state DW_fetch_state() dwb_res Output dwrs_builder() dwee_res Output dw_eval_element() returned UD_fetch_state().","code":""},{"path":"/reference/DW_add_wrangling_element.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adding Wrangling Element to Current Data View — DW_add_wrangling_element","text":"state data set attached","code":""},{"path":"/reference/DW_add_wrangling_element.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adding Wrangling Element to Current Data View — DW_add_wrangling_element","text":"","code":"library(formods) # The example requires a formods DW state object state = DW_test_mksession(session=list())$state #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b state[[\"DW\"]][[\"ui\"]][[\"select_dw_element\"]] = \"filter\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_column\"]] = \"EVID\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_operator\"]] = \"==\" state[[\"DW\"]][[\"ui\"]][[\"fds_filter_rhs\"]] = 0 # This builds the data wrangling statement based on # elemets scraped from the UI dwb_res = dwrs_builder(state) # Here we evaluate the resulting command: dwee_res = dw_eval_element(state, dwb_res[[\"cmd\"]]) # Next we add this wrangling element to the state state = DW_add_wrangling_element(state, dwb_res, dwee_res) #> → DW: module checksum updated:28a679e132fa3cd0e47f9d941d4facdc # This creates a new data view and makes it active state = DW_new_view(state) # Here we can pluck out that data view from the state current_view = DW_fetch_current_view(state) # This will update the key in this view current_view[[\"key\"]] = \"My new view\" # And this will place it back into the state state = DW_set_current_view(state, current_view) #> → DW: module checksum updated:18070dc40a79230360b4e93daa19a2cc"},{"path":"/reference/DW_append_report.html","id":null,"dir":"Reference","previous_headings":"","what":"Append Report Elements — DW_append_report","title":"Append Report Elements — DW_append_report","text":"Takes current state app appends data views xlsx report object.","code":""},{"path":"/reference/DW_append_report.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append Report Elements — DW_append_report","text":"","code":"DW_append_report(state, rpt, rpttype, gen_code_only = FALSE)"},{"path":"/reference/DW_append_report.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append Report Elements — DW_append_report","text":"state DW state DW_fetch_state() rpt Report current content report appended function. details structure see documentation FM_generate_report. rpttype Type report generate (supported \"xlsx\"). gen_code_only Boolean value indicating code generated (FALSE).","code":""},{"path":"/reference/DW_append_report.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Append Report Elements — DW_append_report","text":"list containing following elements isgood: Return status function. hasrptele: Boolean indicator module reportable elements. code: Code generate reporting elements. msgs: Messages passed back user. rpt: Report additions passed back user.","code":""},{"path":[]},{"path":"/reference/DW_append_report.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Append Report Elements — DW_append_report","text":"","code":"# We need a state object to use below sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b state = sess_res$state rpt = list(summary = list(), sheets=list()) rpt_res = DW_append_report(state, rpt = rpt, rpttype = \"xlsx\") # Shows if report elements are present rpt_res$hasrptele #> [1] TRUE # Code chunk to generate report element cat(paste(rpt_res$code, collapse=\"\\n\")) #> rpt[[\"sheets\"]][[\"DW_myDS_1\"]]=DW_myDS_1 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_1\", #> Description=\"Observations\" #> ) #> ) #> rpt[[\"sheets\"]][[\"DW_myDS_2\"]]=DW_myDS_2 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_2\", #> Description=\"PK 3mg SD IV\" #> ) #> ) #> rpt[[\"sheets\"]][[\"DW_myDS_3\"]]=DW_myDS_3 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_3\", #> Description=\"PK 3mg MD SC (first dose)\" #> ) #> ) #> rpt[[\"sheets\"]][[\"DW_myDS_4\"]]=DW_myDS_4 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_4\", #> Description=\"Parameters\" #> ) #> ) #> rpt[[\"sheets\"]][[\"DW_myDS_5\"]]=DW_myDS_5 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_5\", #> Description=\"PK/PD 3mg SD IV w/BQL\" #> ) #> ) #> rpt[[\"sheets\"]][[\"DW_myDS_6\"]]=DW_myDS_6 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_6\", #> Description=\"PK/PD 3mg MD SC (first dose) w/BQL\" #> ) #> ) #> rpt[[\"sheets\"]][[\"DW_myDS_7\"]]=DW_myDS_7 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_7\", #> Description=\"PK 3mg SD IV w/BQL\" #> ) #> ) #> rpt[[\"sheets\"]][[\"DW_myDS_8\"]]=DW_myDS_8 #> rpt[[\"summary\"]] = rbind(rpt[[\"summary\"]], #> data.frame( #> Sheet_Name=\"DW_myDS_8\", #> Description=\"PK 3mg SD IV w/BQL w/dosing\" #> ) #> ) # Tabular summary of data views rpt_res$rpt$summary #> Sheet_Name Description #> 1 DW_myDS_1 Observations #> 2 DW_myDS_2 PK 3mg SD IV #> 3 DW_myDS_3 PK 3mg MD SC (first dose) #> 4 DW_myDS_4 Parameters #> 5 DW_myDS_5 PK/PD 3mg SD IV w/BQL #> 6 DW_myDS_6 PK/PD 3mg MD SC (first dose) w/BQL #> 7 DW_myDS_7 PK 3mg SD IV w/BQL #> 8 DW_myDS_8 PK 3mg SD IV w/BQL w/dosing"},{"path":"/reference/DW_attach_ds.html","id":null,"dir":"Reference","previous_headings":"","what":"Attach Data Set to DW State — DW_attach_ds","title":"Attach Data Set to DW State — DW_attach_ds","text":"Attaches dataset DW state supplied.","code":""},{"path":"/reference/DW_attach_ds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Attach Data Set to DW State — DW_attach_ds","text":"","code":"DW_attach_ds(state, id_UD, session)"},{"path":"/reference/DW_attach_ds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Attach Data Set to DW State — DW_attach_ds","text":"state DW state DW_fetch_state() id_UD ID string upload data module used handle uploads session Shiny session variable","code":""},{"path":"/reference/DW_attach_ds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Attach Data Set to DW State — DW_attach_ds","text":"state data set attached","code":""},{"path":"/reference/DW_attach_ds.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Attach Data Set to DW State — DW_attach_ds","text":"","code":"# Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b session = sess_res$session input = sess_res$input # We also need a state variable state = sess_res$state # We need to identify the UD module with the data id_UD = \"UD\" state = DW_attach_ds(state, id_UD, session)"},{"path":"/reference/DW_fetch_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Module Code — DW_fetch_code","title":"Fetch Module Code — DW_fetch_code","text":"Fetches code generate results seen app","code":""},{"path":"/reference/DW_fetch_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Module Code — DW_fetch_code","text":"","code":"DW_fetch_code(state)"},{"path":"/reference/DW_fetch_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Module Code — DW_fetch_code","text":"state DW state DW_fetch_state()","code":""},{"path":"/reference/DW_fetch_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Module Code — DW_fetch_code","text":"Character object vector lines code isgood)","code":""},{"path":"/reference/DW_fetch_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Module Code — DW_fetch_code","text":"","code":"# This will create a formods DW state object for the example sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b state = sess_res$state code = DW_fetch_code(state) cat(code) #> # Observations ============================================================ #> DW_myDS_1 = myDS #> DW_myDS_1 = dplyr::filter(DW_myDS_1,EVID == 0) #> DW_myDS_1 = dplyr::filter(DW_myDS_1,DV != 0) #> DW_myDS_1 = dplyr::mutate(DW_myDS_1,IDCMT = paste0(ID, ', ', CMT)) #> #> # PK 3mg SD IV ============================================================ #> DW_myDS_2 = myDS #> DW_myDS_2 = dplyr::filter(DW_myDS_2,EVID == 0) #> DW_myDS_2 = dplyr::filter(DW_myDS_2,DV != 0) #> DW_myDS_2 = dplyr::filter(DW_myDS_2,Cohort %in% c(\"SD 3 mg IV\")) #> DW_myDS_2 = dplyr::filter(DW_myDS_2,CMT %in% c(\"C_ng_ml\")) #> #> # PK 3mg MD SC (first dose) =============================================== #> DW_myDS_3 = myDS #> DW_myDS_3 = dplyr::filter(DW_myDS_3,EVID == 0) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,DV != 0) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,Cohort %in% c(\"MD 3 mg SC\")) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,DOSE_NUM == 1) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,CMT %in% c(\"C_ng_ml\")) #> #> # Parameters ============================================================== #> DW_myDS_4 = myDS #> DW_myDS_4 = dplyr::group_by(DW_myDS_4,ID) #> DW_myDS_4 = dplyr::filter(DW_myDS_4,row_number()==1) #> DW_myDS_4 = dplyr::select(DW_myDS_4,ID, DOSE, DOSE_STR, Cohort, ROUTE, ka, CL, Vc, Vp, Q) #> DW_myDS_4 = tidyr::pivot_longer(DW_myDS_4, cols = c(\"ka\", \"CL\", \"Vc\", \"Vp\", \"Q\"), names_to = \"parameter\", values_to = \"values\") #> #> # PK/PD 3mg SD IV w/BQL =================================================== #> DW_myDS_5 = myDS #> DW_myDS_5 = dplyr::filter(DW_myDS_5,EVID == 0) #> DW_myDS_5 = dplyr::filter(DW_myDS_5,Cohort %in% c(\"SD 3 mg IV\")) #> #> # PK/PD 3mg MD SC (first dose) w/BQL ====================================== #> DW_myDS_6 = myDS #> DW_myDS_6 = dplyr::filter(DW_myDS_6,EVID == 0) #> DW_myDS_6 = dplyr::filter(DW_myDS_6,Cohort %in% c(\"MD 3 mg SC\")) #> DW_myDS_6 = dplyr::filter(DW_myDS_6,DOSE_NUM == 1) #> #> # PK 3mg SD IV w/BQL ====================================================== #> DW_myDS_7 = myDS #> DW_myDS_7 = dplyr::filter(DW_myDS_7,EVID == 0) #> DW_myDS_7 = dplyr::filter(DW_myDS_7,Cohort %in% c(\"SD 3 mg IV\")) #> DW_myDS_7 = dplyr::filter(DW_myDS_7,CMT %in% c(\"C_ng_ml\")) #> #> # PK 3mg SD IV w/BQL w/dosing ============================================= #> DW_myDS_8 = myDS #> DW_myDS_8 = dplyr::filter(DW_myDS_8,Cohort %in% c(\"MD 3 mg IV\"))"},{"path":"/reference/DW_fetch_current_view.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches Current Data View — DW_fetch_current_view","title":"Fetches Current Data View — DW_fetch_current_view","text":"Takes DW state returns current active view","code":""},{"path":"/reference/DW_fetch_current_view.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches Current Data View — DW_fetch_current_view","text":"","code":"DW_fetch_current_view(state)"},{"path":"/reference/DW_fetch_current_view.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches Current Data View — DW_fetch_current_view","text":"state DW state DW_fetch_state()","code":""},{"path":"/reference/DW_fetch_current_view.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches Current Data View — DW_fetch_current_view","text":"List containing details active data view. structure list structure state$DW$views output DW_fetch_state().","code":""},{"path":"/reference/DW_fetch_current_view.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches Current Data View — DW_fetch_current_view","text":"","code":"library(formods) # The example requires a formods DW state object state = DW_test_mksession(session=list())$state #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b state[[\"DW\"]][[\"ui\"]][[\"select_dw_element\"]] = \"filter\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_column\"]] = \"EVID\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_operator\"]] = \"==\" state[[\"DW\"]][[\"ui\"]][[\"fds_filter_rhs\"]] = 0 # This builds the data wrangling statement based on # elemets scraped from the UI dwb_res = dwrs_builder(state) # Here we evaluate the resulting command: dwee_res = dw_eval_element(state, dwb_res[[\"cmd\"]]) # Next we add this wrangling element to the state state = DW_add_wrangling_element(state, dwb_res, dwee_res) #> → DW: module checksum updated:28a679e132fa3cd0e47f9d941d4facdc # This creates a new data view and makes it active state = DW_new_view(state) # Here we can pluck out that data view from the state current_view = DW_fetch_current_view(state) # This will update the key in this view current_view[[\"key\"]] = \"My new view\" # And this will place it back into the state state = DW_set_current_view(state, current_view) #> → DW: module checksum updated:18070dc40a79230360b4e93daa19a2cc"},{"path":"/reference/DW_fetch_ds.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Module Datasets — DW_fetch_ds","title":"Fetch Module Datasets — DW_fetch_ds","text":"Fetches datasets contained module.","code":""},{"path":"/reference/DW_fetch_ds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Module Datasets — DW_fetch_ds","text":"","code":"DW_fetch_ds(state)"},{"path":"/reference/DW_fetch_ds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Module Datasets — DW_fetch_ds","text":"state UD state UD_fetch_state()","code":""},{"path":"/reference/DW_fetch_ds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Module Datasets — DW_fetch_ds","text":"Character object vector lines code list containing following elements isgood: Return status function. hasds: Boolean indicator module datasets msgs: Messages passed back user. ds: List datasets. list element name R-object dataset. element following structure: label: Text label dataset MOD_TYPE: Short name type module. id: module ID DS: Dataframe containing actual dataset. DSMETA: Metadata describing DS, see FM_fetch_ds() details format. code: Complete code build dataset. checksum: Module checksum. DSchecksum: Dataset checksum.","code":""},{"path":"/reference/DW_fetch_ds.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Module Datasets — DW_fetch_ds","text":"","code":"# We need a state variable sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b state = sess_res$state ds = DW_fetch_ds(state)"},{"path":"/reference/DW_fetch_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Data Wrangling State — DW_fetch_state","title":"Fetch Data Wrangling State — DW_fetch_state","text":"Merges default app options changes made UI","code":""},{"path":"/reference/DW_fetch_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Data Wrangling State — DW_fetch_state","text":"","code":"DW_fetch_state( id, input, session, FM_yaml_file, MOD_yaml_file, id_UD, react_state )"},{"path":"/reference/DW_fetch_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Data Wrangling State — DW_fetch_state","text":"id Shiny module ID input Shiny input variable session Shiny session variable FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. id_UD ID string upload data module used handle uploads name list element react_state data set stored. react_state Variable passed server allow reaction outside module (NULL)","code":""},{"path":"/reference/DW_fetch_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Data Wrangling State — DW_fetch_state","text":"List containing current state DM module including default values yaml file well changes made user. structure list defined . yaml: Contents yaml file. MC: Module components yaml file. DW: Data wrangling state isgood: Boolean status state. FALSE dataset identified id_UD bad. checksum: MD5 sum indicating change datasets within view. Use trigger updates respose changes module. button_counters: List counters detect button clicks. code_previous: Loading code UD field. current_view: View id current active data wrangling view. UD: Copy \"UD\" field id_UD react_state input. ui: Current value form elements UI ui_hold: List hold elements disable updates full ui referesh complete. view_cntr: Counter tracking view ids, value contains id last view created. views: List data wrangling views. view following structure: checksum: MD5 sum WDS code: Code generate WDS start finish code_dw_only: Code just wrangling portion. code_previous: Code load data assign view object. elements_table: Table data wrangling elements. id: Character id (view_idx) idx: Numeric id (1) isgood: Boolean status data view. False evaluation fails key: User key (short description) view_ds_object_name: Object name data view WDS: Current value data view successful commands elements_table evaluated. MOD_TYPE: Character data containing type module \"DW\" id: Character data containing module id FM_yaml_file: App configuration file FM main section. MOD_yaml_file: Module configuration file MC main section. module session variable.","code":""},{"path":"/reference/DW_fetch_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Data Wrangling State — DW_fetch_state","text":"","code":"# Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b session = sess_res$session input = sess_res$input # Configuration files FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\") MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"DW.yaml\") # We need to specify both the DW module id as well as the # id of the UD module that feeds into it. id = \"DW\" id_UD = \"UD\" # Creating an empty state object state = DW_fetch_state(id = id, input = input, session = session, FM_yaml_file = FM_yaml_file, MOD_yaml_file = MOD_yaml_file, id_UD = \"UD\", react_state = NULL)"},{"path":"/reference/DW_init_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize DW Module State — DW_init_state","title":"Initialize DW Module State — DW_init_state","text":"Creates list initialized module state","code":""},{"path":"/reference/DW_init_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize DW Module State — DW_init_state","text":"","code":"DW_init_state(FM_yaml_file, MOD_yaml_file, id, id_UD, session)"},{"path":"/reference/DW_init_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize DW Module State — DW_init_state","text":"FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. id Shiny module ID id_UD ID string upload data module used handle uploads name list element react_state data set stored. session Shiny session variable module (NULL)","code":""},{"path":"/reference/DW_init_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize DW Module State — DW_init_state","text":"list containing empty DW state","code":""},{"path":"/reference/DW_init_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize DW Module State — DW_init_state","text":"","code":"# Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b session = sess_res$session input = sess_res$input state = DW_init_state( FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"DW.yaml\"), id = \"DW\", id_UD = \"UD\", session = session) #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad state #> $yaml #> $yaml$FM #> $yaml$FM$include #> $yaml$FM$include$files #> $yaml$FM$include$files[[1]] #> $yaml$FM$include$files[[1]]$file #> $yaml$FM$include$files[[1]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.docx\\\")\" #> #> $yaml$FM$include$files[[1]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.docx\\\")\" #> #> #> #> $yaml$FM$include$files[[2]] #> $yaml$FM$include$files[[2]]$file #> $yaml$FM$include$files[[2]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.pptx\\\")\" #> #> $yaml$FM$include$files[[2]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.pptx\\\")\" #> #> #> #> $yaml$FM$include$files[[3]] #> $yaml$FM$include$files[[3]]$file #> $yaml$FM$include$files[[3]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.yaml\\\")\" #> #> $yaml$FM$include$files[[3]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.yaml\\\")\" #> #> #> #> #> #> $yaml$FM$deployed #> [1] FALSE #> #> $yaml$FM$code #> $yaml$FM$code$theme #> [1] \"vibrant_ink\" #> #> $yaml$FM$code$showLineNumbers #> [1] TRUE #> #> $yaml$FM$code$gen_file #> [1] \"run_analysis.R\" #> #> $yaml$FM$code$gen_preamble #> [1] \"# formods automated output ------------------------------------------------\\n# https://formods.ubiquity.tools/\\nrm(list=ls())\" #> #> $yaml$FM$code$packages #> [1] \"onbrand\" \"writexl\" #> #> #> $yaml$FM$notifications #> $yaml$FM$notifications$config #> $yaml$FM$notifications$config$success #> $yaml$FM$notifications$config$success$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$success$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$success$background #> [1] \"#5bb85b\" #> #> #> $yaml$FM$notifications$config$failure #> $yaml$FM$notifications$config$failure$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$background #> [1] \"#d9534f\" #> #> #> $yaml$FM$notifications$config$info #> $yaml$FM$notifications$config$info$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$info$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$info$background #> [1] \"#5bc0de\" #> #> #> $yaml$FM$notifications$config$warning #> $yaml$FM$notifications$config$warning$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$background #> [1] \"#f0ac4d\" #> #> #> #> #> $yaml$FM$reporting #> $yaml$FM$reporting$enabled #> [1] TRUE #> #> $yaml$FM$reporting$content_init #> $yaml$FM$reporting$content_init$xlsx #> [1] \"rpt = list(summary = NULL,\\n sheets = list())\" #> #> $yaml$FM$reporting$content_init$docx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.docx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> $yaml$FM$reporting$content_init$pptx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.pptx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> #> #> $yaml$FM$ui #> $yaml$FM$ui$button_style #> [1] \"fill\" #> #> $yaml$FM$ui$select_size #> [1] 10 #> #> $yaml$FM$ui$color_green #> [1] \"#00BB8A\" #> #> $yaml$FM$ui$color_red #> [1] \"#FF475E\" #> #> $yaml$FM$ui$color_blue #> [1] \"#0088FF\" #> #> $yaml$FM$ui$color_purple #> [1] \"#bd2cf4\" #> #> #> $yaml$FM$data_meta #> $yaml$FM$data_meta$data_header #> [1] \"===NAME===<\/b>
===LABEL===<\/font><\/span>\" #> #> $yaml$FM$data_meta$subtext #> [1] \"===LABEL===: ===RANGE===\" #> #> $yaml$FM$data_meta$many_sep #> [1] \",⋅⋅⋅,\" #> #> $yaml$FM$data_meta$data_types #> $yaml$FM$data_meta$data_types$character #> $yaml$FM$data_meta$data_types$character$color #> [1] \"#DD4B39\" #> #> $yaml$FM$data_meta$data_types$character$label #> [1] \"text\" #> #> #> $yaml$FM$data_meta$data_types$double #> $yaml$FM$data_meta$data_types$double$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$double$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$integer #> $yaml$FM$data_meta$data_types$integer$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$integer$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$other #> $yaml$FM$data_meta$data_types$other$color #> [1] \"black\" #> #> $yaml$FM$data_meta$data_types$other$label #> [1] \"other\" #> #> #> #> #> $yaml$FM$labels #> $yaml$FM$labels$default_ds #> [1] \"Original data set\" #> #> #> $yaml$FM$user_files #> $yaml$FM$user_files$use_tmpdir #> [1] TRUE #> #> #> $yaml$FM$logging #> $yaml$FM$logging$enabled #> [1] TRUE #> #> $yaml$FM$logging$timestamp #> [1] TRUE #> #> $yaml$FM$logging$timestamp_fmt #> [1] \"%Y-%m-%d %H:%M:%S\" #> #> $yaml$FM$logging$log_file #> [1] \"formods_log.txt\" #> #> $yaml$FM$logging$console #> [1] TRUE #> #> #> #> #> $MC #> $MC$compact #> $MC$compact$code #> [1] TRUE #> #> $MC$compact$preview #> [1] TRUE #> #> $MC$compact$clip #> [1] TRUE #> #> #> $MC$reporting #> $MC$reporting$enabled #> [1] TRUE #> #> $MC$reporting$priority #> [1] 1 #> #> #> $MC$notifications #> $MC$notifications$new_dw_element #> [1] \"Added element: ===ACTION=== (===DESC===)\" #> #> $MC$notifications$del_dw_element #> [1] \"Removed element: ===ACTION=== (===DESC===)\" #> #> #> $MC$tooltips #> $MC$tooltips$include #> [1] TRUE #> #> $MC$tooltips$show_code #> [1] \"Show data wrangling code\" #> #> $MC$tooltips$dw_elements #> [1] \"Current wrangling elements\" #> #> #> $MC$labels #> $MC$labels$tab_main #> [1] \"Wrangle\" #> #> $MC$labels$tab_code #> [1] \"Code\" #> #> $MC$labels$add_element #> [1] \"Add Operation/Action\" #> #> $MC$labels$fds_filter_column #> [1] \"Filter by Column\" #> #> $MC$labels$fds_filter_operator #> [1] \"Condition\" #> #> $MC$labels$fds_filter_rhs #> [1] \"Matching\" #> #> $MC$labels$fds_mutate_column #> [1] \"New or current column to alter\" #> #> $MC$labels$fds_mutate_rhs #> [1] \"New Value\" #> #> $MC$labels$fds_rename_column #> [1] \"Curret Column\" #> #> $MC$labels$fds_rename_rhs #> [1] \"New Name\" #> #> $MC$labels$fds_group_column #> [1] \"Columns to group\" #> #> $MC$labels$fds_longer_column #> [1] \"Columns to make longer\" #> #> $MC$labels$fds_longer_names #> [1] \"New column to contain names\" #> #> $MC$labels$fds_longer_values #> [1] \"New column to contain values\" #> #> $MC$labels$fds_wider_names #> [1] \"Column with names\" #> #> $MC$labels$fds_wider_values #> [1] \"Column with values\" #> #> $MC$labels$new_dw #> [1] \"New\" #> #> $MC$labels$del_dw #> [1] \"Delete\" #> #> $MC$labels$save_dw #> [1] \"Save\" #> #> $MC$labels$copy_dw #> [1] \"Copy\" #> #> $MC$labels$clip_dw #> [1] \"Code\" #> #> $MC$labels$ungroup_data #> [1] \"Removing current grouping\" #> #> $MC$labels$keep_onerow #> [1] \"Keep first row in current grouping\" #> #> $MC$labels$no_dataset #> [1] \"No dataset available to wrangle. You need to load a dataset to use this module.\" #> #> $MC$labels$no_dw_elements #> [1] \"No data wrangling elements defined yet\" #> #> $MC$labels$busy #> $MC$labels$busy$dv_update #> [1] \"Updating data views. Please be patient...\" #> #> #> #> $MC$errors #> $MC$errors$fds_filter_column #> [1] \"Filter column not specified.\" #> #> $MC$errors$fds_filter_operator #> [1] \"Filter condition not specified.\" #> #> $MC$errors$fds_filter_rhs #> [1] \"Filter RHS not specified.\" #> #> $MC$errors$fds_mutate_column #> [1] \"Mutate column not specified.\" #> #> $MC$errors$fds_mutate_rhs #> [1] \"Mutate RHS not specified.\" #> #> $MC$errors$fds_rename_column #> [1] \"Column to rename not specified.\" #> #> $MC$errors$fds_rename_rhs #> [1] \"New column name not specified.\" #> #> $MC$errors$fds_group_column #> [1] \"No columns to group specified.\" #> #> $MC$errors$fds_select_column #> [1] \"You must select at least one column to keep.\" #> #> $MC$errors$fds_longer_column #> [1] \"You must select at least one column to make longer.\" #> #> $MC$errors$fds_longer_names #> [1] \"You must supply a column for the names of the new longer dataset\" #> #> $MC$errors$fds_longer_values #> [1] \"You must supply a column for the values of the new longer dataset\" #> #> $MC$errors$fds_wider_names #> [1] \"You must select a column with the names.\" #> #> $MC$errors$`fds_wider_value s` #> [1] \"You must select a column with the values.\" #> #> $MC$errors$current_key #> [1] \"Short description\" #> #> $MC$errors$current_key_empty #> [1] \"The data view description field cannot be empty\" #> #> $MC$errors$unknown_action #> [1] \"The selection action is not supported.\" #> #> $MC$errors$no_rows #> [1] \"There are no rows in the data set.\" #> #> $MC$errors$element_not_added #> [1] \"Unable to add the data wrangling element:\" #> #> $MC$errors$fix_bad_element #> [1] \"There is a bad element in the data wrangling chain,\\nyou need to fix that before adding new elements\" #> #> #> $MC$operators #> $MC$operators[[1]] #> $MC$operators[[1]]$type #> [1] \"factor\" #> #> $MC$operators[[1]]$text #> [1] \"is one of\" #> #> $MC$operators[[1]]$rop #> [1] \"%in%\" #> #> #> $MC$operators[[2]] #> $MC$operators[[2]]$type #> [1] \"factor\" #> #> $MC$operators[[2]]$text #> [1] \"is not\" #> #> $MC$operators[[2]]$rop #> [1] \"!%in%\" #> #> #> $MC$operators[[3]] #> $MC$operators[[3]]$type #> [1] \"not_factor\" #> #> $MC$operators[[3]]$text #> [1] \"is within the range\" #> #> $MC$operators[[3]]$rop #> [1] \"within\" #> #> #> $MC$operators[[4]] #> $MC$operators[[4]]$type #> [1] \"not_factor\" #> #> $MC$operators[[4]]$text #> [1] \"is equal to\" #> #> $MC$operators[[4]]$rop #> [1] \"==\" #> #> #> $MC$operators[[5]] #> $MC$operators[[5]]$type #> [1] \"not_factor\" #> #> $MC$operators[[5]]$text #> [1] \"is not equal to\" #> #> $MC$operators[[5]]$rop #> [1] \"!=\" #> #> #> #> $MC$actions #> $MC$actions$filter #> $MC$actions$filter$choice #> [1] \"Filter\" #> #> $MC$actions$filter$subtext #> [1] \"Filter data\" #> #> #> $MC$actions$mutate #> $MC$actions$mutate$choice #> [1] \"Alter\" #> #> $MC$actions$mutate$subtext #> [1] \"Create new column or change existing column\" #> #> #> $MC$actions$rename #> $MC$actions$rename$choice #> [1] \"Rename\" #> #> $MC$actions$rename$subtext #> [1] \"Rename column\" #> #> #> $MC$actions$group #> $MC$actions$group$choice #> [1] \"Group\" #> #> $MC$actions$group$subtext #> [1] \"Group subsequent operations by columns\" #> #> #> $MC$actions$ungroup #> $MC$actions$ungroup$choice #> [1] \"Ungroup\" #> #> $MC$actions$ungroup$subtext #> [1] \"Removing groping\" #> #> #> $MC$actions$longer #> $MC$actions$longer$choice #> [1] \"Elongate\" #> #> $MC$actions$longer$subtext #> [1] \"Make Longer: rows to columns\" #> #> #> $MC$actions$wider #> $MC$actions$wider$choice #> [1] \"Widen\" #> #> $MC$actions$wider$subtext #> [1] \"Make Wider: columns to rows\" #> #> #> $MC$actions$onerow #> $MC$actions$onerow$choice #> [1] \"First Row\" #> #> $MC$actions$onerow$subtext #> [1] \"Keep only first row of grouped data\" #> #> #> $MC$actions$select #> $MC$actions$select$choice #> [1] \"Select\" #> #> $MC$actions$select$subtext #> [1] \"Choose columns to keep\" #> #> #> #> $MC$formatting #> $MC$formatting$preview #> $MC$formatting$preview$width #> [1] 800 #> #> $MC$formatting$preview$height #> [1] 400 #> #> #> $MC$formatting$dw_elements #> $MC$formatting$dw_elements$width #> [1] 600 #> #> $MC$formatting$dw_elements$height #> [1] 200 #> #> #> $MC$formatting$current_key #> $MC$formatting$current_key$width #> [1] 300 #> #> #> $MC$formatting$code #> $MC$formatting$code$width #> [1] 800 #> #> $MC$formatting$code$height #> [1] 300 #> #> #> $MC$formatting$button_dw_del #> $MC$formatting$button_dw_del$size #> [1] \"sm\" #> #> $MC$formatting$button_dw_del$block #> [1] TRUE #> #> $MC$formatting$button_dw_del$tooltip #> [1] \"Delete the current data view.\" #> #> $MC$formatting$button_dw_del$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_dw_clip #> $MC$formatting$button_dw_clip$size #> [1] \"sm\" #> #> $MC$formatting$button_dw_clip$block #> [1] TRUE #> #> $MC$formatting$button_dw_clip$tooltip #> [1] \"Copy code to generate current data view to the clipboard.\" #> #> $MC$formatting$button_dw_clip$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_dw_save #> $MC$formatting$button_dw_save$size #> [1] \"sm\" #> #> $MC$formatting$button_dw_save$block #> [1] TRUE #> #> $MC$formatting$button_dw_save$tooltip #> [1] \"Save changes to data view name\" #> #> $MC$formatting$button_dw_save$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_dw_copy #> $MC$formatting$button_dw_copy$size #> [1] \"sm\" #> #> $MC$formatting$button_dw_copy$block #> [1] TRUE #> #> $MC$formatting$button_dw_copy$tooltip #> [1] \"Copy current data view to a new data view.\" #> #> $MC$formatting$button_dw_copy$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_dw_new #> $MC$formatting$button_dw_new$size #> [1] \"sm\" #> #> $MC$formatting$button_dw_new$block #> [1] TRUE #> #> $MC$formatting$button_dw_new$tooltip #> [1] \"Create a new empty data view.\" #> #> $MC$formatting$button_dw_new$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_dw_add_element #> $MC$formatting$button_dw_add_element$size #> [1] \"sm\" #> #> $MC$formatting$button_dw_add_element$block #> [1] TRUE #> #> #> #> $MC$code #> $MC$code$readOnly #> [1] TRUE #> #> $MC$code$mode #> [1] \"r\" #> #> $MC$code$packages #> [1] \"dplyr\" \"tidyr\" #> #> $MC$code$preamble #> [1] \"# Data wrangling ----------------------------------------------------------\" #> #> #> $MC$ds_object_name #> [1] \"DW_myDS\" #> #> #> $DW #> $DW$button_counters #> $DW$button_counters$button_dw_add_element #> [1] 0 #> #> $DW$button_counters$button_dw_new #> [1] 0 #> #> $DW$button_counters$button_dw_del #> [1] 0 #> #> $DW$button_counters$button_dw_save #> [1] 0 #> #> $DW$button_counters$button_dw_copy #> [1] 0 #> #> #> $DW$ui_hold #> $DW$ui_hold$hot_dw_elements #> [1] FALSE #> #> $DW$ui_hold$current_key #> [1] FALSE #> #> $DW$ui_hold$select_dw_views #> [1] FALSE #> #> #> $DW$ui_ids #> [1] \"hot_dw_elements\" \"button_dw_add_element\" #> [3] \"button_dw_new\" \"button_dw_del\" #> [5] \"button_dw_copy\" \"button_dw_save\" #> [7] \"select_fds_filter_column\" \"select_fds_filter_operator\" #> [9] \"fds_filter_rhs\" \"select_fds_mutate_column\" #> [11] \"select_fds_mutate_rhs\" \"select_fds_rename_column\" #> [13] \"fds_rename_rhs\" \"current_key\" #> [15] \"select_fds_group_column\" \"select_fds_select_column\" #> [17] \"select_fds_longer_column\" \"select_fds_longer_values\" #> [19] \"select_fds_longer_names\" \"select_fds_wider_values\" #> [21] \"select_fds_wider_names\" \"select_dw_views\" #> [23] \"select_dw_element\" #> #> $DW$isgood #> [1] TRUE #> #> $DW$op_choices #> $DW$op_choices$factor #> is one of is not #> \"%in%\" \"!%in%\" #> #> $DW$op_choices$not_factor #> is within the range is equal to is not equal to #> \"within\" \"==\" \"!=\" #> #> #> $DW$view_cntr #> [1] 1 #> #> $DW$UD #> $DW$UD$isgood #> [1] TRUE #> #> $DW$UD$checksum #> [1] \"897d952fecbc804999396a96f9df4b20\" #> #> $DW$UD$contents #> # A tibble: 10,680 × 33 #> ID TIME_DY TIME_HR NTIME_DY NTIME_HR TIME AMT DV RECDESC DOSE #> #> 1 1 0 0 0 0 0 3000000 0 dose 3000000 #> 2 1 0 0 0 0 0 0 1250 BM_ng_ml 3000000 #> 3 1 0 0 0 0 0 0 0 C_ng_ml 3000000 #> 4 1 1 24 1 24 24 0 1647 BM_ng_ml 3000000 #> 5 1 1 24 1 24 24 0 690. C_ng_ml 3000000 #> 6 1 2 48 2 48 48 0 1947 BM_ng_ml 3000000 #> 7 1 2 48 2 48 48 0 588. C_ng_ml 3000000 #> 8 1 3 72 3 72 72 0 2170 BM_ng_ml 3000000 #> 9 1 3 72 3 72 72 0 506. C_ng_ml 3000000 #> 10 1 4 96 4 96 96 0 2332 BM_ng_ml 3000000 #> # ℹ 10,670 more rows #> # ℹ 23 more variables: DOSE_STR , Cohort , ROUTE , WT , #> # SUBTYPE , SEX , F1 , ka , CL , Vc , Vp , #> # Q , BM_IC , kdeg_BM , Emax , EC50 , CMT , #> # DUR , EVID , NDose , DOSE_NUM , SUBTYPE_ID , #> # SEX_ID #> #> $DW$UD$object_name #> [1] \"myDS\" #> #> #> $DW$code_previous #> [1] \"myDS = readxl::read_excel(path=\\\"TEST_DATA.xlsx\\\", sheet=\\\"DATA\\\")\\nmyDS = janitor::clean_names(myDS, case=\\\"none\\\")\" #> #> $DW$views #> $DW$views$view_1 #> $DW$views$view_1$isgood #> [1] TRUE #> #> $DW$views$view_1$id #> [1] \"view_1\" #> #> $DW$views$view_1$idx #> [1] 1 #> #> $DW$views$view_1$view_ds_object_name #> [1] \"DW_myDS_1\" #> #> $DW$views$view_1$code_previous #> [1] \"DW_myDS_1 = myDS\" #> #> $DW$views$view_1$key #> [1] \"data_view_1\" #> #> $DW$views$view_1$WDS #> # A tibble: 10,680 × 33 #> ID TIME_DY TIME_HR NTIME_DY NTIME_HR TIME AMT DV RECDESC DOSE #> #> 1 1 0 0 0 0 0 3000000 0 dose 3000000 #> 2 1 0 0 0 0 0 0 1250 BM_ng_ml 3000000 #> 3 1 0 0 0 0 0 0 0 C_ng_ml 3000000 #> 4 1 1 24 1 24 24 0 1647 BM_ng_ml 3000000 #> 5 1 1 24 1 24 24 0 690. C_ng_ml 3000000 #> 6 1 2 48 2 48 48 0 1947 BM_ng_ml 3000000 #> 7 1 2 48 2 48 48 0 588. C_ng_ml 3000000 #> 8 1 3 72 3 72 72 0 2170 BM_ng_ml 3000000 #> 9 1 3 72 3 72 72 0 506. C_ng_ml 3000000 #> 10 1 4 96 4 96 96 0 2332 BM_ng_ml 3000000 #> # ℹ 10,670 more rows #> # ℹ 23 more variables: DOSE_STR , Cohort , ROUTE , WT , #> # SUBTYPE , SEX , F1 , ka , CL , Vc , Vp , #> # Q , BM_IC , kdeg_BM , Emax , EC50 , CMT , #> # DUR , EVID , NDose , DOSE_NUM , SUBTYPE_ID , #> # SEX_ID #> #> $DW$views$view_1$elements_table #> NULL #> #> $DW$views$view_1$checksum #> [1] \"b18a369b1e4d93010a04a56c7cde00c8\" #> #> $DW$views$view_1$code #> NULL #> #> $DW$views$view_1$code_dw_only #> NULL #> #> #> #> $DW$current_view #> [1] \"view_1\" #> #> $DW$checksum #> [1] \"5b0f0b05ee3ac7336a74c564bb6efdad\" #> #> #> $MOD_TYPE #> [1] \"DW\" #> #> $id #> [1] \"DW\" #> #> $dep_mod_ids #> [1] \"UD\" #> #> $FM_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/formods.yaml\" #> #> $MOD_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/DW.yaml\" #> #> $shiny_token #> [1] \"non_shiny\" #>"},{"path":"/reference/DW_new_view.html","id":null,"dir":"Reference","previous_headings":"","what":"New Data Wrangling View — DW_new_view","title":"New Data Wrangling View — DW_new_view","text":"Appends new empty data wrangling view DW state object makes new view active view.","code":""},{"path":"/reference/DW_new_view.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"New Data Wrangling View — DW_new_view","text":"","code":"DW_new_view(state)"},{"path":"/reference/DW_new_view.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"New Data Wrangling View — DW_new_view","text":"state DW state DW_fetch_state()","code":""},{"path":"/reference/DW_new_view.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"New Data Wrangling View — DW_new_view","text":"DW state object containing new data view view set current active view. See help DW_fetch_state() view format.","code":""},{"path":"/reference/DW_new_view.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"New Data Wrangling View — DW_new_view","text":"","code":"library(formods) # The example requires a formods DW state object state = DW_test_mksession(session=list())$state #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b state[[\"DW\"]][[\"ui\"]][[\"select_dw_element\"]] = \"filter\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_column\"]] = \"EVID\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_operator\"]] = \"==\" state[[\"DW\"]][[\"ui\"]][[\"fds_filter_rhs\"]] = 0 # This builds the data wrangling statement based on # elemets scraped from the UI dwb_res = dwrs_builder(state) # Here we evaluate the resulting command: dwee_res = dw_eval_element(state, dwb_res[[\"cmd\"]]) # Next we add this wrangling element to the state state = DW_add_wrangling_element(state, dwb_res, dwee_res) #> → DW: module checksum updated:28a679e132fa3cd0e47f9d941d4facdc # This creates a new data view and makes it active state = DW_new_view(state) # Here we can pluck out that data view from the state current_view = DW_fetch_current_view(state) # This will update the key in this view current_view[[\"key\"]] = \"My new view\" # And this will place it back into the state state = DW_set_current_view(state, current_view) #> → DW: module checksum updated:18070dc40a79230360b4e93daa19a2cc"},{"path":"/reference/DW_set_current_view.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets Current Data View — DW_set_current_view","title":"Sets Current Data View — DW_set_current_view","text":"Takes DW state updated view sets view current view_id","code":""},{"path":"/reference/DW_set_current_view.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets Current Data View — DW_set_current_view","text":"","code":"DW_set_current_view(state, dw_view)"},{"path":"/reference/DW_set_current_view.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sets Current Data View — DW_set_current_view","text":"state DW state DW_fetch_state() dw_view Data view list format returned DW_fetch_current_view() (see structure state$DW$views output DW_fetch_state()).","code":""},{"path":"/reference/DW_set_current_view.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets Current Data View — DW_set_current_view","text":"DW state object value dw_view set current view id.","code":""},{"path":"/reference/DW_set_current_view.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sets Current Data View — DW_set_current_view","text":"","code":"library(formods) # The example requires a formods DW state object state = DW_test_mksession(session=list())$state #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b state[[\"DW\"]][[\"ui\"]][[\"select_dw_element\"]] = \"filter\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_column\"]] = \"EVID\" state[[\"DW\"]][[\"ui\"]][[\"select_fds_filter_operator\"]] = \"==\" state[[\"DW\"]][[\"ui\"]][[\"fds_filter_rhs\"]] = 0 # This builds the data wrangling statement based on # elemets scraped from the UI dwb_res = dwrs_builder(state) # Here we evaluate the resulting command: dwee_res = dw_eval_element(state, dwb_res[[\"cmd\"]]) # Next we add this wrangling element to the state state = DW_add_wrangling_element(state, dwb_res, dwee_res) #> → DW: module checksum updated:28a679e132fa3cd0e47f9d941d4facdc # This creates a new data view and makes it active state = DW_new_view(state) # Here we can pluck out that data view from the state current_view = DW_fetch_current_view(state) # This will update the key in this view current_view[[\"key\"]] = \"My new view\" # And this will place it back into the state state = DW_set_current_view(state, current_view) #> → DW: module checksum updated:18070dc40a79230360b4e93daa19a2cc"},{"path":"/reference/DW_test_mksession.html","id":null,"dir":"Reference","previous_headings":"","what":"Populate Session Data for Module Testing — DW_test_mksession","title":"Populate Session Data for Module Testing — DW_test_mksession","text":"Populates supplied session variable testing.","code":""},{"path":"/reference/DW_test_mksession.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Populate Session Data for Module Testing — DW_test_mksession","text":"","code":"DW_test_mksession(session, id = \"DW\", id_UD = \"UD\")"},{"path":"/reference/DW_test_mksession.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Populate Session Data for Module Testing — DW_test_mksession","text":"session Shiny session variable (app) list (outside app) id ID string corresponds ID used call modules UI elements id_UD ID string corresponds ID used call UD modules UI elements","code":""},{"path":"/reference/DW_test_mksession.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Populate Session Data for Module Testing — DW_test_mksession","text":"list following elements isgood: Boolean indicating exit status function. session: value Shiny session variable (app) list (outside app) initialization. input: value shiny input end session initialization. state: App state. rsc: react_state components.","code":""},{"path":"/reference/DW_test_mksession.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Populate Session Data for Module Testing — DW_test_mksession","text":"","code":"sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b"},{"path":"/reference/DW_update_checksum.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates DW Module Checksum — DW_update_checksum","title":"Updates DW Module Checksum — DW_update_checksum","text":"Takes DW state updates checksum used trigger downstream updates","code":""},{"path":"/reference/DW_update_checksum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates DW Module Checksum — DW_update_checksum","text":"","code":"DW_update_checksum(state)"},{"path":"/reference/DW_update_checksum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates DW Module Checksum — DW_update_checksum","text":"state DW state DW_fetch_state()","code":""},{"path":"/reference/DW_update_checksum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates DW Module Checksum — DW_update_checksum","text":"DW state object checksum updated","code":""},{"path":"/reference/DW_update_checksum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Updates DW Module Checksum — DW_update_checksum","text":"","code":"# Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b session = sess_res$session input = sess_res$input # We also need a state variable state = sess_res$state state = DW_update_checksum(state) #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b"},{"path":"/reference/FG_Server.html","id":null,"dir":"Reference","previous_headings":"","what":"Figure Generation Server — FG_Server","title":"Figure Generation Server — FG_Server","text":"Server function figure generation module","code":""},{"path":"/reference/FG_Server.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Figure Generation Server — FG_Server","text":"","code":"FG_Server( id, FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"FG.yaml\"), id_ASM = \"ASM\", id_UD = \"UD\", id_DW = \"DW\", deployed = FALSE, react_state = NULL )"},{"path":"/reference/FG_Server.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Figure Generation Server — FG_Server","text":"id ID string corresponds ID used call module's UI function FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. id_ASM ID string app state management module used save load app states id_UD ID string upload data module used handle uploads name list element react_state data set stored. id_DW ID string data wrangling module process uploaded data deployed Boolean variable indicating whether app deployed . react_state Variable passed server allow reaction outside module (NULL)","code":""},{"path":"/reference/FG_Server.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Figure Generation Server — FG_Server","text":"FG Server object","code":""},{"path":"/reference/FG_Server.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Figure Generation Server — FG_Server","text":"","code":"if(interactive()){ # These are suggested packages library(shinydashboard) library(ggpubr) library(plotly) library(shinybusy) library(prompter) library(utils) library(clipr) library(formods) CSS <- \" .wrapfig { float: right; shape-margin: 20px; margin-right: 20px; margin-bottom: 20px; } \" # Default to not deployed if(!exists(\"deployed\")){ deployed = FALSE } #https://fontawesome.com/icons?from=io data_url = \"https://github.com/john-harrold/formods/raw/master/inst/test_data/TEST_DATA.xlsx\" ui <- dashboardPage( skin=\"black\", dashboardHeader(title=\"formods\"), dashboardSidebar( sidebarMenu( menuItem(\"Source Data\", tabName=\"upload\", icon=icon(\"table\")) , menuItem(\"Wrangle\", tabName=\"wrangle\", icon=icon(\"hat-cowboy\")), menuItem(\"Plot\", tabName=\"plot\", icon=icon(\"chart-line\")), menuItem(\"App State\", tabName=\"app_state\", icon=icon(\"archive\")), menuItem(\"App Info\", tabName=\"sysinfo\", icon=icon(\"book-medical\")) ) ), dashboardBody( tags$head( tags$style(HTML(CSS)) ), tabItems( tabItem(tabName=\"app_state\", box(title=\"Manage App State\", htmlOutput(NS(\"ASM\", \"ui_asm_compact\")))), tabItem(tabName=\"upload\", box(title=\"Load Data\", width=12, fluidRow( prompter::use_prompt(), column(width=6, htmlOutput(NS(\"UD\", \"UD_ui_compact\"))), column(width=6, tags$p( tags$img( class = \"wrapfig\", src = \"https://github.com/john-harrold/formods/raw/master/man/figures/logo.png\", width = 100, alt = \"formods logo\" ), 'Formods is a set of modules and an framework for developing modules which interact and create code to replicate analyses performed within an app. To experiment download this', tags$a(\"test dataset\", href=data_url), 'and upload it into the App using the form on the left.')) ) ) ), tabItem(tabName=\"wrangle\", box(title=\"Transform and Create Views of Your Data\", width=12, htmlOutput(NS(\"DW\", \"DW_ui_compact\")))), tabItem(tabName=\"plot\", box(title=\"Visualize Data\", width=12, htmlOutput(NS(\"FG\", \"FG_ui_compact\")))), tabItem(tabName=\"sysinfo\", box(title=\"System Details\", width=12, shinydashboard::tabBox( width = 12, title = NULL, shiny::tabPanel(id=\"sys_modules\", title=tagList(shiny::icon(\"ghost\"), \"Modules\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_modules\")) ), shiny::tabPanel(id=\"sys_packages\", title=tagList(shiny::icon(\"ghost\"), \"Packages\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_packages\")) ), shiny::tabPanel(id=\"sys_log\", title=tagList(shiny::icon(\"clipboard-list\"), \"App Log\"), verbatimTextOutput(NS(\"ASM\", \"ui_asm_sys_log\")) ), shiny::tabPanel(id=\"sys_options\", title=tagList(shiny::icon(\"sliders\"), \"R Options\"), htmlOutput(NS(\"ASM\", \"ui_asm_sys_options\")) ) ) )) ) ) ) # Main app server server <- function(input, output, session) { # Empty reactive object to track and react to # changes in the module state outside of the module react_FM = reactiveValues() # This is the list of module ids used for reproducible script generation. The # order here is important. mod_ids = c(\"UD\", \"DW\", \"FG\") #Populating with test data FG_test_mksession(session) # Module servers formods::ASM_Server(id=\"ASM\", deployed = deployed, react_state = react_FM, mod_ids = mod_ids) formods::UD_Server( id=\"UD\", id_ASM = \"ASM\", deployed = deployed, react_state = react_FM) formods::DW_Server( id=\"DW\", id_ASM = \"ASM\",id_UD = \"UD\", deployed = deployed, react_state = react_FM) formods::FG_Server( id=\"FG\", id_ASM = \"ASM\",id_UD = \"UD\", id_DW = \"DW\", deployed = deployed, react_state = react_FM) } shinyApp(ui, server) }"},{"path":"/reference/FG_append_report.html","id":null,"dir":"Reference","previous_headings":"","what":"Append Report Elements — FG_append_report","title":"Append Report Elements — FG_append_report","text":"Description","code":""},{"path":"/reference/FG_append_report.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append Report Elements — FG_append_report","text":"","code":"FG_append_report(state, rpt, rpttype, gen_code_only = FALSE)"},{"path":"/reference/FG_append_report.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append Report Elements — FG_append_report","text":"state FG state FG_fetch_state() rpt Report current content report appended function. details structure see documentation FM_generate_report. rpttype Type report generate (supported \"xlsx\", \"pptx\", \"docx\"). gen_code_only Boolean value indicating code generated (FALSE).","code":""},{"path":"/reference/FG_append_report.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Append Report Elements — FG_append_report","text":"list containing following elements isgood: Return status function. hasrptele: Boolean indicator module reportable elements. code: Data wrangling R command. msgs: Messages passed back user. rpt: Report additions passed back user.","code":""},{"path":[]},{"path":"/reference/FG_append_report.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Append Report Elements — FG_append_report","text":"","code":"# \\donttest{ sess_res = FG_test_mksession(session=list(), full_session=FALSE) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → FG: dest: file.path(\"config\",\"report.docx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → FG: dest: file.path(\"config\",\"report.pptx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → FG: dest: file.path(\"config\",\"report.yaml\") #> → FG: State initialized #> → FG: module checksum updated:49305b1f42ca13ff15881186db5740a2 #> → FG: module checksum updated:cd8600191428b21b7e5d47f90df95aa0 #> → FG: module checksum updated:6365492678ef133590bab11275d57adb #> → FG: module checksum updated:527e5e6fcbde41d1c076662d828d424d state = sess_res$state # This will read in the default PowerPoint report template rpt = onbrand::read_template( template = system.file(package=\"onbrand\",\"templates\",\"report.pptx\"), mapping = system.file(package=\"onbrand\",\"templates\",\"report.yaml\")) rpt_res = FG_append_report(state = state, rpt = rpt, rpttype = \"pptx\", gen_code_only=TRUE) # Shows if report elements are present rpt_res$hasrptele #> [1] TRUE # Code chunk to generate report element cat(paste(rpt_res$code, collapse=\"\\n\")) #> # Figure Fig_1(1): Individual profiles by cohort #> rpt = onbrand::report_add_slide(rpt, #> template = \"content_list\", #> elements = list( #> title = list( content = \"Individual profiles by cohort\", #> type = \"text\"), #> content_body = list( content = ( FG_myp_1 + ggforce::facet_wrap_paginate(vars(Cohort), nrow = 3, ncol = 4, page=1)), #> type = \"ggplot\"))) #> # Figure Fig_1(2): Individual profiles by cohort #> rpt = onbrand::report_add_slide(rpt, #> template = \"content_list\", #> elements = list( #> title = list( content = \"Individual profiles by cohort\", #> type = \"text\"), #> content_body = list( content = ( FG_myp_1 + ggforce::facet_wrap_paginate(vars(Cohort), nrow = 3, ncol = 4, page=2)), #> type = \"ggplot\"))) # }"},{"path":"/reference/FG_build.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluates Figure Generation Code — FG_build","title":"Evaluates Figure Generation Code — FG_build","text":"Takes current state rebuilds active figure. elements table row flagged deletion, deleted. cmd input NULL attempt append element figure.","code":""},{"path":"/reference/FG_build.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluates Figure Generation Code — FG_build","text":"","code":"FG_build( state, del_row = NULL, cmd = NULL, element = \"unknown\", desc = \"unknown\" )"},{"path":"/reference/FG_build.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluates Figure Generation Code — FG_build","text":"state FG state FG_fetch_state() del_row Row number deleted (NULL rows need deleted) cmd String containing plotting command. Set NULL initialize new figure force rebuild dataset update. element Short name figure element performed, eg. point desc Verbose description action performed","code":""},{"path":"/reference/FG_build.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluates Figure Generation Code — FG_build","text":"list following elements isgood: Return status function. msgs: Messages passed back user. pages: List element containing ggplot object (p) code generate object (code)","code":""},{"path":"/reference/FG_build.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluates Figure Generation Code — FG_build","text":"","code":"if(interactive()){ library(formods) # Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = FG_test_mksession(session=list(), full_session=FALSE) session = sess_res$session input = sess_res$input # This will create a populated FG state object: state = sess_res$state # This sets the current active figure to Fig_1 state[[\"FG\"]][[\"current_fig\"]] = \"Fig_1\" # This is a paginated figure, and we can access a specific # figure using the following: pg_1 = FG_extract_page(state, 1) pg_2 = FG_extract_page(state, 2) # This will give you access to the current figure directly: current_fig = FG_fetch_current_fig(state) # For example this will set the key for that figure: current_fig$key = \"Individual profiles by cohort (multiple pages)\" # Once you're done you can put it back into the state: state = FG_set_current_fig(state, current_fig) # If you made any changes to the actual figure, this will # force a rebuild of the current figure: state = FG_build( state=state, del_row = NULL, cmd = NULL) # To create a new empty figure you can do this: state = FG_new_fig(state) }"},{"path":"/reference/FG_extract_page.html","id":null,"dir":"Reference","previous_headings":"","what":"Extracts Specific Page from Paginated Figure — FG_extract_page","title":"Extracts Specific Page from Paginated Figure — FG_extract_page","text":"Used extract specified page current figure.","code":""},{"path":"/reference/FG_extract_page.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracts Specific Page from Paginated Figure — FG_extract_page","text":"","code":"FG_extract_page(state, page)"},{"path":"/reference/FG_extract_page.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracts Specific Page from Paginated Figure — FG_extract_page","text":"state FG state FG_fetch_state() page Page number extract","code":""},{"path":"/reference/FG_extract_page.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracts Specific Page from Paginated Figure — FG_extract_page","text":"ggplot object specified page.","code":""},{"path":"/reference/FG_extract_page.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extracts Specific Page from Paginated Figure — FG_extract_page","text":"","code":"if(interactive()){ library(formods) # Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = FG_test_mksession(session=list(), full_session=FALSE) session = sess_res$session input = sess_res$input # This will create a populated FG state object: state = sess_res$state # This sets the current active figure to Fig_1 state[[\"FG\"]][[\"current_fig\"]] = \"Fig_1\" # This is a paginated figure, and we can access a specific # figure using the following: pg_1 = FG_extract_page(state, 1) pg_2 = FG_extract_page(state, 2) # This will give you access to the current figure directly: current_fig = FG_fetch_current_fig(state) # For example this will set the key for that figure: current_fig$key = \"Individual profiles by cohort (multiple pages)\" # Once you're done you can put it back into the state: state = FG_set_current_fig(state, current_fig) # If you made any changes to the actual figure, this will # force a rebuild of the current figure: state = FG_build( state=state, del_row = NULL, cmd = NULL) # To create a new empty figure you can do this: state = FG_new_fig(state) }"},{"path":"/reference/FG_fetch_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Module Code — FG_fetch_code","title":"Fetch Module Code — FG_fetch_code","text":"Fetches code generate results seen app","code":""},{"path":"/reference/FG_fetch_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Module Code — FG_fetch_code","text":"","code":"FG_fetch_code(state)"},{"path":"/reference/FG_fetch_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Module Code — FG_fetch_code","text":"state UD state FG_fetch_state()","code":""},{"path":"/reference/FG_fetch_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Module Code — FG_fetch_code","text":"Character object vector lines code","code":""},{"path":"/reference/FG_fetch_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Module Code — FG_fetch_code","text":"","code":"# \\donttest{ # This will create a populated FG state object: sess_res = FG_test_mksession(session=list(), full_session=FALSE) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → FG: dest: file.path(\"config\",\"report.docx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → FG: dest: file.path(\"config\",\"report.pptx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → FG: dest: file.path(\"config\",\"report.yaml\") #> → FG: State initialized #> → FG: module checksum updated:49305b1f42ca13ff15881186db5740a2 #> → FG: module checksum updated:cd8600191428b21b7e5d47f90df95aa0 #> → FG: module checksum updated:6365492678ef133590bab11275d57adb #> → FG: module checksum updated:527e5e6fcbde41d1c076662d828d424d state = sess_res$state code = FG_fetch_code(state) cat(paste(code, collapse=\"\\n\")) #> # Individual profiles by cohort =========================================== #> FG_myp_1 = ggplot2::ggplot(data=DW_myDS_1) #> FG_myp_1 = FG_myp_1 + geom_line(aes(x=TIME_DY, y=DV, color=CMT, group=IDCMT)) #> FG_myp_1 = FG_myp_1 + ggforce::facet_wrap_paginate(vars(Cohort), nrow = 3, ncol = 4, page=1) #> FG_myp_1 = FG_myp_1 + scale_y_log10(limits=NULL) #> FG_myp_1 = FG_myp_1 + ggplot2::theme_light() # }"},{"path":"/reference/FG_fetch_current_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches Current Figure — FG_fetch_current_fig","title":"Fetches Current Figure — FG_fetch_current_fig","text":"Takes FG state returns current active figure","code":""},{"path":"/reference/FG_fetch_current_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches Current Figure — FG_fetch_current_fig","text":"","code":"FG_fetch_current_fig(state)"},{"path":"/reference/FG_fetch_current_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches Current Figure — FG_fetch_current_fig","text":"state FG state FG_fetch_state()","code":""},{"path":"/reference/FG_fetch_current_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches Current Figure — FG_fetch_current_fig","text":"List containing details active figure. structure list structure state$FG$figs output FG_fetch_state().","code":""},{"path":"/reference/FG_fetch_current_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches Current Figure — FG_fetch_current_fig","text":"","code":"if(interactive()){ library(formods) # Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = FG_test_mksession(session=list(), full_session=FALSE) session = sess_res$session input = sess_res$input # This will create a populated FG state object: state = sess_res$state # This sets the current active figure to Fig_1 state[[\"FG\"]][[\"current_fig\"]] = \"Fig_1\" # This is a paginated figure, and we can access a specific # figure using the following: pg_1 = FG_extract_page(state, 1) pg_2 = FG_extract_page(state, 2) # This will give you access to the current figure directly: current_fig = FG_fetch_current_fig(state) # For example this will set the key for that figure: current_fig$key = \"Individual profiles by cohort (multiple pages)\" # Once you're done you can put it back into the state: state = FG_set_current_fig(state, current_fig) # If you made any changes to the actual figure, this will # force a rebuild of the current figure: state = FG_build( state=state, del_row = NULL, cmd = NULL) # To create a new empty figure you can do this: state = FG_new_fig(state) }"},{"path":"/reference/FG_fetch_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch Figure Generation State — FG_fetch_state","title":"Fetch Figure Generation State — FG_fetch_state","text":"Merges default app options changes made UI","code":""},{"path":"/reference/FG_fetch_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch Figure Generation State — FG_fetch_state","text":"","code":"FG_fetch_state( id, input, session, FM_yaml_file, MOD_yaml_file, id_ASM = NULL, id_UD = NULL, id_DW = NULL, react_state )"},{"path":"/reference/FG_fetch_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch Figure Generation State — FG_fetch_state","text":"id Shiny module ID input Shiny input variable session Shiny session variable FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. id_ASM ID string app state management module used save load app states id_UD ID string upload data module used handle uploads name list element react_state data set stored. id_DW ID string data wrangling module process uploaded data react_state Variable passed server allow reaction outside module (NULL)","code":""},{"path":"/reference/FG_fetch_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch Figure Generation State — FG_fetch_state","text":"list containing current state app including default values yaml file well changes made user. structure list defined : yaml: Contents yaml file. MC: Module components yaml file. FG: Data wrangling state isgood: Boolean status state. Currently just TRUE button_counters: List counters detect button clicks. ui_msg: Message returned users perform actions. ui: Current value form elements UI. ui_ids: Vector UI elements module. ui_hold: List hold elements disable updates full ui referesh complete. checksum: checksum FG module used detect changes module. aes_elements: Plot elements defined aesthetics (.e. X geom_X) current_fig: fig_id currently figure. fig_cntr: Counter figures, incremented time new figure created. DSV: Available data sets UD DW modules. figs: List figures. view following structure: add_isgood: JMH checksum: Checksum figure used detect changes figure. code: Code generate figure start finish. code_fg_only: Code just generate figure. code_previous: Code load /wrangle dataset. elements_table: Table figure generation elements. fg_object_name: JMH fig_dsview: Name dataset view current figure (also R object name dataset view). fobj: JMH id: Character id (fig_idx) idx: Numeric id (1) isgood: Boolean status figure. FALSE evaluation/build fails. key: Figure key acts title/caption (user editable) msgs: JMH notes: Figure notes (user editable) num_pages: JMH page: JMH MOD_TYPE: Character data containing type module \"DW\" id: Character data containing module id module session variable. FM_yaml_file: App configuration file FM main section. MOD_yaml_file: Module configuration file MC main section.","code":""},{"path":"/reference/FG_fetch_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch Figure Generation State — FG_fetch_state","text":"","code":"# Configuration files FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\") MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"FG.yaml\") # We need to specify both the FG module id as well as the # id of the UD module that feeds into it. id = \"FG\" id_UD = \"UD\" id_DW = \"DW\" # These would be the Shiny input and session variables input = list() session = list() # Creating an empty state object state = FG_fetch_state(id = id, input = input, session = session, FM_yaml_file = FM_yaml_file, MOD_yaml_file = MOD_yaml_file, id_UD = id_UD, id_DW = id_DW, react_state = NULL) #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → FG: dest: file.path(\"config\",\"report.docx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → FG: dest: file.path(\"config\",\"report.pptx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → FG: dest: file.path(\"config\",\"report.yaml\") #> → FG: State initialized #> → FG: figure page change detected state #> $yaml #> $yaml$FM #> $yaml$FM$include #> $yaml$FM$include$files #> $yaml$FM$include$files[[1]] #> $yaml$FM$include$files[[1]]$file #> $yaml$FM$include$files[[1]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.docx\\\")\" #> #> $yaml$FM$include$files[[1]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.docx\\\")\" #> #> #> #> $yaml$FM$include$files[[2]] #> $yaml$FM$include$files[[2]]$file #> $yaml$FM$include$files[[2]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.pptx\\\")\" #> #> $yaml$FM$include$files[[2]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.pptx\\\")\" #> #> #> #> $yaml$FM$include$files[[3]] #> $yaml$FM$include$files[[3]]$file #> $yaml$FM$include$files[[3]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.yaml\\\")\" #> #> $yaml$FM$include$files[[3]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.yaml\\\")\" #> #> #> #> #> #> $yaml$FM$deployed #> [1] FALSE #> #> $yaml$FM$code #> $yaml$FM$code$theme #> [1] \"vibrant_ink\" #> #> $yaml$FM$code$showLineNumbers #> [1] TRUE #> #> $yaml$FM$code$gen_file #> [1] \"run_analysis.R\" #> #> $yaml$FM$code$gen_preamble #> [1] \"# formods automated output ------------------------------------------------\\n# https://formods.ubiquity.tools/\\nrm(list=ls())\" #> #> $yaml$FM$code$packages #> [1] \"onbrand\" \"writexl\" #> #> #> $yaml$FM$notifications #> $yaml$FM$notifications$config #> $yaml$FM$notifications$config$success #> $yaml$FM$notifications$config$success$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$success$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$success$background #> [1] \"#5bb85b\" #> #> #> $yaml$FM$notifications$config$failure #> $yaml$FM$notifications$config$failure$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$background #> [1] \"#d9534f\" #> #> #> $yaml$FM$notifications$config$info #> $yaml$FM$notifications$config$info$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$info$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$info$background #> [1] \"#5bc0de\" #> #> #> $yaml$FM$notifications$config$warning #> $yaml$FM$notifications$config$warning$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$background #> [1] \"#f0ac4d\" #> #> #> #> #> $yaml$FM$reporting #> $yaml$FM$reporting$enabled #> [1] TRUE #> #> $yaml$FM$reporting$content_init #> $yaml$FM$reporting$content_init$xlsx #> [1] \"rpt = list(summary = NULL,\\n sheets = list())\" #> #> $yaml$FM$reporting$content_init$docx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.docx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> $yaml$FM$reporting$content_init$pptx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.pptx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> #> #> $yaml$FM$ui #> $yaml$FM$ui$button_style #> [1] \"fill\" #> #> $yaml$FM$ui$select_size #> [1] 10 #> #> $yaml$FM$ui$color_green #> [1] \"#00BB8A\" #> #> $yaml$FM$ui$color_red #> [1] \"#FF475E\" #> #> $yaml$FM$ui$color_blue #> [1] \"#0088FF\" #> #> $yaml$FM$ui$color_purple #> [1] \"#bd2cf4\" #> #> #> $yaml$FM$data_meta #> $yaml$FM$data_meta$data_header #> [1] \"===NAME===<\/b>
===LABEL===<\/font><\/span>\" #> #> $yaml$FM$data_meta$subtext #> [1] \"===LABEL===: ===RANGE===\" #> #> $yaml$FM$data_meta$many_sep #> [1] \",⋅⋅⋅,\" #> #> $yaml$FM$data_meta$data_types #> $yaml$FM$data_meta$data_types$character #> $yaml$FM$data_meta$data_types$character$color #> [1] \"#DD4B39\" #> #> $yaml$FM$data_meta$data_types$character$label #> [1] \"text\" #> #> #> $yaml$FM$data_meta$data_types$double #> $yaml$FM$data_meta$data_types$double$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$double$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$integer #> $yaml$FM$data_meta$data_types$integer$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$integer$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$other #> $yaml$FM$data_meta$data_types$other$color #> [1] \"black\" #> #> $yaml$FM$data_meta$data_types$other$label #> [1] \"other\" #> #> #> #> #> $yaml$FM$labels #> $yaml$FM$labels$default_ds #> [1] \"Original data set\" #> #> #> $yaml$FM$user_files #> $yaml$FM$user_files$use_tmpdir #> [1] TRUE #> #> #> $yaml$FM$logging #> $yaml$FM$logging$enabled #> [1] TRUE #> #> $yaml$FM$logging$timestamp #> [1] TRUE #> #> $yaml$FM$logging$timestamp_fmt #> [1] \"%Y-%m-%d %H:%M:%S\" #> #> $yaml$FM$logging$log_file #> [1] \"formods_log.txt\" #> #> $yaml$FM$logging$console #> [1] TRUE #> #> #> #> #> $MC #> $MC$compact #> $MC$compact$code #> [1] TRUE #> #> $MC$compact$preview #> [1] \"ggplot\" #> #> $MC$compact$clip #> [1] TRUE #> #> #> $MC$reporting #> $MC$reporting$enabled #> [1] TRUE #> #> $MC$reporting$priority #> [1] 1 #> #> #> $MC$tooltips #> $MC$tooltips$include #> [1] TRUE #> #> $MC$tooltips$components #> $MC$tooltips$components$manual #> $MC$tooltips$components$manual$x #> [1] \"Numeric location on the x-axis\" #> #> $MC$tooltips$components$manual$y #> [1] \"Numeric location on the y-axis\" #> #> $MC$tooltips$components$manual$color #> [1] \"A named color red, blue, green\" #> #> $MC$tooltips$components$manual$linetype #> [1] \"Specify either solid, dashed, dotted, dotdash, longdash or twodash\" #> #> $MC$tooltips$components$manual$shape #> [1] \"Open shapes: square (0), circle (1), triangle (2); Filled shapes: square (15), circle (16), triangle (17)\" #> #> $MC$tooltips$components$manual$size #> [1] \"Numeric value\" #> #> $MC$tooltips$components$manual$alpha #> [1] \"Numeric value between 0 (completely transparent) and 1 (solid)\" #> #> $MC$tooltips$components$manual$group #> NULL #> #> $MC$tooltips$components$manual$xintercept #> NULL #> #> $MC$tooltips$components$manual$yintercept #> NULL #> #> #> #> $MC$tooltips$ph #> $MC$tooltips$ph$notes #> [1] \"Optional figure notes that will be carried over and used in other elements (e.g. reporting).\" #> #> $MC$tooltips$ph$fig_key #> [1] \"Unique description used for referencing figures and in other elements (e.g. reporting).\" #> #> #> $MC$tooltips$show_code #> [1] \"Show figure generation code\" #> #> $MC$tooltips$fg_elements #> [1] \"Current figure elements\" #> #> #> $MC$labels #> $MC$labels$components #> $MC$labels$components$x #> [1] \"x-axis\" #> #> $MC$labels$components$y #> [1] \"y-axis\" #> #> $MC$labels$components$color #> [1] \"color\" #> #> $MC$labels$components$linetype #> [1] \"line type\" #> #> $MC$labels$components$fill #> [1] \"fill color\" #> #> $MC$labels$components$weight #> [1] \"weight\" #> #> $MC$labels$components$ymin #> [1] \"ymin\" #> #> $MC$labels$components$ymax #> [1] \"ymax\" #> #> $MC$labels$components$lower #> [1] \"lower\" #> #> $MC$labels$components$middle #> [1] \"middle\" #> #> $MC$labels$components$upper #> [1] \"upper\" #> #> $MC$labels$components$shape #> [1] \"shape\" #> #> $MC$labels$components$size #> [1] \"size\" #> #> $MC$labels$components$alpha #> [1] \"transparency\" #> #> $MC$labels$components$group #> [1] \"group\" #> #> $MC$labels$components$xintercept #> [1] \"x intercept\" #> #> $MC$labels$components$yintercept #> [1] \"y intercept\" #> #> $MC$labels$components$yscale #> [1] \"y-scale\" #> #> $MC$labels$components$xscale #> [1] \"x-scale\" #> #> $MC$labels$components$ylim #> [1] \"y limits\" #> #> $MC$labels$components$xlim #> [1] \"x limits\" #> #> #> $MC$labels$ph #> $MC$labels$ph$xlab #> [1] \"x-axis label\" #> #> $MC$labels$ph$ylab #> [1] \"y-axis label\" #> #> $MC$labels$ph$ggtitle #> [1] \"plot title\" #> #> $MC$labels$ph$notes #> [1] \"optional notes here\" #> #> $MC$labels$ph$fig_key #> [1] \"title/caption\" #> #> $MC$labels$ph$manual #> [1] \"Manual\" #> #> $MC$labels$ph$axlim #> [1] \"0.1, 1000 # Empty for auto\" #> #> #> $MC$labels$manual #> [1] \"Manual\" #> #> $MC$labels$not_used #> [1] \"Not Used\" #> #> $MC$labels$curr_figs_none #> [1] \"No figures yet created\" #> #> $MC$labels$no_fig_elements #> [1] \"Add figure elements\" #> #> $MC$labels$new_fig #> [1] \"New\" #> #> $MC$labels$save_fig #> [1] \"Save\" #> #> $MC$labels$del_fig #> [1] \"Delete\" #> #> $MC$labels$copy_fig #> [1] \"Copy\" #> #> $MC$labels$clip_fig #> [1] \"Code\" #> #> $MC$labels$upds_fig #> [1] \"Data set\" #> #> $MC$labels$add_ele #> [1] \"Add Figure Element\" #> #> $MC$labels$msg_bad_label #> [1] \"No labels were specified, unable to add element.\" #> #> $MC$labels$msg_bad_facet #> [1] \"At least one column must be selected to add a faceting element.\" #> #> $MC$labels$msg_bad_element #> [1] \"Unable to add the specified element: ===ELEMENT===\" #> #> $MC$labels$msg_bad_manual_comp #> [1] \"The plot element component ===COMP=== was specified manually but \\nno manual value was provided.\" #> #> $MC$labels$select_current_fig #> [1] \"Current figure\" #> #> $MC$labels$select_current_view #> [1] \"Data from\" #> #> $MC$labels$no_figures_defined #> [1] \"No figures have been defined. There are no data sources to create figures. You need to load data and create data views to use this module.\" #> #> $MC$labels$busy #> $MC$labels$busy$fig_update #> [1] \"Updating the current figure. Please be patient...\" #> #> #> #> $MC$errors #> $MC$errors$element_not_added #> [1] \"Unable to add the data figure element:\" #> #> $MC$errors$current_key_empty #> [1] \"The figure description field cannot be empty.\" #> #> $MC$errors$only_one_element #> [1] \"Only one element of ===ELEMENT=== type is allowed. The old ===ELEMENT=== will be replaced.\" #> #> #> $MC$elements #> $MC$elements$line #> $MC$elements$line$choice #> [1] \"Line\" #> #> $MC$elements$line$subtext #> [1] \"Continuous line\" #> #> $MC$elements$line$ui_aes #> [1] \"x\" \"y\" \"color\" \"group\" \"linetype\" \"size\" \"alpha\" #> #> $MC$elements$line$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$line$fcn #> [1] \"geom_line\" #> #> #> $MC$elements$point #> $MC$elements$point$choice #> [1] \"Point\" #> #> $MC$elements$point$subtext #> [1] \"Scatter plot\" #> #> $MC$elements$point$ui_aes #> [1] \"x\" \"y\" \"color\" \"group\" \"shape\" \"size\" \"alpha\" #> #> $MC$elements$point$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$point$fcn #> [1] \"geom_point\" #> #> #> $MC$elements$errorbar #> $MC$elements$errorbar$choice #> [1] \"Errobar\" #> #> $MC$elements$errorbar$subtext #> [1] \"Errorbars around points\" #> #> $MC$elements$errorbar$ui_aes #> [1] \"x\" \"ymin\" \"ymax\" \"color\" \"group\" \"size\" \"alpha\" #> #> $MC$elements$errorbar$aes_req #> [1] \"x\" \"ymin\" \"ymax\" #> #> $MC$elements$errorbar$fcn #> [1] \"geom_errorbar\" #> #> #> $MC$elements$hguide #> $MC$elements$hguide$choice #> [1] \"H-Guide\" #> #> $MC$elements$hguide$subtext #> [1] \"Horizontal guide\" #> #> $MC$elements$hguide$ui_aes #> [1] \"yintercept\" \"linetype\" \"color\" \"size\" #> #> $MC$elements$hguide$aes_req #> [1] \"yintercept\" #> #> $MC$elements$hguide$fcn #> [1] \"geom_hline\" #> #> #> $MC$elements$vguide #> $MC$elements$vguide$choice #> [1] \"V-Guide\" #> #> $MC$elements$vguide$subtext #> [1] \"Vertical guide\" #> #> $MC$elements$vguide$ui_aes #> [1] \"xintercept\" \"linetype\" \"color\" \"size\" #> #> $MC$elements$vguide$aes_req #> [1] \"xintercept\" #> #> $MC$elements$vguide$fcn #> [1] \"geom_vline\" #> #> #> $MC$elements$facet #> $MC$elements$facet$choice #> [1] \"Facet\" #> #> $MC$elements$facet$subtext #> [1] \"Facet by one or more variables\" #> #> #> $MC$elements$label #> $MC$elements$label$choice #> [1] \"Label\" #> #> $MC$elements$label$subtext #> [1] \"Label axes or plot title\" #> #> $MC$elements$label$ui_text #> [1] \"xlab\" \"ylab\" \"ggtitle\" #> #> #> $MC$elements$scales #> $MC$elements$scales$choice #> [1] \"Format Axes\" #> #> $MC$elements$scales$subtext #> [1] \"Axis scales and limits\" #> #> #> $MC$elements$smooth #> $MC$elements$smooth$choice #> [1] \"Smooth Trend\" #> #> $MC$elements$smooth$subtext #> [1] \"Smoothed conditional means\" #> #> $MC$elements$smooth$ui_aes #> [1] \"x\" \"y\" \"color\" \"group\" \"fill\" \"weight\" #> [7] \"linetype\" \"size\" \"alpha\" \"ymax\" \"ymin\" #> #> $MC$elements$smooth$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$smooth$fcn #> [1] \"geom_smooth\" #> #> #> $MC$elements$ribbon #> $MC$elements$ribbon$choice #> [1] \"Shaded Area\" #> #> $MC$elements$ribbon$subtext #> [1] \"Creating prediction intervals\" #> #> $MC$elements$ribbon$ui_aes #> [1] \"x\" \"ymin\" \"ymax\" \"color\" \"group\" \"fill\" \"linetype\" #> [8] \"size\" \"alpha\" #> #> $MC$elements$ribbon$aes_req #> [1] \"x\" \"ymin\" \"ymax\" #> #> $MC$elements$ribbon$fcn #> [1] \"geom_ribbon\" #> #> #> $MC$elements$boxplot #> $MC$elements$boxplot$choice #> [1] \"Boxplot\" #> #> $MC$elements$boxplot$subtext #> [1] \"Box and whiskers plot\" #> #> $MC$elements$boxplot$ui_aes #> [1] \"x\" \"y\" \"lower\" \"middle\" \"upper\" \"ymin\" #> [7] \"ymax\" \"color\" \"group\" \"fill\" \"weight\" \"linetype\" #> [13] \"size\" \"shape\" \"alpha\" #> #> $MC$elements$boxplot$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$boxplot$fcn #> [1] \"geom_boxplot\" #> #> #> #> $MC$formatting #> $MC$formatting$code #> $MC$formatting$code$width #> [1] 800 #> #> $MC$formatting$code$height #> [1] 300 #> #> #> $MC$formatting$preview #> $MC$formatting$preview$width #> [1] 800 #> #> $MC$formatting$preview$height #> [1] 400 #> #> #> $MC$formatting$select_fg_page #> $MC$formatting$select_fg_page$width #> [1] 1000 #> #> #> $MC$formatting$notes #> $MC$formatting$notes$width #> [1] \"560px\" #> #> $MC$formatting$notes$height #> [1] \"75px\" #> #> #> $MC$formatting$components #> $MC$formatting$components$aes #> $MC$formatting$components$aes$width #> [1] \"100px\" #> #> #> $MC$formatting$components$facet #> $MC$formatting$components$facet$width #> [1] \"200px\" #> #> #> $MC$formatting$components$label #> $MC$formatting$components$label$width #> [1] \"150px\" #> #> #> $MC$formatting$components$axscale #> $MC$formatting$components$axscale$width #> [1] \"150px\" #> #> #> $MC$formatting$components$axlim #> $MC$formatting$components$axlim$width #> [1] \"150px\" #> #> #> #> $MC$formatting$select_current_fig #> $MC$formatting$select_current_fig$width #> [1] 200 #> #> #> $MC$formatting$select_current_view #> $MC$formatting$select_current_view$width #> [1] 200 #> #> #> $MC$formatting$fg_elements #> $MC$formatting$fg_elements$width #> [1] 600 #> #> $MC$formatting$fg_elements$height #> [1] 200 #> #> #> $MC$formatting$faceting #> $MC$formatting$faceting$nrow #> [1] 3 #> #> $MC$formatting$faceting$ncol #> [1] 4 #> #> #> $MC$formatting$button_fig_del #> $MC$formatting$button_fig_del$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_del$block #> [1] TRUE #> #> $MC$formatting$button_fig_del$tooltip #> [1] \"Delete the current figure.\" #> #> $MC$formatting$button_fig_del$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_save #> $MC$formatting$button_fig_save$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_save$block #> [1] TRUE #> #> $MC$formatting$button_fig_save$tooltip #> [1] \"Save changes to caption, notes and data source.\" #> #> $MC$formatting$button_fig_save$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_clip #> $MC$formatting$button_fig_clip$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_clip$block #> [1] TRUE #> #> $MC$formatting$button_fig_clip$tooltip #> [1] \"Copy code to generate current figure to the clipboard.\" #> #> $MC$formatting$button_fig_clip$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_copy #> $MC$formatting$button_fig_copy$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_copy$block #> [1] TRUE #> #> $MC$formatting$button_fig_copy$tooltip #> [1] \"Copy current figure to a new figure.\" #> #> $MC$formatting$button_fig_copy$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_new #> $MC$formatting$button_fig_new$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_new$block #> [1] TRUE #> #> $MC$formatting$button_fig_new$tooltip #> [1] \"Create a new empty figure.\" #> #> $MC$formatting$button_fig_new$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_add #> $MC$formatting$button_fig_add$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_add$block #> [1] TRUE #> #> #> #> $MC$post_processing #> [1] \"===FGOBJ=== = ===FGOBJ=== + ggplot2::theme_light()\" #> #> $MC$fg_object_name #> [1] \"myp\" #> #> $MC$code #> $MC$code$packages #> [1] \"ggplot2\" \"ggforce\" #> #> $MC$code$readOnly #> [1] TRUE #> #> $MC$code$mode #> [1] \"r\" #> #> $MC$code$preamble #> [1] \"# Generating figures ------------------------------------------------------\" #> #> #> #> $FG #> $FG$button_counters #> $FG$button_counters$button_element_add #> [1] 0 #> #> $FG$button_counters$button_fig_save #> [1] 0 #> #> $FG$button_counters$button_fig_new #> [1] 0 #> #> $FG$button_counters$button_fig_del #> [1] 0 #> #> $FG$button_counters$button_fig_copy #> [1] 0 #> #> #> $FG$ui_hold #> $FG$ui_hold$hot_fg_elements #> [1] FALSE #> #> $FG$ui_hold$text_fig_key #> [1] FALSE #> #> $FG$ui_hold$text_fig_notes #> [1] FALSE #> #> $FG$ui_hold$select_current_view #> [1] FALSE #> #> $FG$ui_hold$select_current_fig #> [1] FALSE #> #> #> $FG$ui_ids #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_color\" \"select_component_group\" #> [5] \"select_component_linetype\" \"select_component_size\" #> [7] \"select_component_alpha\" \"text_component_x_manual\" #> [9] \"text_component_y_manual\" \"text_component_color_manual\" #> [11] \"text_component_group_manual\" \"text_component_linetype_manual\" #> [13] \"text_component_size_manual\" \"text_component_alpha_manual\" #> [15] \"select_component_shape\" \"text_component_shape_manual\" #> [17] \"select_component_ymin\" \"select_component_ymax\" #> [19] \"text_component_ymin_manual\" \"text_component_ymax_manual\" #> [21] \"select_component_yintercept\" \"text_component_yintercept_manual\" #> [23] \"select_component_xintercept\" \"text_component_xintercept_manual\" #> [25] \"select_component_fill\" \"select_component_weight\" #> [27] \"text_component_fill_manual\" \"text_component_weight_manual\" #> [29] \"select_component_lower\" \"select_component_middle\" #> [31] \"select_component_upper\" \"text_component_lower_manual\" #> [33] \"text_component_middle_manual\" \"text_component_upper_manual\" #> [35] \"button_fig_new\" \"button_fig_save\" #> [37] \"button_fig_del\" \"button_fig_copy\" #> [39] \"button_element_add\" \"hot_fg_elements\" #> [41] \"text_fig_key\" \"text_fig_notes\" #> [43] \"text_component_xlab\" \"text_component_ylab\" #> [45] \"text_component_xlim\" \"text_component_ylim\" #> [47] \"text_component_ggtitle\" \"select_fg_page\" #> [49] \"select_current_fig\" \"select_current_view\" #> [51] \"select_component_facet\" \"select_component_xscale\" #> [53] \"select_component_yscale\" \"select_fg_element\" #> #> $FG$isgood #> [1] FALSE #> #> $FG$DSV #> $FG$DSV$isgood #> [1] FALSE #> #> $FG$DSV$hasds #> [1] FALSE #> #> $FG$DSV$catalog #> NULL #> #> $FG$DSV$modules #> list() #> #> $FG$DSV$ds #> list() #> #> #> $FG$fig_cntr #> [1] 0 #> #> $FG$aes_elements #> [1] \"line\" \"point\" \"errorbar\" \"hguide\" \"vguide\" \"smooth\" \"ribbon\" #> [8] \"boxplot\" #> #> $FG$auto_elements #> $FG$auto_elements$line #> $FG$auto_elements$line$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_color\" \"select_component_group\" #> [5] \"select_component_linetype\" \"select_component_size\" #> [7] \"select_component_alpha\" #> #> $FG$auto_elements$line$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_color_manual\" \"text_component_group_manual\" #> [5] \"text_component_linetype_manual\" \"text_component_size_manual\" #> [7] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$point #> $FG$auto_elements$point$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" \"select_component_color\" #> [4] \"select_component_group\" \"select_component_shape\" \"select_component_size\" #> [7] \"select_component_alpha\" #> #> $FG$auto_elements$point$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_color_manual\" \"text_component_group_manual\" #> [5] \"text_component_shape_manual\" \"text_component_size_manual\" #> [7] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$errorbar #> $FG$auto_elements$errorbar$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_ymin\" \"select_component_ymax\" #> [4] \"select_component_color\" \"select_component_group\" \"select_component_size\" #> [7] \"select_component_alpha\" #> #> $FG$auto_elements$errorbar$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_ymin_manual\" #> [3] \"text_component_ymax_manual\" \"text_component_color_manual\" #> [5] \"text_component_group_manual\" \"text_component_size_manual\" #> [7] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$hguide #> $FG$auto_elements$hguide$ui_aes_select_id #> [1] \"select_component_yintercept\" \"select_component_linetype\" #> [3] \"select_component_color\" \"select_component_size\" #> #> $FG$auto_elements$hguide$ui_aes_manual_id #> [1] \"text_component_yintercept_manual\" \"text_component_linetype_manual\" #> [3] \"text_component_color_manual\" \"text_component_size_manual\" #> #> #> $FG$auto_elements$vguide #> $FG$auto_elements$vguide$ui_aes_select_id #> [1] \"select_component_xintercept\" \"select_component_linetype\" #> [3] \"select_component_color\" \"select_component_size\" #> #> $FG$auto_elements$vguide$ui_aes_manual_id #> [1] \"text_component_xintercept_manual\" \"text_component_linetype_manual\" #> [3] \"text_component_color_manual\" \"text_component_size_manual\" #> #> #> $FG$auto_elements$smooth #> $FG$auto_elements$smooth$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_color\" \"select_component_group\" #> [5] \"select_component_fill\" \"select_component_weight\" #> [7] \"select_component_linetype\" \"select_component_size\" #> [9] \"select_component_alpha\" \"select_component_ymax\" #> [11] \"select_component_ymin\" #> #> $FG$auto_elements$smooth$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_color_manual\" \"text_component_group_manual\" #> [5] \"text_component_fill_manual\" \"text_component_weight_manual\" #> [7] \"text_component_linetype_manual\" \"text_component_size_manual\" #> [9] \"text_component_alpha_manual\" \"text_component_ymax_manual\" #> [11] \"text_component_ymin_manual\" #> #> #> $FG$auto_elements$ribbon #> $FG$auto_elements$ribbon$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_ymin\" #> [3] \"select_component_ymax\" \"select_component_color\" #> [5] \"select_component_group\" \"select_component_fill\" #> [7] \"select_component_linetype\" \"select_component_size\" #> [9] \"select_component_alpha\" #> #> $FG$auto_elements$ribbon$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_ymin_manual\" #> [3] \"text_component_ymax_manual\" \"text_component_color_manual\" #> [5] \"text_component_group_manual\" \"text_component_fill_manual\" #> [7] \"text_component_linetype_manual\" \"text_component_size_manual\" #> [9] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$boxplot #> $FG$auto_elements$boxplot$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_lower\" \"select_component_middle\" #> [5] \"select_component_upper\" \"select_component_ymin\" #> [7] \"select_component_ymax\" \"select_component_color\" #> [9] \"select_component_group\" \"select_component_fill\" #> [11] \"select_component_weight\" \"select_component_linetype\" #> [13] \"select_component_size\" \"select_component_shape\" #> [15] \"select_component_alpha\" #> #> $FG$auto_elements$boxplot$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_lower_manual\" \"text_component_middle_manual\" #> [5] \"text_component_upper_manual\" \"text_component_ymin_manual\" #> [7] \"text_component_ymax_manual\" \"text_component_color_manual\" #> [9] \"text_component_group_manual\" \"text_component_fill_manual\" #> [11] \"text_component_weight_manual\" \"text_component_linetype_manual\" #> [13] \"text_component_size_manual\" \"text_component_shape_manual\" #> [15] \"text_component_alpha_manual\" #> #> #> #> $FG$ui #> $FG$ui$select_component_x #> [1] \"\" #> #> $FG$ui$select_component_y #> [1] \"\" #> #> $FG$ui$select_component_color #> [1] \"\" #> #> $FG$ui$select_component_group #> [1] \"\" #> #> $FG$ui$select_component_linetype #> [1] \"\" #> #> $FG$ui$select_component_size #> [1] \"\" #> #> $FG$ui$select_component_alpha #> [1] \"\" #> #> $FG$ui$text_component_x_manual #> [1] \"\" #> #> $FG$ui$text_component_y_manual #> [1] \"\" #> #> $FG$ui$text_component_color_manual #> [1] \"\" #> #> $FG$ui$text_component_group_manual #> [1] \"\" #> #> $FG$ui$text_component_linetype_manual #> [1] \"\" #> #> $FG$ui$text_component_size_manual #> [1] \"\" #> #> $FG$ui$text_component_alpha_manual #> [1] \"\" #> #> $FG$ui$select_component_shape #> [1] \"\" #> #> $FG$ui$text_component_shape_manual #> [1] \"\" #> #> $FG$ui$select_component_ymin #> [1] \"\" #> #> $FG$ui$select_component_ymax #> [1] \"\" #> #> $FG$ui$text_component_ymin_manual #> [1] \"\" #> #> $FG$ui$text_component_ymax_manual #> [1] \"\" #> #> $FG$ui$select_component_yintercept #> [1] \"\" #> #> $FG$ui$text_component_yintercept_manual #> [1] \"\" #> #> $FG$ui$select_component_xintercept #> [1] \"\" #> #> $FG$ui$text_component_xintercept_manual #> [1] \"\" #> #> $FG$ui$select_component_fill #> [1] \"\" #> #> $FG$ui$select_component_weight #> [1] \"\" #> #> $FG$ui$text_component_fill_manual #> [1] \"\" #> #> $FG$ui$text_component_weight_manual #> [1] \"\" #> #> $FG$ui$select_component_lower #> [1] \"\" #> #> $FG$ui$select_component_middle #> [1] \"\" #> #> $FG$ui$select_component_upper #> [1] \"\" #> #> $FG$ui$text_component_lower_manual #> [1] \"\" #> #> $FG$ui$text_component_middle_manual #> [1] \"\" #> #> $FG$ui$text_component_upper_manual #> [1] \"\" #> #> $FG$ui$button_fig_new #> [1] \"\" #> #> $FG$ui$button_fig_save #> [1] \"\" #> #> $FG$ui$button_fig_del #> [1] \"\" #> #> $FG$ui$button_fig_copy #> [1] \"\" #> #> $FG$ui$button_element_add #> [1] \"\" #> #> $FG$ui$hot_fg_elements #> [1] \"\" #> #> $FG$ui$text_fig_key #> [1] \"\" #> #> $FG$ui$text_fig_notes #> [1] \"\" #> #> $FG$ui$text_component_xlab #> [1] \"\" #> #> $FG$ui$text_component_ylab #> [1] \"\" #> #> $FG$ui$text_component_xlim #> [1] \"\" #> #> $FG$ui$text_component_ylim #> [1] \"\" #> #> $FG$ui$text_component_ggtitle #> [1] \"\" #> #> $FG$ui$select_fg_page #> [1] \"\" #> #> $FG$ui$select_current_fig #> [1] \"\" #> #> $FG$ui$select_current_view #> [1] \"\" #> #> $FG$ui$select_component_facet #> [1] \"\" #> #> $FG$ui$select_component_xscale #> [1] \"\" #> #> $FG$ui$select_component_yscale #> [1] \"\" #> #> $FG$ui$select_fg_element #> [1] \"\" #> #> #> $FG$current_fig #> [1] \"\" #> #> $FG$figs #> $FG$figs[[1]] #> $FG$figs[[1]]$page #> [1] \"\" #> #> #> #> #> $MOD_TYPE #> [1] \"FG\" #> #> $id #> [1] \"FG\" #> #> $dep_mod_ids #> [1] \"UD\" \"DW\" #> #> $FM_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/formods.yaml\" #> #> $MOD_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/FG.yaml\" #> #> $shiny_token #> [1] \"non_shiny\" #>"},{"path":"/reference/FG_init_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize FG Module State — FG_init_state","title":"Initialize FG Module State — FG_init_state","text":"Creates list initialized module state","code":""},{"path":"/reference/FG_init_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize FG Module State — FG_init_state","text":"","code":"FG_init_state(FM_yaml_file, MOD_yaml_file, id, id_UD, id_DW, session)"},{"path":"/reference/FG_init_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize FG Module State — FG_init_state","text":"FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. id Shiny module ID id_UD ID string upload data module used handle uploads name list element react_state data set stored. id_DW ID string data wrangling module process uploaded data session Shiny session variable","code":""},{"path":"/reference/FG_init_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize FG Module State — FG_init_state","text":"list containing empty app state object","code":""},{"path":"/reference/FG_init_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize FG Module State — FG_init_state","text":"","code":"# These would be the Shiny input and session variables input = list() session = list() state = FG_init_state( FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"FG.yaml\"), id = \"FG\", id_UD = \"UD\", id_DW = \"DW\", session = session) #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → FG: dest: file.path(\"config\",\"report.docx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → FG: dest: file.path(\"config\",\"report.pptx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → FG: dest: file.path(\"config\",\"report.yaml\") #> → FG: State initialized state #> $yaml #> $yaml$FM #> $yaml$FM$include #> $yaml$FM$include$files #> $yaml$FM$include$files[[1]] #> $yaml$FM$include$files[[1]]$file #> $yaml$FM$include$files[[1]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.docx\\\")\" #> #> $yaml$FM$include$files[[1]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.docx\\\")\" #> #> #> #> $yaml$FM$include$files[[2]] #> $yaml$FM$include$files[[2]]$file #> $yaml$FM$include$files[[2]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.pptx\\\")\" #> #> $yaml$FM$include$files[[2]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.pptx\\\")\" #> #> #> #> $yaml$FM$include$files[[3]] #> $yaml$FM$include$files[[3]]$file #> $yaml$FM$include$files[[3]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.yaml\\\")\" #> #> $yaml$FM$include$files[[3]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.yaml\\\")\" #> #> #> #> #> #> $yaml$FM$deployed #> [1] FALSE #> #> $yaml$FM$code #> $yaml$FM$code$theme #> [1] \"vibrant_ink\" #> #> $yaml$FM$code$showLineNumbers #> [1] TRUE #> #> $yaml$FM$code$gen_file #> [1] \"run_analysis.R\" #> #> $yaml$FM$code$gen_preamble #> [1] \"# formods automated output ------------------------------------------------\\n# https://formods.ubiquity.tools/\\nrm(list=ls())\" #> #> $yaml$FM$code$packages #> [1] \"onbrand\" \"writexl\" #> #> #> $yaml$FM$notifications #> $yaml$FM$notifications$config #> $yaml$FM$notifications$config$success #> $yaml$FM$notifications$config$success$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$success$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$success$background #> [1] \"#5bb85b\" #> #> #> $yaml$FM$notifications$config$failure #> $yaml$FM$notifications$config$failure$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$background #> [1] \"#d9534f\" #> #> #> $yaml$FM$notifications$config$info #> $yaml$FM$notifications$config$info$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$info$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$info$background #> [1] \"#5bc0de\" #> #> #> $yaml$FM$notifications$config$warning #> $yaml$FM$notifications$config$warning$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$background #> [1] \"#f0ac4d\" #> #> #> #> #> $yaml$FM$reporting #> $yaml$FM$reporting$enabled #> [1] TRUE #> #> $yaml$FM$reporting$content_init #> $yaml$FM$reporting$content_init$xlsx #> [1] \"rpt = list(summary = NULL,\\n sheets = list())\" #> #> $yaml$FM$reporting$content_init$docx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.docx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> $yaml$FM$reporting$content_init$pptx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.pptx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> #> #> $yaml$FM$ui #> $yaml$FM$ui$button_style #> [1] \"fill\" #> #> $yaml$FM$ui$select_size #> [1] 10 #> #> $yaml$FM$ui$color_green #> [1] \"#00BB8A\" #> #> $yaml$FM$ui$color_red #> [1] \"#FF475E\" #> #> $yaml$FM$ui$color_blue #> [1] \"#0088FF\" #> #> $yaml$FM$ui$color_purple #> [1] \"#bd2cf4\" #> #> #> $yaml$FM$data_meta #> $yaml$FM$data_meta$data_header #> [1] \"===NAME===<\/b>
===LABEL===<\/font><\/span>\" #> #> $yaml$FM$data_meta$subtext #> [1] \"===LABEL===: ===RANGE===\" #> #> $yaml$FM$data_meta$many_sep #> [1] \",⋅⋅⋅,\" #> #> $yaml$FM$data_meta$data_types #> $yaml$FM$data_meta$data_types$character #> $yaml$FM$data_meta$data_types$character$color #> [1] \"#DD4B39\" #> #> $yaml$FM$data_meta$data_types$character$label #> [1] \"text\" #> #> #> $yaml$FM$data_meta$data_types$double #> $yaml$FM$data_meta$data_types$double$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$double$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$integer #> $yaml$FM$data_meta$data_types$integer$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$integer$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$other #> $yaml$FM$data_meta$data_types$other$color #> [1] \"black\" #> #> $yaml$FM$data_meta$data_types$other$label #> [1] \"other\" #> #> #> #> #> $yaml$FM$labels #> $yaml$FM$labels$default_ds #> [1] \"Original data set\" #> #> #> $yaml$FM$user_files #> $yaml$FM$user_files$use_tmpdir #> [1] TRUE #> #> #> $yaml$FM$logging #> $yaml$FM$logging$enabled #> [1] TRUE #> #> $yaml$FM$logging$timestamp #> [1] TRUE #> #> $yaml$FM$logging$timestamp_fmt #> [1] \"%Y-%m-%d %H:%M:%S\" #> #> $yaml$FM$logging$log_file #> [1] \"formods_log.txt\" #> #> $yaml$FM$logging$console #> [1] TRUE #> #> #> #> #> $MC #> $MC$compact #> $MC$compact$code #> [1] TRUE #> #> $MC$compact$preview #> [1] \"ggplot\" #> #> $MC$compact$clip #> [1] TRUE #> #> #> $MC$reporting #> $MC$reporting$enabled #> [1] TRUE #> #> $MC$reporting$priority #> [1] 1 #> #> #> $MC$tooltips #> $MC$tooltips$include #> [1] TRUE #> #> $MC$tooltips$components #> $MC$tooltips$components$manual #> $MC$tooltips$components$manual$x #> [1] \"Numeric location on the x-axis\" #> #> $MC$tooltips$components$manual$y #> [1] \"Numeric location on the y-axis\" #> #> $MC$tooltips$components$manual$color #> [1] \"A named color red, blue, green\" #> #> $MC$tooltips$components$manual$linetype #> [1] \"Specify either solid, dashed, dotted, dotdash, longdash or twodash\" #> #> $MC$tooltips$components$manual$shape #> [1] \"Open shapes: square (0), circle (1), triangle (2); Filled shapes: square (15), circle (16), triangle (17)\" #> #> $MC$tooltips$components$manual$size #> [1] \"Numeric value\" #> #> $MC$tooltips$components$manual$alpha #> [1] \"Numeric value between 0 (completely transparent) and 1 (solid)\" #> #> $MC$tooltips$components$manual$group #> NULL #> #> $MC$tooltips$components$manual$xintercept #> NULL #> #> $MC$tooltips$components$manual$yintercept #> NULL #> #> #> #> $MC$tooltips$ph #> $MC$tooltips$ph$notes #> [1] \"Optional figure notes that will be carried over and used in other elements (e.g. reporting).\" #> #> $MC$tooltips$ph$fig_key #> [1] \"Unique description used for referencing figures and in other elements (e.g. reporting).\" #> #> #> $MC$tooltips$show_code #> [1] \"Show figure generation code\" #> #> $MC$tooltips$fg_elements #> [1] \"Current figure elements\" #> #> #> $MC$labels #> $MC$labels$components #> $MC$labels$components$x #> [1] \"x-axis\" #> #> $MC$labels$components$y #> [1] \"y-axis\" #> #> $MC$labels$components$color #> [1] \"color\" #> #> $MC$labels$components$linetype #> [1] \"line type\" #> #> $MC$labels$components$fill #> [1] \"fill color\" #> #> $MC$labels$components$weight #> [1] \"weight\" #> #> $MC$labels$components$ymin #> [1] \"ymin\" #> #> $MC$labels$components$ymax #> [1] \"ymax\" #> #> $MC$labels$components$lower #> [1] \"lower\" #> #> $MC$labels$components$middle #> [1] \"middle\" #> #> $MC$labels$components$upper #> [1] \"upper\" #> #> $MC$labels$components$shape #> [1] \"shape\" #> #> $MC$labels$components$size #> [1] \"size\" #> #> $MC$labels$components$alpha #> [1] \"transparency\" #> #> $MC$labels$components$group #> [1] \"group\" #> #> $MC$labels$components$xintercept #> [1] \"x intercept\" #> #> $MC$labels$components$yintercept #> [1] \"y intercept\" #> #> $MC$labels$components$yscale #> [1] \"y-scale\" #> #> $MC$labels$components$xscale #> [1] \"x-scale\" #> #> $MC$labels$components$ylim #> [1] \"y limits\" #> #> $MC$labels$components$xlim #> [1] \"x limits\" #> #> #> $MC$labels$ph #> $MC$labels$ph$xlab #> [1] \"x-axis label\" #> #> $MC$labels$ph$ylab #> [1] \"y-axis label\" #> #> $MC$labels$ph$ggtitle #> [1] \"plot title\" #> #> $MC$labels$ph$notes #> [1] \"optional notes here\" #> #> $MC$labels$ph$fig_key #> [1] \"title/caption\" #> #> $MC$labels$ph$manual #> [1] \"Manual\" #> #> $MC$labels$ph$axlim #> [1] \"0.1, 1000 # Empty for auto\" #> #> #> $MC$labels$manual #> [1] \"Manual\" #> #> $MC$labels$not_used #> [1] \"Not Used\" #> #> $MC$labels$curr_figs_none #> [1] \"No figures yet created\" #> #> $MC$labels$no_fig_elements #> [1] \"Add figure elements\" #> #> $MC$labels$new_fig #> [1] \"New\" #> #> $MC$labels$save_fig #> [1] \"Save\" #> #> $MC$labels$del_fig #> [1] \"Delete\" #> #> $MC$labels$copy_fig #> [1] \"Copy\" #> #> $MC$labels$clip_fig #> [1] \"Code\" #> #> $MC$labels$upds_fig #> [1] \"Data set\" #> #> $MC$labels$add_ele #> [1] \"Add Figure Element\" #> #> $MC$labels$msg_bad_label #> [1] \"No labels were specified, unable to add element.\" #> #> $MC$labels$msg_bad_facet #> [1] \"At least one column must be selected to add a faceting element.\" #> #> $MC$labels$msg_bad_element #> [1] \"Unable to add the specified element: ===ELEMENT===\" #> #> $MC$labels$msg_bad_manual_comp #> [1] \"The plot element component ===COMP=== was specified manually but \\nno manual value was provided.\" #> #> $MC$labels$select_current_fig #> [1] \"Current figure\" #> #> $MC$labels$select_current_view #> [1] \"Data from\" #> #> $MC$labels$no_figures_defined #> [1] \"No figures have been defined. There are no data sources to create figures. You need to load data and create data views to use this module.\" #> #> $MC$labels$busy #> $MC$labels$busy$fig_update #> [1] \"Updating the current figure. Please be patient...\" #> #> #> #> $MC$errors #> $MC$errors$element_not_added #> [1] \"Unable to add the data figure element:\" #> #> $MC$errors$current_key_empty #> [1] \"The figure description field cannot be empty.\" #> #> $MC$errors$only_one_element #> [1] \"Only one element of ===ELEMENT=== type is allowed. The old ===ELEMENT=== will be replaced.\" #> #> #> $MC$elements #> $MC$elements$line #> $MC$elements$line$choice #> [1] \"Line\" #> #> $MC$elements$line$subtext #> [1] \"Continuous line\" #> #> $MC$elements$line$ui_aes #> [1] \"x\" \"y\" \"color\" \"group\" \"linetype\" \"size\" \"alpha\" #> #> $MC$elements$line$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$line$fcn #> [1] \"geom_line\" #> #> #> $MC$elements$point #> $MC$elements$point$choice #> [1] \"Point\" #> #> $MC$elements$point$subtext #> [1] \"Scatter plot\" #> #> $MC$elements$point$ui_aes #> [1] \"x\" \"y\" \"color\" \"group\" \"shape\" \"size\" \"alpha\" #> #> $MC$elements$point$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$point$fcn #> [1] \"geom_point\" #> #> #> $MC$elements$errorbar #> $MC$elements$errorbar$choice #> [1] \"Errobar\" #> #> $MC$elements$errorbar$subtext #> [1] \"Errorbars around points\" #> #> $MC$elements$errorbar$ui_aes #> [1] \"x\" \"ymin\" \"ymax\" \"color\" \"group\" \"size\" \"alpha\" #> #> $MC$elements$errorbar$aes_req #> [1] \"x\" \"ymin\" \"ymax\" #> #> $MC$elements$errorbar$fcn #> [1] \"geom_errorbar\" #> #> #> $MC$elements$hguide #> $MC$elements$hguide$choice #> [1] \"H-Guide\" #> #> $MC$elements$hguide$subtext #> [1] \"Horizontal guide\" #> #> $MC$elements$hguide$ui_aes #> [1] \"yintercept\" \"linetype\" \"color\" \"size\" #> #> $MC$elements$hguide$aes_req #> [1] \"yintercept\" #> #> $MC$elements$hguide$fcn #> [1] \"geom_hline\" #> #> #> $MC$elements$vguide #> $MC$elements$vguide$choice #> [1] \"V-Guide\" #> #> $MC$elements$vguide$subtext #> [1] \"Vertical guide\" #> #> $MC$elements$vguide$ui_aes #> [1] \"xintercept\" \"linetype\" \"color\" \"size\" #> #> $MC$elements$vguide$aes_req #> [1] \"xintercept\" #> #> $MC$elements$vguide$fcn #> [1] \"geom_vline\" #> #> #> $MC$elements$facet #> $MC$elements$facet$choice #> [1] \"Facet\" #> #> $MC$elements$facet$subtext #> [1] \"Facet by one or more variables\" #> #> #> $MC$elements$label #> $MC$elements$label$choice #> [1] \"Label\" #> #> $MC$elements$label$subtext #> [1] \"Label axes or plot title\" #> #> $MC$elements$label$ui_text #> [1] \"xlab\" \"ylab\" \"ggtitle\" #> #> #> $MC$elements$scales #> $MC$elements$scales$choice #> [1] \"Format Axes\" #> #> $MC$elements$scales$subtext #> [1] \"Axis scales and limits\" #> #> #> $MC$elements$smooth #> $MC$elements$smooth$choice #> [1] \"Smooth Trend\" #> #> $MC$elements$smooth$subtext #> [1] \"Smoothed conditional means\" #> #> $MC$elements$smooth$ui_aes #> [1] \"x\" \"y\" \"color\" \"group\" \"fill\" \"weight\" #> [7] \"linetype\" \"size\" \"alpha\" \"ymax\" \"ymin\" #> #> $MC$elements$smooth$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$smooth$fcn #> [1] \"geom_smooth\" #> #> #> $MC$elements$ribbon #> $MC$elements$ribbon$choice #> [1] \"Shaded Area\" #> #> $MC$elements$ribbon$subtext #> [1] \"Creating prediction intervals\" #> #> $MC$elements$ribbon$ui_aes #> [1] \"x\" \"ymin\" \"ymax\" \"color\" \"group\" \"fill\" \"linetype\" #> [8] \"size\" \"alpha\" #> #> $MC$elements$ribbon$aes_req #> [1] \"x\" \"ymin\" \"ymax\" #> #> $MC$elements$ribbon$fcn #> [1] \"geom_ribbon\" #> #> #> $MC$elements$boxplot #> $MC$elements$boxplot$choice #> [1] \"Boxplot\" #> #> $MC$elements$boxplot$subtext #> [1] \"Box and whiskers plot\" #> #> $MC$elements$boxplot$ui_aes #> [1] \"x\" \"y\" \"lower\" \"middle\" \"upper\" \"ymin\" #> [7] \"ymax\" \"color\" \"group\" \"fill\" \"weight\" \"linetype\" #> [13] \"size\" \"shape\" \"alpha\" #> #> $MC$elements$boxplot$aes_req #> [1] \"x\" \"y\" #> #> $MC$elements$boxplot$fcn #> [1] \"geom_boxplot\" #> #> #> #> $MC$formatting #> $MC$formatting$code #> $MC$formatting$code$width #> [1] 800 #> #> $MC$formatting$code$height #> [1] 300 #> #> #> $MC$formatting$preview #> $MC$formatting$preview$width #> [1] 800 #> #> $MC$formatting$preview$height #> [1] 400 #> #> #> $MC$formatting$select_fg_page #> $MC$formatting$select_fg_page$width #> [1] 1000 #> #> #> $MC$formatting$notes #> $MC$formatting$notes$width #> [1] \"560px\" #> #> $MC$formatting$notes$height #> [1] \"75px\" #> #> #> $MC$formatting$components #> $MC$formatting$components$aes #> $MC$formatting$components$aes$width #> [1] \"100px\" #> #> #> $MC$formatting$components$facet #> $MC$formatting$components$facet$width #> [1] \"200px\" #> #> #> $MC$formatting$components$label #> $MC$formatting$components$label$width #> [1] \"150px\" #> #> #> $MC$formatting$components$axscale #> $MC$formatting$components$axscale$width #> [1] \"150px\" #> #> #> $MC$formatting$components$axlim #> $MC$formatting$components$axlim$width #> [1] \"150px\" #> #> #> #> $MC$formatting$select_current_fig #> $MC$formatting$select_current_fig$width #> [1] 200 #> #> #> $MC$formatting$select_current_view #> $MC$formatting$select_current_view$width #> [1] 200 #> #> #> $MC$formatting$fg_elements #> $MC$formatting$fg_elements$width #> [1] 600 #> #> $MC$formatting$fg_elements$height #> [1] 200 #> #> #> $MC$formatting$faceting #> $MC$formatting$faceting$nrow #> [1] 3 #> #> $MC$formatting$faceting$ncol #> [1] 4 #> #> #> $MC$formatting$button_fig_del #> $MC$formatting$button_fig_del$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_del$block #> [1] TRUE #> #> $MC$formatting$button_fig_del$tooltip #> [1] \"Delete the current figure.\" #> #> $MC$formatting$button_fig_del$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_save #> $MC$formatting$button_fig_save$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_save$block #> [1] TRUE #> #> $MC$formatting$button_fig_save$tooltip #> [1] \"Save changes to caption, notes and data source.\" #> #> $MC$formatting$button_fig_save$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_clip #> $MC$formatting$button_fig_clip$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_clip$block #> [1] TRUE #> #> $MC$formatting$button_fig_clip$tooltip #> [1] \"Copy code to generate current figure to the clipboard.\" #> #> $MC$formatting$button_fig_clip$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_copy #> $MC$formatting$button_fig_copy$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_copy$block #> [1] TRUE #> #> $MC$formatting$button_fig_copy$tooltip #> [1] \"Copy current figure to a new figure.\" #> #> $MC$formatting$button_fig_copy$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_new #> $MC$formatting$button_fig_new$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_new$block #> [1] TRUE #> #> $MC$formatting$button_fig_new$tooltip #> [1] \"Create a new empty figure.\" #> #> $MC$formatting$button_fig_new$tooltip_position #> [1] \"right\" #> #> #> $MC$formatting$button_fig_add #> $MC$formatting$button_fig_add$size #> [1] \"sm\" #> #> $MC$formatting$button_fig_add$block #> [1] TRUE #> #> #> #> $MC$post_processing #> [1] \"===FGOBJ=== = ===FGOBJ=== + ggplot2::theme_light()\" #> #> $MC$fg_object_name #> [1] \"myp\" #> #> $MC$code #> $MC$code$packages #> [1] \"ggplot2\" \"ggforce\" #> #> $MC$code$readOnly #> [1] TRUE #> #> $MC$code$mode #> [1] \"r\" #> #> $MC$code$preamble #> [1] \"# Generating figures ------------------------------------------------------\" #> #> #> #> $FG #> $FG$button_counters #> $FG$button_counters$button_element_add #> [1] 0 #> #> $FG$button_counters$button_fig_save #> [1] 0 #> #> $FG$button_counters$button_fig_new #> [1] 0 #> #> $FG$button_counters$button_fig_del #> [1] 0 #> #> $FG$button_counters$button_fig_copy #> [1] 0 #> #> #> $FG$ui_hold #> $FG$ui_hold$hot_fg_elements #> [1] FALSE #> #> $FG$ui_hold$text_fig_key #> [1] FALSE #> #> $FG$ui_hold$text_fig_notes #> [1] FALSE #> #> $FG$ui_hold$select_current_view #> [1] FALSE #> #> $FG$ui_hold$select_current_fig #> [1] FALSE #> #> #> $FG$ui_ids #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_color\" \"select_component_group\" #> [5] \"select_component_linetype\" \"select_component_size\" #> [7] \"select_component_alpha\" \"text_component_x_manual\" #> [9] \"text_component_y_manual\" \"text_component_color_manual\" #> [11] \"text_component_group_manual\" \"text_component_linetype_manual\" #> [13] \"text_component_size_manual\" \"text_component_alpha_manual\" #> [15] \"select_component_shape\" \"text_component_shape_manual\" #> [17] \"select_component_ymin\" \"select_component_ymax\" #> [19] \"text_component_ymin_manual\" \"text_component_ymax_manual\" #> [21] \"select_component_yintercept\" \"text_component_yintercept_manual\" #> [23] \"select_component_xintercept\" \"text_component_xintercept_manual\" #> [25] \"select_component_fill\" \"select_component_weight\" #> [27] \"text_component_fill_manual\" \"text_component_weight_manual\" #> [29] \"select_component_lower\" \"select_component_middle\" #> [31] \"select_component_upper\" \"text_component_lower_manual\" #> [33] \"text_component_middle_manual\" \"text_component_upper_manual\" #> [35] \"button_fig_new\" \"button_fig_save\" #> [37] \"button_fig_del\" \"button_fig_copy\" #> [39] \"button_element_add\" \"hot_fg_elements\" #> [41] \"text_fig_key\" \"text_fig_notes\" #> [43] \"text_component_xlab\" \"text_component_ylab\" #> [45] \"text_component_xlim\" \"text_component_ylim\" #> [47] \"text_component_ggtitle\" \"select_fg_page\" #> [49] \"select_current_fig\" \"select_current_view\" #> [51] \"select_component_facet\" \"select_component_xscale\" #> [53] \"select_component_yscale\" \"select_fg_element\" #> #> $FG$isgood #> [1] FALSE #> #> $FG$DSV #> $FG$DSV$isgood #> [1] FALSE #> #> $FG$DSV$hasds #> [1] FALSE #> #> $FG$DSV$catalog #> NULL #> #> $FG$DSV$modules #> list() #> #> $FG$DSV$ds #> list() #> #> #> $FG$fig_cntr #> [1] 0 #> #> $FG$aes_elements #> [1] \"line\" \"point\" \"errorbar\" \"hguide\" \"vguide\" \"smooth\" \"ribbon\" #> [8] \"boxplot\" #> #> $FG$auto_elements #> $FG$auto_elements$line #> $FG$auto_elements$line$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_color\" \"select_component_group\" #> [5] \"select_component_linetype\" \"select_component_size\" #> [7] \"select_component_alpha\" #> #> $FG$auto_elements$line$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_color_manual\" \"text_component_group_manual\" #> [5] \"text_component_linetype_manual\" \"text_component_size_manual\" #> [7] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$point #> $FG$auto_elements$point$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" \"select_component_color\" #> [4] \"select_component_group\" \"select_component_shape\" \"select_component_size\" #> [7] \"select_component_alpha\" #> #> $FG$auto_elements$point$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_color_manual\" \"text_component_group_manual\" #> [5] \"text_component_shape_manual\" \"text_component_size_manual\" #> [7] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$errorbar #> $FG$auto_elements$errorbar$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_ymin\" \"select_component_ymax\" #> [4] \"select_component_color\" \"select_component_group\" \"select_component_size\" #> [7] \"select_component_alpha\" #> #> $FG$auto_elements$errorbar$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_ymin_manual\" #> [3] \"text_component_ymax_manual\" \"text_component_color_manual\" #> [5] \"text_component_group_manual\" \"text_component_size_manual\" #> [7] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$hguide #> $FG$auto_elements$hguide$ui_aes_select_id #> [1] \"select_component_yintercept\" \"select_component_linetype\" #> [3] \"select_component_color\" \"select_component_size\" #> #> $FG$auto_elements$hguide$ui_aes_manual_id #> [1] \"text_component_yintercept_manual\" \"text_component_linetype_manual\" #> [3] \"text_component_color_manual\" \"text_component_size_manual\" #> #> #> $FG$auto_elements$vguide #> $FG$auto_elements$vguide$ui_aes_select_id #> [1] \"select_component_xintercept\" \"select_component_linetype\" #> [3] \"select_component_color\" \"select_component_size\" #> #> $FG$auto_elements$vguide$ui_aes_manual_id #> [1] \"text_component_xintercept_manual\" \"text_component_linetype_manual\" #> [3] \"text_component_color_manual\" \"text_component_size_manual\" #> #> #> $FG$auto_elements$smooth #> $FG$auto_elements$smooth$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_color\" \"select_component_group\" #> [5] \"select_component_fill\" \"select_component_weight\" #> [7] \"select_component_linetype\" \"select_component_size\" #> [9] \"select_component_alpha\" \"select_component_ymax\" #> [11] \"select_component_ymin\" #> #> $FG$auto_elements$smooth$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_color_manual\" \"text_component_group_manual\" #> [5] \"text_component_fill_manual\" \"text_component_weight_manual\" #> [7] \"text_component_linetype_manual\" \"text_component_size_manual\" #> [9] \"text_component_alpha_manual\" \"text_component_ymax_manual\" #> [11] \"text_component_ymin_manual\" #> #> #> $FG$auto_elements$ribbon #> $FG$auto_elements$ribbon$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_ymin\" #> [3] \"select_component_ymax\" \"select_component_color\" #> [5] \"select_component_group\" \"select_component_fill\" #> [7] \"select_component_linetype\" \"select_component_size\" #> [9] \"select_component_alpha\" #> #> $FG$auto_elements$ribbon$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_ymin_manual\" #> [3] \"text_component_ymax_manual\" \"text_component_color_manual\" #> [5] \"text_component_group_manual\" \"text_component_fill_manual\" #> [7] \"text_component_linetype_manual\" \"text_component_size_manual\" #> [9] \"text_component_alpha_manual\" #> #> #> $FG$auto_elements$boxplot #> $FG$auto_elements$boxplot$ui_aes_select_id #> [1] \"select_component_x\" \"select_component_y\" #> [3] \"select_component_lower\" \"select_component_middle\" #> [5] \"select_component_upper\" \"select_component_ymin\" #> [7] \"select_component_ymax\" \"select_component_color\" #> [9] \"select_component_group\" \"select_component_fill\" #> [11] \"select_component_weight\" \"select_component_linetype\" #> [13] \"select_component_size\" \"select_component_shape\" #> [15] \"select_component_alpha\" #> #> $FG$auto_elements$boxplot$ui_aes_manual_id #> [1] \"text_component_x_manual\" \"text_component_y_manual\" #> [3] \"text_component_lower_manual\" \"text_component_middle_manual\" #> [5] \"text_component_upper_manual\" \"text_component_ymin_manual\" #> [7] \"text_component_ymax_manual\" \"text_component_color_manual\" #> [9] \"text_component_group_manual\" \"text_component_fill_manual\" #> [11] \"text_component_weight_manual\" \"text_component_linetype_manual\" #> [13] \"text_component_size_manual\" \"text_component_shape_manual\" #> [15] \"text_component_alpha_manual\" #> #> #> #> #> $MOD_TYPE #> [1] \"FG\" #> #> $id #> [1] \"FG\" #> #> $dep_mod_ids #> [1] \"UD\" \"DW\" #> #> $FM_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/formods.yaml\" #> #> $MOD_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/FG.yaml\" #> #> $shiny_token #> [1] \"non_shiny\" #>"},{"path":"/reference/FG_new_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize New Figure — FG_new_fig","title":"Initialize New Figure — FG_new_fig","text":"Creates new figure FG module","code":""},{"path":"/reference/FG_new_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize New Figure — FG_new_fig","text":"","code":"FG_new_fig(state)"},{"path":"/reference/FG_new_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize New Figure — FG_new_fig","text":"state FG state FG_fetch_state()","code":""},{"path":"/reference/FG_new_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize New Figure — FG_new_fig","text":"FG state object containing new empty figure figure set current active figure","code":""},{"path":"/reference/FG_new_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize New Figure — FG_new_fig","text":"","code":"if(interactive()){ library(formods) # Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = FG_test_mksession(session=list(), full_session=FALSE) session = sess_res$session input = sess_res$input # This will create a populated FG state object: state = sess_res$state # This sets the current active figure to Fig_1 state[[\"FG\"]][[\"current_fig\"]] = \"Fig_1\" # This is a paginated figure, and we can access a specific # figure using the following: pg_1 = FG_extract_page(state, 1) pg_2 = FG_extract_page(state, 2) # This will give you access to the current figure directly: current_fig = FG_fetch_current_fig(state) # For example this will set the key for that figure: current_fig$key = \"Individual profiles by cohort (multiple pages)\" # Once you're done you can put it back into the state: state = FG_set_current_fig(state, current_fig) # If you made any changes to the actual figure, this will # force a rebuild of the current figure: state = FG_build( state=state, del_row = NULL, cmd = NULL) # To create a new empty figure you can do this: state = FG_new_fig(state) }"},{"path":"/reference/FG_set_current_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets Current Figure — FG_set_current_fig","title":"Sets Current Figure — FG_set_current_fig","text":"Takes FG state figure list sets figure list value active figure","code":""},{"path":"/reference/FG_set_current_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets Current Figure — FG_set_current_fig","text":"","code":"FG_set_current_fig(state, fig)"},{"path":"/reference/FG_set_current_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sets Current Figure — FG_set_current_fig","text":"state FG state FG_fetch_state() fig Figure list FG_fetch_current_fig","code":""},{"path":"/reference/FG_set_current_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets Current Figure — FG_set_current_fig","text":"State current figure updated","code":""},{"path":"/reference/FG_set_current_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sets Current Figure — FG_set_current_fig","text":"","code":"if(interactive()){ library(formods) # Within shiny both session and input variables will exist, # this creates examples here for testing purposes: sess_res = FG_test_mksession(session=list(), full_session=FALSE) session = sess_res$session input = sess_res$input # This will create a populated FG state object: state = sess_res$state # This sets the current active figure to Fig_1 state[[\"FG\"]][[\"current_fig\"]] = \"Fig_1\" # This is a paginated figure, and we can access a specific # figure using the following: pg_1 = FG_extract_page(state, 1) pg_2 = FG_extract_page(state, 2) # This will give you access to the current figure directly: current_fig = FG_fetch_current_fig(state) # For example this will set the key for that figure: current_fig$key = \"Individual profiles by cohort (multiple pages)\" # Once you're done you can put it back into the state: state = FG_set_current_fig(state, current_fig) # If you made any changes to the actual figure, this will # force a rebuild of the current figure: state = FG_build( state=state, del_row = NULL, cmd = NULL) # To create a new empty figure you can do this: state = FG_new_fig(state) }"},{"path":"/reference/FG_test_mksession.html","id":null,"dir":"Reference","previous_headings":"","what":"Populate Session Data for Module Testing — FG_test_mksession","title":"Populate Session Data for Module Testing — FG_test_mksession","text":"Populates supplied session variable testing.","code":""},{"path":"/reference/FG_test_mksession.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Populate Session Data for Module Testing — FG_test_mksession","text":"","code":"FG_test_mksession( session, id = \"FG\", id_UD = \"UD\", id_DW = \"DW\", full_session = TRUE )"},{"path":"/reference/FG_test_mksession.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Populate Session Data for Module Testing — FG_test_mksession","text":"session Shiny session variable (app) list (outside app) id ID string corresponds ID used call modules UI elements id_UD ID string corresponds ID used call UD modules UI elements id_DW ID string corresponds ID used call DW modules UI elements full_session Boolean indicate full test session created (default TRUE).","code":""},{"path":"/reference/FG_test_mksession.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Populate Session Data for Module Testing — FG_test_mksession","text":"list following elements isgood: Boolean indicating exit status function. session: value Shiny session variable (app) list (outside app) initialization. input: value shiny input end session initialization. state: App state. rsc: react_state components.","code":""},{"path":"/reference/FG_test_mksession.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Populate Session Data for Module Testing — FG_test_mksession","text":"","code":"# \\donttest{ sess_res = FG_test_mksession(session=list(), full_session=FALSE) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → FG: dest: file.path(\"config\",\"report.docx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → FG: dest: file.path(\"config\",\"report.pptx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → FG: dest: file.path(\"config\",\"report.yaml\") #> → FG: State initialized #> → FG: module checksum updated:49305b1f42ca13ff15881186db5740a2 #> → FG: module checksum updated:cd8600191428b21b7e5d47f90df95aa0 #> → FG: module checksum updated:6365492678ef133590bab11275d57adb #> → FG: module checksum updated:527e5e6fcbde41d1c076662d828d424d # }"},{"path":"/reference/FG_update_checksum.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates FG Module Checksum — FG_update_checksum","title":"Updates FG Module Checksum — FG_update_checksum","text":"Called changes figures, function update checksum module. allows modules determine changes figures within .","code":""},{"path":"/reference/FG_update_checksum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates FG Module Checksum — FG_update_checksum","text":"","code":"FG_update_checksum(state)"},{"path":"/reference/FG_update_checksum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates FG Module Checksum — FG_update_checksum","text":"state FG state FG_fetch_state()","code":""},{"path":"/reference/FG_update_checksum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates FG Module Checksum — FG_update_checksum","text":"state checksum updated.","code":""},{"path":"/reference/FG_update_checksum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Updates FG Module Checksum — FG_update_checksum","text":"","code":"# This will create a populated FG state object: sess_res = FG_test_mksession(session=list(), full_session=FALSE) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → FG: dest: file.path(\"config\",\"report.docx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → FG: dest: file.path(\"config\",\"report.pptx\") #> → FG: including file #> → FG: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → FG: dest: file.path(\"config\",\"report.yaml\") #> → FG: State initialized #> → FG: module checksum updated:49305b1f42ca13ff15881186db5740a2 #> → FG: module checksum updated:cd8600191428b21b7e5d47f90df95aa0 #> → FG: module checksum updated:6365492678ef133590bab11275d57adb #> → FG: module checksum updated:527e5e6fcbde41d1c076662d828d424d state = sess_res$state state = FG_update_checksum(state) #> → FG: module checksum updated:527e5e6fcbde41d1c076662d828d424d"},{"path":"/reference/FM_add_ui_tooltip.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Tooltip to UI Element — FM_add_ui_tooltip","title":"Add Tooltip to UI Element — FM_add_ui_tooltip","text":"Adds tool tip user element.","code":""},{"path":"/reference/FM_add_ui_tooltip.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Tooltip to UI Element — FM_add_ui_tooltip","text":"","code":"FM_add_ui_tooltip( state, uiele, tooltip = \"mytooltip\", position = \"right\", size = \"medium\" )"},{"path":"/reference/FM_add_ui_tooltip.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Tooltip to UI Element — FM_add_ui_tooltip","text":"state Current module state yaml file read. uiele UI element add toooltip . tooltip Text containing tool tip. position Position tooltip. size size tooltip","code":""},{"path":"/reference/FM_add_ui_tooltip.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Tooltip to UI Element — FM_add_ui_tooltip","text":"tooltips enabled suggested packages installed uiele tooltip added returned. Otherwise just return original uiele unchanged.","code":""},{"path":"/reference/FM_add_ui_tooltip.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Tooltip to UI Element — FM_add_ui_tooltip","text":"","code":"if(interactive()){ # We need a module state object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) state = sess_res$state uiele = shiny::textInput(inputId = \"my input\", label=\"example input\") uiele = FM_add_ui_tooltip(state, uiele) }"},{"path":"/reference/FM_build_comment.html","id":null,"dir":"Reference","previous_headings":"","what":"Create RStudio Formatted Comments — FM_build_comment","title":"Create RStudio Formatted Comments — FM_build_comment","text":"Takes character string builds comment formatted section specified level RStudio","code":""},{"path":"/reference/FM_build_comment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create RStudio Formatted Comments — FM_build_comment","text":"","code":"FM_build_comment(level = 1, comment_str)"},{"path":"/reference/FM_build_comment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create RStudio Formatted Comments — FM_build_comment","text":"level Integer (1 (default),2, 3) indicating section level comment. comment_str Character object.","code":""},{"path":"/reference/FM_build_comment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create RStudio Formatted Comments — FM_build_comment","text":"Formatted comment.","code":""},{"path":"/reference/FM_build_comment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create RStudio Formatted Comments — FM_build_comment","text":"","code":"FM_build_comment(1, \"This is a level 1 header\") #> [1] \"# This is a level 1 header ------------------------------------------------\" FM_build_comment(2, paste0(rep(\"Long string repeated.\", 5), collapse=\" \")) #> [1] \"# Long string repeated. Long string repeated. Long string repeated. L =====\""},{"path":"/reference/FM_fetch_app_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches the Code to Reproduce Analysis — FM_fetch_app_code","title":"Fetches the Code to Reproduce Analysis — FM_fetch_app_code","text":"Takes current state app builds script reproduce analysis within app.","code":""},{"path":"/reference/FM_fetch_app_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches the Code to Reproduce Analysis — FM_fetch_app_code","text":"","code":"FM_fetch_app_code(session, state, mod_ids)"},{"path":"/reference/FM_fetch_app_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches the Code to Reproduce Analysis — FM_fetch_app_code","text":"session Shiny session variable state module state yaml read mod_ids Vector module IDs order needed (used code generation).","code":""},{"path":"/reference/FM_fetch_app_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches the Code to Reproduce Analysis — FM_fetch_app_code","text":"list following elements: isgood: Boolean indicating whether code generation successful (TRUE) msgs: messages generated code: Code regenerate app","code":""},{"path":"/reference/FM_fetch_app_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches the Code to Reproduce Analysis — FM_fetch_app_code","text":"","code":"# We need a Shiny session object to use this function: sess_res = DW_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → DW: dest: file.path(\"config\",\"report.docx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → DW: dest: file.path(\"config\",\"report.pptx\") #> → DW: including file #> → DW: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → DW: dest: file.path(\"config\",\"report.yaml\") #> → DW: State initialized #> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad #> → DW: module checksum updated:65801ab4b3c645aabf7edf91fc2f0d2c #> → DW: module checksum updated:7fb2dd3b16b1780c4c24f64d658dd7c7 #> → DW: module checksum updated:5ab04ea00be44c0040695a4ed6243c90 #> → DW: module checksum updated:960db107cfe9db93578f79f0ae6283e2 #> → DW: module checksum updated:f0b5d122dcb04f207cba233253b61c4b #> → DW: module checksum updated:189ed77a84bd9fcdd7b26abff8bea34a #> → DW: module checksum updated:669ec77d50652669cd3fcfd949469b37 #> → DW: module checksum updated:dd6cafa0be3b6b195d230a11e9f07f9f #> → DW: module checksum updated:5c2022c376ca8f56b839347156559890 #> → DW: module checksum updated:43640500a04674debd8e2399056c384a #> → DW: module checksum updated:f81c45ac1ef4e7b43153d8c8eaf7aed6 #> → DW: module checksum updated:207cde891d98e20c4afbb7fb5fb0aba2 #> → DW: module checksum updated:0a673e81c01cbbf33533dd65d6baf9e3 #> → DW: module checksum updated:af3f3aefd0115ed9dfdd4d6ef9d5182f #> → DW: module checksum updated:b0ccaee21e859322df0bf79d00c4b347 #> → DW: module checksum updated:2d3d6e9e38be6dea813b2d4d679e34b5 #> → DW: module checksum updated:2b60dd49b48a4e65200dc7241ad270e3 #> → DW: module checksum updated:3c92f397181a4fcdbdf2bd7dd7425e77 #> → DW: module checksum updated:92b81d7573def603649370b87c123b55 #> → DW: module checksum updated:9210264aabc0339e832b0c6bcfda32af #> → DW: module checksum updated:fe62fde1e7e738a1a35c479de9d5007b #> → DW: module checksum updated:ff3edcd4c1e58c96ea2707361916ffbc #> → DW: module checksum updated:b6cdfcef0432c5d9b1fa2bd46122ffa2 #> → DW: module checksum updated:4fa4283f1fd8fd6cf6e6e7df0669723a #> → DW: module checksum updated:cf3e139cef554b2d09dca619ee6aff41 #> → DW: module checksum updated:a9154d91a9e4b5d21f9585a6f68dd083 #> → DW: module checksum updated:4b5c6ad66658ddfa92d10ae1b0b7afa8 #> → DW: module checksum updated:591ac875a490b66a1fa7f4e7d4ba1c62 #> → DW: module checksum updated:afa3ca309cc3e6a48f542f4e8eadd54a #> → DW: module checksum updated:5c918dd4f53a4f1e56115abb09c4f332 #> → DW: module checksum updated:159ddf8c8cd26b178dfda5434bbecfa1 #> → DW: module checksum updated:8bb3c97e700998f2f73353189bd07831 #> → DW: module checksum updated:a1eceffec3ff7d9f9961683b3d07088b session = sess_res$session state = sess_res$state app_code = FM_fetch_app_code(session = session, state = state, mod_ids = c(\"UD\", \"DW\")) cat(app_code$code) #> # formods automated output ------------------------------------------------ #> # https://formods.ubiquity.tools/ #> rm(list=ls()) #> library(\"dplyr\") #> library(\"janitor\") #> library(\"readr\") #> library(\"readxl\") #> library(\"tidyr\") #> #> #> # This reporting object has the formatting #> # information for table generation #> rpt = onbrand::read_template( #> template = file.path(\"config\", \"report.docx\"), #> mapping = file.path(\"config\", \"report.yaml\")) #> #> # Loading data ------------------------------------------------------------ #> myDS = readxl::read_excel(path=\"TEST_DATA.xlsx\", sheet=\"DATA\") #> myDS = janitor::clean_names(myDS, case=\"none\") #> #> # Data wrangling ---------------------------------------------------------- #> # Observations ============================================================ #> DW_myDS_1 = myDS #> DW_myDS_1 = dplyr::filter(DW_myDS_1,EVID == 0) #> DW_myDS_1 = dplyr::filter(DW_myDS_1,DV != 0) #> DW_myDS_1 = dplyr::mutate(DW_myDS_1,IDCMT = paste0(ID, ', ', CMT)) #> #> # PK 3mg SD IV ============================================================ #> DW_myDS_2 = myDS #> DW_myDS_2 = dplyr::filter(DW_myDS_2,EVID == 0) #> DW_myDS_2 = dplyr::filter(DW_myDS_2,DV != 0) #> DW_myDS_2 = dplyr::filter(DW_myDS_2,Cohort %in% c(\"SD 3 mg IV\")) #> DW_myDS_2 = dplyr::filter(DW_myDS_2,CMT %in% c(\"C_ng_ml\")) #> #> # PK 3mg MD SC (first dose) =============================================== #> DW_myDS_3 = myDS #> DW_myDS_3 = dplyr::filter(DW_myDS_3,EVID == 0) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,DV != 0) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,Cohort %in% c(\"MD 3 mg SC\")) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,DOSE_NUM == 1) #> DW_myDS_3 = dplyr::filter(DW_myDS_3,CMT %in% c(\"C_ng_ml\")) #> #> # Parameters ============================================================== #> DW_myDS_4 = myDS #> DW_myDS_4 = dplyr::group_by(DW_myDS_4,ID) #> DW_myDS_4 = dplyr::filter(DW_myDS_4,row_number()==1) #> DW_myDS_4 = dplyr::select(DW_myDS_4,ID, DOSE, DOSE_STR, Cohort, ROUTE, ka, CL, Vc, Vp, Q) #> DW_myDS_4 = tidyr::pivot_longer(DW_myDS_4, cols = c(\"ka\", \"CL\", \"Vc\", \"Vp\", \"Q\"), names_to = \"parameter\", values_to = \"values\") #> #> # PK/PD 3mg SD IV w/BQL =================================================== #> DW_myDS_5 = myDS #> DW_myDS_5 = dplyr::filter(DW_myDS_5,EVID == 0) #> DW_myDS_5 = dplyr::filter(DW_myDS_5,Cohort %in% c(\"SD 3 mg IV\")) #> #> # PK/PD 3mg MD SC (first dose) w/BQL ====================================== #> DW_myDS_6 = myDS #> DW_myDS_6 = dplyr::filter(DW_myDS_6,EVID == 0) #> DW_myDS_6 = dplyr::filter(DW_myDS_6,Cohort %in% c(\"MD 3 mg SC\")) #> DW_myDS_6 = dplyr::filter(DW_myDS_6,DOSE_NUM == 1) #> #> # PK 3mg SD IV w/BQL ====================================================== #> DW_myDS_7 = myDS #> DW_myDS_7 = dplyr::filter(DW_myDS_7,EVID == 0) #> DW_myDS_7 = dplyr::filter(DW_myDS_7,Cohort %in% c(\"SD 3 mg IV\")) #> DW_myDS_7 = dplyr::filter(DW_myDS_7,CMT %in% c(\"C_ng_ml\")) #> #> # PK 3mg SD IV w/BQL w/dosing ============================================= #> DW_myDS_8 = myDS #> DW_myDS_8 = dplyr::filter(DW_myDS_8,Cohort %in% c(\"MD 3 mg IV\")) #>"},{"path":"/reference/FM_fetch_app_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches Informaiton About the App — FM_fetch_app_info","title":"Fetches Informaiton About the App — FM_fetch_app_info","text":"Returns diagnostic information app","code":""},{"path":"/reference/FM_fetch_app_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches Informaiton About the App — FM_fetch_app_info","text":"","code":"FM_fetch_app_info(session)"},{"path":"/reference/FM_fetch_app_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches Informaiton About the App — FM_fetch_app_info","text":"session Shiny session variable.","code":""},{"path":"/reference/FM_fetch_app_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches Informaiton About the App — FM_fetch_app_info","text":"List information app following structure uiele: system information UI elements used shiny apps. uiele_packages: UI element installed packages used shiny apps. uiele_options: UI element current options. uiele_modules: UI element loaded formods modules used shiny apps. msgs: System information text used report/terminal. si_packages Dataframe currently used packages. si_options Dataframe current options","code":""},{"path":"/reference/FM_fetch_app_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches Informaiton About the App — FM_fetch_app_info","text":"","code":"# We need a Shiny session object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session app_info = FM_fetch_app_info(session) app_info$msgs #> [1] \"Modules\" #> [2] \"ID: UD\" #> [3] \"type: UD\" #> [4] \"FM_yaml_file: /private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/formods.yaml\" #> [5] \"MOD_yaml_file: /private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/UD.yaml\" #> [6] \"User files: /var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/non_shiny/FM\" #> [7] \"Log file: /var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/non_shiny/FM/formods_log.txt\" #> [8] \"Package dependencies: janitor, readr, readxl\" #> [9] \" package * version date (UTC) lib source\" #> [10] \" abind 1.4-5 2016-07-21 [2] CRAN (R 4.2.0)\" #> [11] \" askpass 1.2.0 2023-09-03 [2] CRAN (R 4.2.0)\" #> [12] \" backports 1.4.1 2021-12-13 [2] CRAN (R 4.2.0)\" #> [13] \" broom 1.0.5 2023-06-09 [2] CRAN (R 4.2.0)\" #> [14] \" bslib 0.6.1 2023-11-28 [2] CRAN (R 4.2.3)\" #> [15] \" cachem 1.0.8 2023-05-01 [2] CRAN (R 4.2.0)\" #> [16] \" car 3.1-2 2023-03-30 [2] CRAN (R 4.2.1)\" #> [17] \" carData 3.0-5 2022-01-06 [2] CRAN (R 4.2.0)\" #> [18] \" cellranger 1.1.0 2016-07-27 [2] CRAN (R 4.2.0)\" #> [19] \" cli 3.6.2 2023-12-11 [2] CRAN (R 4.2.3)\" #> [20] \" clipr 0.8.0 2022-02-22 [2] CRAN (R 4.2.0)\" #> [21] \" colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.2.0)\" #> [22] \" crayon 1.5.2 2022-09-29 [2] CRAN (R 4.2.0)\" #> [23] \" crul 1.4.0 2023-05-17 [2] CRAN (R 4.2.0)\" #> [24] \" curl 5.2.1 2024-03-01 [2] CRAN (R 4.2.3)\" #> [25] \" data.table 1.15.2 2024-02-29 [2] CRAN (R 4.2.3)\" #> [26] \" desc 1.4.3 2023-12-10 [2] CRAN (R 4.2.3)\" #> [27] \" devtools 2.4.5 2022-10-11 [2] CRAN (R 4.2.0)\" #> [28] \" digest 0.6.34 2024-01-11 [2] CRAN (R 4.2.3)\" #> [29] \" downlit 0.4.3 2023-06-29 [2] CRAN (R 4.2.0)\" #> [30] \" dplyr 1.1.4 2023-11-17 [2] CRAN (R 4.2.3)\" #> [31] \" DT 0.32 2024-02-19 [2] CRAN (R 4.2.1)\" #> [32] \" ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.2.0)\" #> [33] \" evaluate 0.23 2023-11-01 [2] CRAN (R 4.2.0)\" #> [34] \" fansi 1.0.6 2023-12-08 [2] CRAN (R 4.2.3)\" #> [35] \" farver 2.1.1 2022-07-06 [2] CRAN (R 4.2.0)\" #> [36] \" fastmap 1.1.1 2023-02-24 [2] CRAN (R 4.2.0)\" #> [37] \" flextable 0.9.6.001 2024-03-07 [2] Github (davidgohel/flextable@ae707a0)\" #> [38] \" fontBitstreamVera 0.1.1 2017-02-01 [2] CRAN (R 4.2.0)\" #> [39] \" fontLiberation 0.1.0 2016-10-15 [2] CRAN (R 4.2.0)\" #> [40] \" fontquiver 0.2.1 2017-02-01 [2] CRAN (R 4.2.0)\" #> [41] \" formods * 0.1.4 2024-03-13 [1] local\" #> [42] \" fs 1.6.3 2023-07-20 [2] CRAN (R 4.2.0)\" #> [43] \" gdtools 0.3.7 2024-03-05 [2] CRAN (R 4.2.3)\" #> [44] \" generics 0.1.3 2022-07-05 [2] CRAN (R 4.2.0)\" #> [45] \" gfonts 0.2.0 2023-01-08 [2] CRAN (R 4.2.0)\" #> [46] \" ggforce 0.4.2 2024-02-19 [2] CRAN (R 4.2.1)\" #> [47] \" ggplot2 3.4.4 2023-10-12 [2] CRAN (R 4.2.0)\" #> [48] \" ggpubr 0.6.0 2023-02-10 [2] CRAN (R 4.2.0)\" #> [49] \" ggsignif 0.6.4 2022-10-13 [2] CRAN (R 4.2.0)\" #> [50] \" glue 1.7.0 2024-01-09 [2] CRAN (R 4.2.3)\" #> [51] \" gtable 0.3.4 2023-08-21 [2] CRAN (R 4.2.0)\" #> [52] \" gtools 3.9.5 2023-11-20 [2] CRAN (R 4.2.3)\" #> [53] \" here 1.0.1 2020-12-13 [2] CRAN (R 4.2.0)\" #> [54] \" hms 1.1.3 2023-03-21 [2] CRAN (R 4.2.0)\" #> [55] \" htmltools 0.5.7 2023-11-03 [2] CRAN (R 4.2.0)\" #> [56] \" htmlwidgets 1.6.4 2023-12-06 [2] CRAN (R 4.2.3)\" #> [57] \" httpcode 0.3.0 2020-04-10 [2] CRAN (R 4.2.0)\" #> [58] \" httpuv 1.6.14 2024-01-26 [2] CRAN (R 4.2.3)\" #> [59] \" httr 1.4.7 2023-08-15 [2] CRAN (R 4.2.0)\" #> [60] \" janitor 2.2.0 2023-02-02 [2] CRAN (R 4.2.0)\" #> [61] \" jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.2.0)\" #> [62] \" jsonlite 1.8.8 2023-12-04 [2] CRAN (R 4.2.3)\" #> [63] \" knitr 1.45 2023-10-30 [2] CRAN (R 4.2.0)\" #> [64] \" labeling 0.4.3 2023-08-29 [2] CRAN (R 4.2.0)\" #> [65] \" later 1.3.2 2023-12-06 [2] CRAN (R 4.2.3)\" #> [66] \" lazyeval 0.2.2 2019-03-15 [2] CRAN (R 4.2.0)\" #> [67] \" lifecycle 1.0.4 2023-11-07 [2] CRAN (R 4.2.3)\" #> [68] \" lubridate 1.9.3 2023-09-27 [2] CRAN (R 4.2.0)\" #> [69] \" magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.2.0)\" #> [70] \" MASS 7.3-60 2023-05-04 [2] CRAN (R 4.2.0)\" #> [71] \" memoise 2.0.1 2021-11-26 [2] CRAN (R 4.2.0)\" #> [72] \" mime 0.12 2021-09-28 [2] CRAN (R 4.2.0)\" #> [73] \" miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.2.0)\" #> [74] \" munsell 0.5.0 2018-06-12 [2] CRAN (R 4.2.0)\" #> [75] \" officer 0.6.5 2024-02-24 [2] CRAN (R 4.2.3)\" #> [76] \" onbrand 1.0.5 2024-02-19 [2] Github (john-harrold/onbrand@f44cc3d)\" #> [77] \" openssl 2.1.1 2023-09-25 [2] CRAN (R 4.2.0)\" #> [78] \" pillar 1.9.0 2023-03-22 [2] CRAN (R 4.2.0)\" #> [79] \" pkgbuild 1.4.3 2023-12-10 [2] CRAN (R 4.2.3)\" #> [80] \" pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.2.0)\" #> [81] \" pkgdown 2.0.7 2022-12-14 [2] CRAN (R 4.2.0)\" #> [82] \" pkgload 1.3.4 2024-01-16 [2] CRAN (R 4.2.3)\" #> [83] \" plotly 4.10.4 2024-01-13 [2] CRAN (R 4.2.3)\" #> [84] \" polyclip 1.10-6 2023-09-27 [2] CRAN (R 4.2.0)\" #> [85] \" profvis 0.3.8 2023-05-02 [2] CRAN (R 4.2.0)\" #> [86] \" promises 1.2.1 2023-08-10 [2] CRAN (R 4.2.0)\" #> [87] \" prompter 1.1.0 2021-10-07 [2] CRAN (R 4.2.0)\" #> [88] \" purrr 1.0.2 2023-08-10 [2] CRAN (R 4.2.0)\" #> [89] \" R6 2.5.1 2021-08-19 [2] CRAN (R 4.2.0)\" #> [90] \" ragg 1.2.7 2023-12-11 [2] CRAN (R 4.2.3)\" #> [91] \" Rcpp 1.0.12 2024-01-09 [2] CRAN (R 4.2.3)\" #> [92] \" readr 2.1.5 2024-01-10 [2] CRAN (R 4.2.3)\" #> [93] \" readxl 1.4.3 2023-07-06 [2] CRAN (R 4.2.0)\" #> [94] \" remotes 2.4.2.1 2023-07-18 [2] CRAN (R 4.2.0)\" #> [95] \" rhandsontable 0.3.8 2021-05-27 [2] CRAN (R 4.2.0)\" #> [96] \" rlang 1.1.3 2024-01-10 [2] CRAN (R 4.2.3)\" #> [97] \" rmarkdown 2.26 2024-03-05 [2] CRAN (R 4.2.3)\" #> [98] \" rprojroot 2.0.4 2023-11-05 [2] CRAN (R 4.2.0)\" #> [99] \" rstatix 0.7.2 2023-02-01 [2] CRAN (R 4.2.0)\" #> [100] \" rstudioapi 0.15.0 2023-07-07 [2] CRAN (R 4.2.0)\" #> [101] \" sass 0.4.8 2023-12-06 [2] CRAN (R 4.2.3)\" #> [102] \" scales 1.3.0 2023-11-28 [2] CRAN (R 4.2.3)\" #> [103] \" sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.2.0)\" #> [104] \" shiny 1.8.0 2023-11-17 [2] CRAN (R 4.2.3)\" #> [105] \" shinyAce 0.4.2 2022-05-06 [2] CRAN (R 4.2.0)\" #> [106] \" shinybusy 0.3.2 2023-11-23 [2] CRAN (R 4.2.3)\" #> [107] \" shinydashboard 0.7.2 2021-09-30 [2] CRAN (R 4.2.0)\" #> [108] \" shinyWidgets 0.8.1 2024-01-10 [2] CRAN (R 4.2.3)\" #> [109] \" snakecase 0.11.1 2023-08-27 [2] CRAN (R 4.2.0)\" #> [110] \" stringi 1.8.3 2023-12-11 [2] CRAN (R 4.2.3)\" #> [111] \" stringr 1.5.1 2023-11-14 [2] CRAN (R 4.2.3)\" #> [112] \" systemfonts 1.0.5 2023-10-09 [2] CRAN (R 4.2.0)\" #> [113] \" textshaping 0.3.7 2023-10-09 [2] CRAN (R 4.2.0)\" #> [114] \" tibble 3.2.1 2023-03-20 [2] CRAN (R 4.2.0)\" #> [115] \" tidyr 1.3.1 2024-01-24 [2] CRAN (R 4.2.3)\" #> [116] \" tidyselect 1.2.0 2022-10-10 [2] CRAN (R 4.2.0)\" #> [117] \" timechange 0.3.0 2024-01-18 [2] CRAN (R 4.2.3)\" #> [118] \" tweenr 2.0.2 2022-09-06 [2] CRAN (R 4.2.0)\" #> [119] \" tzdb 0.4.0 2023-05-12 [2] CRAN (R 4.2.0)\" #> [120] \" urlchecker 1.0.1 2021-11-30 [2] CRAN (R 4.2.0)\" #> [121] \" usethis 2.2.3 2024-02-19 [2] CRAN (R 4.2.1)\" #> [122] \" utf8 1.2.4 2023-10-22 [2] CRAN (R 4.2.0)\" #> [123] \" uuid 1.2-0 2024-01-14 [2] CRAN (R 4.2.3)\" #> [124] \" vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.2.3)\" #> [125] \" viridisLite 0.4.2 2023-05-02 [2] CRAN (R 4.2.0)\" #> [126] \" whisker 0.4.1 2022-12-05 [2] CRAN (R 4.2.0)\" #> [127] \" withr 3.0.0 2024-01-16 [2] CRAN (R 4.2.3)\" #> [128] \" writexl 1.5.0 2024-02-09 [2] CRAN (R 4.2.3)\" #> [129] \" xfun 0.42 2024-02-08 [2] CRAN (R 4.2.3)\" #> [130] \" xml2 1.3.6 2023-12-04 [2] CRAN (R 4.2.3)\" #> [131] \" xtable 1.8-4 2019-04-21 [2] CRAN (R 4.2.0)\" #> [132] \" yaml 2.3.8 2023-12-11 [2] CRAN (R 4.2.3)\" #> [133] \" zip 2.3.1 2024-01-27 [2] CRAN (R 4.2.3)\" #> [134] \"\" #> [135] \" [1] /private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8\" #> [136] \" [2] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library\""},{"path":"/reference/FM_fetch_app_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches the App State — FM_fetch_app_state","title":"Fetches the App State — FM_fetch_app_state","text":"Returns entire state App","code":""},{"path":"/reference/FM_fetch_app_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches the App State — FM_fetch_app_state","text":"","code":"FM_fetch_app_state(session)"},{"path":"/reference/FM_fetch_app_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches the App State — FM_fetch_app_state","text":"session Shiny session variable.","code":""},{"path":"/reference/FM_fetch_app_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches the App State — FM_fetch_app_state","text":"App state NULL defined.","code":""},{"path":"/reference/FM_fetch_app_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches the App State — FM_fetch_app_state","text":"","code":"# We need a Shiny session object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session app_state = FM_fetch_app_state(session) app_state #> $FM_UD #> $FM_UD$yaml #> $FM_UD$yaml$FM #> $FM_UD$yaml$FM$include #> $FM_UD$yaml$FM$include$files #> $FM_UD$yaml$FM$include$files[[1]] #> $FM_UD$yaml$FM$include$files[[1]]$file #> $FM_UD$yaml$FM$include$files[[1]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.docx\\\")\" #> #> $FM_UD$yaml$FM$include$files[[1]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.docx\\\")\" #> #> #> #> $FM_UD$yaml$FM$include$files[[2]] #> $FM_UD$yaml$FM$include$files[[2]]$file #> $FM_UD$yaml$FM$include$files[[2]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.pptx\\\")\" #> #> $FM_UD$yaml$FM$include$files[[2]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.pptx\\\")\" #> #> #> #> $FM_UD$yaml$FM$include$files[[3]] #> $FM_UD$yaml$FM$include$files[[3]]$file #> $FM_UD$yaml$FM$include$files[[3]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.yaml\\\")\" #> #> $FM_UD$yaml$FM$include$files[[3]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.yaml\\\")\" #> #> #> #> #> #> $FM_UD$yaml$FM$deployed #> [1] FALSE #> #> $FM_UD$yaml$FM$code #> $FM_UD$yaml$FM$code$theme #> [1] \"vibrant_ink\" #> #> $FM_UD$yaml$FM$code$showLineNumbers #> [1] TRUE #> #> $FM_UD$yaml$FM$code$gen_file #> [1] \"run_analysis.R\" #> #> $FM_UD$yaml$FM$code$gen_preamble #> [1] \"# formods automated output ------------------------------------------------\\n# https://formods.ubiquity.tools/\\nrm(list=ls())\" #> #> $FM_UD$yaml$FM$code$packages #> [1] \"onbrand\" \"writexl\" #> #> #> $FM_UD$yaml$FM$notifications #> $FM_UD$yaml$FM$notifications$config #> $FM_UD$yaml$FM$notifications$config$success #> $FM_UD$yaml$FM$notifications$config$success$useFontAwesome #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$success$useIcon #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$success$background #> [1] \"#5bb85b\" #> #> #> $FM_UD$yaml$FM$notifications$config$failure #> $FM_UD$yaml$FM$notifications$config$failure$useFontAwesome #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$failure$useIcon #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$failure$background #> [1] \"#d9534f\" #> #> #> $FM_UD$yaml$FM$notifications$config$info #> $FM_UD$yaml$FM$notifications$config$info$useFontAwesome #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$info$useIcon #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$info$background #> [1] \"#5bc0de\" #> #> #> $FM_UD$yaml$FM$notifications$config$warning #> $FM_UD$yaml$FM$notifications$config$warning$useFontAwesome #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$warning$useIcon #> [1] FALSE #> #> $FM_UD$yaml$FM$notifications$config$warning$background #> [1] \"#f0ac4d\" #> #> #> #> #> $FM_UD$yaml$FM$reporting #> $FM_UD$yaml$FM$reporting$enabled #> [1] TRUE #> #> $FM_UD$yaml$FM$reporting$content_init #> $FM_UD$yaml$FM$reporting$content_init$xlsx #> [1] \"rpt = list(summary = NULL,\\n sheets = list())\" #> #> $FM_UD$yaml$FM$reporting$content_init$docx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.docx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> $FM_UD$yaml$FM$reporting$content_init$pptx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.pptx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> #> #> $FM_UD$yaml$FM$ui #> $FM_UD$yaml$FM$ui$button_style #> [1] \"fill\" #> #> $FM_UD$yaml$FM$ui$select_size #> [1] 10 #> #> $FM_UD$yaml$FM$ui$color_green #> [1] \"#00BB8A\" #> #> $FM_UD$yaml$FM$ui$color_red #> [1] \"#FF475E\" #> #> $FM_UD$yaml$FM$ui$color_blue #> [1] \"#0088FF\" #> #> $FM_UD$yaml$FM$ui$color_purple #> [1] \"#bd2cf4\" #> #> #> $FM_UD$yaml$FM$data_meta #> $FM_UD$yaml$FM$data_meta$data_header #> [1] \"===NAME===<\/b>
===LABEL===<\/font><\/span>\" #> #> $FM_UD$yaml$FM$data_meta$subtext #> [1] \"===LABEL===: ===RANGE===\" #> #> $FM_UD$yaml$FM$data_meta$many_sep #> [1] \",⋅⋅⋅,\" #> #> $FM_UD$yaml$FM$data_meta$data_types #> $FM_UD$yaml$FM$data_meta$data_types$character #> $FM_UD$yaml$FM$data_meta$data_types$character$color #> [1] \"#DD4B39\" #> #> $FM_UD$yaml$FM$data_meta$data_types$character$label #> [1] \"text\" #> #> #> $FM_UD$yaml$FM$data_meta$data_types$double #> $FM_UD$yaml$FM$data_meta$data_types$double$color #> [1] \"#3C8DBC\" #> #> $FM_UD$yaml$FM$data_meta$data_types$double$label #> [1] \"num\" #> #> #> $FM_UD$yaml$FM$data_meta$data_types$integer #> $FM_UD$yaml$FM$data_meta$data_types$integer$color #> [1] \"#3C8DBC\" #> #> $FM_UD$yaml$FM$data_meta$data_types$integer$label #> [1] \"num\" #> #> #> $FM_UD$yaml$FM$data_meta$data_types$other #> $FM_UD$yaml$FM$data_meta$data_types$other$color #> [1] \"black\" #> #> $FM_UD$yaml$FM$data_meta$data_types$other$label #> [1] \"other\" #> #> #> #> #> $FM_UD$yaml$FM$labels #> $FM_UD$yaml$FM$labels$default_ds #> [1] \"Original data set\" #> #> #> $FM_UD$yaml$FM$user_files #> $FM_UD$yaml$FM$user_files$use_tmpdir #> [1] TRUE #> #> #> $FM_UD$yaml$FM$logging #> $FM_UD$yaml$FM$logging$enabled #> [1] TRUE #> #> $FM_UD$yaml$FM$logging$timestamp #> [1] TRUE #> #> $FM_UD$yaml$FM$logging$timestamp_fmt #> [1] \"%Y-%m-%d %H:%M:%S\" #> #> $FM_UD$yaml$FM$logging$log_file #> [1] \"formods_log.txt\" #> #> $FM_UD$yaml$FM$logging$console #> [1] TRUE #> #> #> #> #> $FM_UD$MC #> $FM_UD$MC$compact #> $FM_UD$MC$compact$code #> [1] FALSE #> #> $FM_UD$MC$compact$preview #> [1] TRUE #> #> #> $FM_UD$MC$reporting #> $FM_UD$MC$reporting$enabled #> [1] FALSE #> #> $FM_UD$MC$reporting$priority #> [1] 1 #> #> #> $FM_UD$MC$labels #> $FM_UD$MC$labels$default_ds #> [1] \"Original data set\" #> #> $FM_UD$MC$labels$upload_button #> [1] \"Select file\" #> #> $FM_UD$MC$labels$tab_main #> [1] \"Upload file\" #> #> $FM_UD$MC$labels$tab_code #> [1] \"Code\" #> #> $FM_UD$MC$labels$tab_preview #> [1] \"Data preview\" #> #> $FM_UD$MC$labels$switch_clean #> [1] \"Clean column names on upload\" #> #> $FM_UD$MC$labels$msg_bad_extension #> [1] \"Incorrect file extension (===EXT===). Unable to load file ===FILE===.\\nOnly the following extesions are allowed: ===ALLOWEDEXT===.\" #> #> #> $FM_UD$MC$tooltips #> $FM_UD$MC$tooltips$include #> [1] TRUE #> #> $FM_UD$MC$tooltips$show_code #> [1] \"Show data reading code\" #> #> #> $FM_UD$MC$formatting #> $FM_UD$MC$formatting$preview #> $FM_UD$MC$formatting$preview$width #> [1] 800 #> #> $FM_UD$MC$formatting$preview$height #> [1] 500 #> #> #> $FM_UD$MC$formatting$code #> $FM_UD$MC$formatting$code$width #> [1] 500 #> #> $FM_UD$MC$formatting$code$height #> [1] 200 #> #> #> $FM_UD$MC$formatting$switch_clean #> $FM_UD$MC$formatting$switch_clean$tooltip #> [1] \"Strange characters in column names can cause problems. When switched on, this will clean up the column headers and fix those that might break things.\" #> #> $FM_UD$MC$formatting$switch_clean$tooltip_position #> [1] \"bottom\" #> #> #> #> $FM_UD$MC$allowed_extensions #> [1] \"csv\" \"tsv\" \"xls\" \"xlsx\" #> #> $FM_UD$MC$code #> $FM_UD$MC$code$packages #> [1] \"readxl\" \"readr\" \"janitor\" #> #> $FM_UD$MC$code$readOnly #> [1] TRUE #> #> $FM_UD$MC$code$mode #> [1] \"r\" #> #> $FM_UD$MC$code$preamble #> [1] \"# Loading data ------------------------------------------------------------\" #> #> #> $FM_UD$MC$ds_object_name #> [1] \"myDS\" #> #> $FM_UD$MC$clean_data #> $FM_UD$MC$clean_data$enabled #> [1] TRUE #> #> $FM_UD$MC$clean_data$default #> [1] TRUE #> #> $FM_UD$MC$clean_data$code #> [1] \"# Make sure you put whatever packages you use here in the packages section\\n# above.\\n#\\n# contents - data frame containing the loaded dataset.\\n# code - code used to load the dataset you need to append any cleaning\\n# code you generate here.\\n# object_name - Name of the dataset object used in generated code.\\nif(system.file(package=\\\"janitor\\\") != \\\"\\\"){\\n contents = janitor::clean_names(contents, case=\\\"none\\\")\\n code = paste0(code, '\\\\n', object_name, ' = janitor::clean_names(', object_name,', case=\\\"none\\\")')\\n}\" #> #> #> #> $FM_UD$UD #> $FM_UD$UD$isgood #> [1] TRUE #> #> $FM_UD$UD$clean #> [1] TRUE #> #> $FM_UD$UD$load_msg #> File loaded.<\/em> #> #> $FM_UD$UD$data_file_local #> [1] \"/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/non_shiny/FM/TEST_DATA.xlsx\" #> #> $FM_UD$UD$data_file_ext #> [1] \"xlsx\" #> #> $FM_UD$UD$data_file #> [1] \"TEST_DATA.xlsx\" #> #> $FM_UD$UD$sheet #> NULL #> #> $FM_UD$UD$sheets #> [1] \"DATA\" \"DDT\" #> #> $FM_UD$UD$code #> [1] \"myDS = readxl::read_excel(path=\\\"TEST_DATA.xlsx\\\", sheet=\\\"DATA\\\")\\nmyDS = janitor::clean_names(myDS, case=\\\"none\\\")\" #> #> $FM_UD$UD$object_name #> [1] \"myDS\" #> #> $FM_UD$UD$checksum #> [1] \"897d952fecbc804999396a96f9df4b20\" #> #> $FM_UD$UD$contents #> # A tibble: 10,680 × 33 #> ID TIME_DY TIME_HR NTIME_DY NTIME_HR TIME AMT DV RECDESC DOSE #> #> 1 1 0 0 0 0 0 3000000 0 dose 3000000 #> 2 1 0 0 0 0 0 0 1250 BM_ng_ml 3000000 #> 3 1 0 0 0 0 0 0 0 C_ng_ml 3000000 #> 4 1 1 24 1 24 24 0 1647 BM_ng_ml 3000000 #> 5 1 1 24 1 24 24 0 690. C_ng_ml 3000000 #> 6 1 2 48 2 48 48 0 1947 BM_ng_ml 3000000 #> 7 1 2 48 2 48 48 0 588. C_ng_ml 3000000 #> 8 1 3 72 3 72 72 0 2170 BM_ng_ml 3000000 #> 9 1 3 72 3 72 72 0 506. C_ng_ml 3000000 #> 10 1 4 96 4 96 96 0 2332 BM_ng_ml 3000000 #> # ℹ 10,670 more rows #> # ℹ 23 more variables: DOSE_STR , Cohort , ROUTE , WT , #> # SUBTYPE , SEX , F1 , ka , CL , Vc , Vp , #> # Q , BM_IC , kdeg_BM , Emax , EC50 , CMT , #> # DUR , EVID , NDose , DOSE_NUM , SUBTYPE_ID , #> # SEX_ID #> #> #> $FM_UD$MOD_TYPE #> [1] \"UD\" #> #> $FM_UD$id #> [1] \"UD\" #> #> $FM_UD$FM_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/formods.yaml\" #> #> $FM_UD$MOD_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/UD.yaml\" #> #> $FM_UD$shiny_token #> [1] \"non_shiny\" #> #>"},{"path":"/reference/FM_fetch_current_mods.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches Details About Current Modules — FM_fetch_current_mods","title":"Fetches Details About Current Modules — FM_fetch_current_mods","text":"Use get information currently supported modules. includes short names, UI elements,","code":""},{"path":"/reference/FM_fetch_current_mods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches Details About Current Modules — FM_fetch_current_mods","text":"","code":"FM_fetch_current_mods()"},{"path":"/reference/FM_fetch_current_mods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches Details About Current Modules — FM_fetch_current_mods","text":"list details currently supported modules.","code":""},{"path":"/reference/FM_fetch_current_mods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches Details About Current Modules — FM_fetch_current_mods","text":"","code":"FM_fetch_current_mods() #> $mods #> $mods$ASM #> $mods$ASM$Name #> [1] \"App State Mangement\" #> #> $mods$ASM$Short_Name #> [1] \"ASM\" #> #> $mods$ASM$UI #> $mods$ASM$UI$htmlOutput #> [1] \"ui_asm_save_name\" \"ui_asm_save_button\" \"ui_asm_load_state\" #> #> $mods$ASM$UI$other #> [1] \"ui_asm_msg\" \"ui_asm_ace_code\" #> #> #> #> $mods$UD #> $mods$UD$Name #> [1] \"Upload Data\" #> #> $mods$UD$Short_Name #> [1] \"UD\" #> #> $mods$UD$UI #> $mods$UD$UI$htmlOutput #> [1] \"ui_ud_load_data\" \"ui_ud_select_sheets\" \"ui_ud_text_load_result\" #> [4] \"ui_ud_data_preview\" #> #> $mods$UD$UI$other #> [1] \"ui_ud_ace_code\" #> #> #> #> $mods$DW #> $mods$DW$Name #> [1] \"Data Wrangling\" #> #> $mods$DW$Short_Name #> [1] \"DW\" #> #> $mods$DW$UI #> $mods$DW$UI$htmlOutput #> [1] \"ui_dw_views\" \"ui_dw_key\" #> [3] \"ui_dw_new_view\" \"ui_dw_save_view\" #> [5] \"ui_dw_del_view\" \"ui_dw_copy_view\" #> [7] \"ui_dw_add_element_button\" \"ui_dw_select\" #> [9] \"ui_dw_new_element_row\" #> #> $mods$DW$UI$other #> [1] \"hot_dw_elements\" \"hot_data_preview\" \"ui_dw_msg\" \"ui_dw_code\" #> #> #> #> $mods$FG #> $mods$FG$Name #> [1] \"Figure Generation\" #> #> $mods$FG$Short_Name #> [1] \"FG\" #> #> $mods$FG$UI #> $mods$FG$UI$htmlOutput #> [1] \"ui_fg_curr_views\" \"ui_fg_curr_figs\" #> [3] \"ui_fg_new_fig\" \"ui_fg_save_fig\" #> [5] \"ui_fg_del_fig\" \"ui_fg_copy_fig\" #> [7] \"ui_fg_fig_name\" \"ui_fg_fig_notes\" #> [9] \"ui_fg_add_element_button\" \"ui_fg_select\" #> [11] \"ui_fg_new_element_row\" \"ui_fg_msg\" #> [13] \"ui_fg_slider_page\" #> #> $mods$FG$UI$other #> [1] \"hot_fg_elements\" \"ui_fg_preview_ggplot\" \"ui_fg_msg\" #> [4] \"ui_fg_code\" #> #> #> #> #> $df #> Module SN #> 1 App State Mangement ASM #> 2 Upload Data UD #> 3 Data Wrangling DW #> 4 Figure Generation FG #> htmlOutput #> 1 ui_asm_save_name, ui_asm_save_button, ui_asm_load_state #> 2 ui_ud_load_data, ui_ud_select_sheets, ui_ud_text_load_result, ui_ud_data_preview #> 3 ui_dw_views, ui_dw_key, ui_dw_new_view, ui_dw_save_view, ui_dw_del_view, ui_dw_copy_view, ui_dw_add_element_button, ui_dw_select, ui_dw_new_element_row #> 4 ui_fg_curr_views, ui_fg_curr_figs, ui_fg_new_fig, ui_fg_save_fig, ui_fg_del_fig, ui_fg_copy_fig, ui_fg_fig_name, ui_fg_fig_notes, ui_fg_add_element_button, ui_fg_select, ui_fg_new_element_row, ui_fg_msg, ui_fg_slider_page #> otherOutput #> 1 ui_asm_msg, ui_asm_ace_code #> 2 ui_ud_ace_code #> 3 hot_dw_elements, hot_data_preview, ui_dw_msg, ui_dw_code #> 4 hot_fg_elements, ui_fg_preview_ggplot, ui_fg_msg, ui_fg_code #>"},{"path":"/reference/FM_fetch_data_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates Formatting Information for Datasets — FM_fetch_data_format","title":"Creates Formatting Information for Datasets — FM_fetch_data_format","text":"Takes data frame information site configureation produce formatting information make easier user see data type information.","code":""},{"path":"/reference/FM_fetch_data_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates Formatting Information for Datasets — FM_fetch_data_format","text":"","code":"FM_fetch_data_format(df, state)"},{"path":"/reference/FM_fetch_data_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates Formatting Information for Datasets — FM_fetch_data_format","text":"df Raw dataframe built rhandsontable. state Current module state yaml file read.","code":""},{"path":"/reference/FM_fetch_data_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates Formatting Information for Datasets — FM_fetch_data_format","text":"list following elements: col_heads: List (element column) formatting information column headers use rhandsontable. col_subtext: List (element column) subtext displayed selections using `pickerInput` `shinyWidgets` package.","code":""},{"path":"/reference/FM_fetch_data_format.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates Formatting Information for Datasets — FM_fetch_data_format","text":"","code":"# We need a module state object to use this function: sess_res = UD_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 state = sess_res$state data_file_local = system.file(package=\"formods\", \"test_data\", \"TEST_DATA.xlsx\") sheet = \"DATA\" df = readxl::read_excel(path=data_file_local, sheet=sheet) hfmt = FM_fetch_data_format(df, state) # Column header formatting head(as.vector(unlist( hfmt[[\"col_heads\"]]))) #> [1] \"ID<\/b>
num<\/font><\/span>\" #> [2] \"TIME_DY<\/b>
num<\/font><\/span>\" #> [3] \"TIME_HR<\/b>
num<\/font><\/span>\" #> [4] \"NTIME_DY<\/b>
num<\/font><\/span>\" #> [5] \"NTIME_HR<\/b>
num<\/font><\/span>\" #> [6] \"TIME<\/b>
num<\/font><\/span>\" # Column select subtext head(as.vector(unlist( hfmt[[\"col_subtext\"]]))) #> [1] \"num: 1,⋅⋅⋅,360\" \"num: 0,⋅⋅⋅,84\" \"num: 0,⋅⋅⋅,2016\" \"num: 0,⋅⋅⋅,42\" #> [5] \"num: 0,⋅⋅⋅,1008\" \"num: 0,⋅⋅⋅,2016\""},{"path":"/reference/FM_fetch_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches Dependency Information — FM_fetch_deps","title":"Fetches Dependency Information — FM_fetch_deps","text":"given state session function determine module ids dependent well packages module elements might depend .","code":""},{"path":"/reference/FM_fetch_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches Dependency Information — FM_fetch_deps","text":"","code":"FM_fetch_deps(state, session)"},{"path":"/reference/FM_fetch_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches Dependency Information — FM_fetch_deps","text":"state Current module state yaml file read session Shiny session variable","code":""},{"path":"/reference/FM_fetch_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches Dependency Information — FM_fetch_deps","text":"list following elements: mod_ids Dependent module ids. packages List package dependencies. package_code Library commands load packages.","code":""},{"path":"/reference/FM_fetch_deps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches Dependency Information — FM_fetch_deps","text":"","code":"# We need a Shiny session object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = sess_res$state mod_deps = FM_fetch_deps(state, session)"},{"path":"/reference/FM_fetch_ds.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches Datasets from Modules in the App — FM_fetch_ds","title":"Fetches Datasets from Modules in the App — FM_fetch_ds","text":"Loops specified module ID modules ID specified. ID, attempt made extract datasets available.","code":""},{"path":"/reference/FM_fetch_ds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches Datasets from Modules in the App — FM_fetch_ds","text":"","code":"FM_fetch_ds(state, session, ids = NULL)"},{"path":"/reference/FM_fetch_ds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches Datasets from Modules in the App — FM_fetch_ds","text":"state Current module state yaml file read session Shiny session variable ids Vector ID strings modules containing datasets NULL datasets available.","code":""},{"path":"/reference/FM_fetch_ds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches Datasets from Modules in the App — FM_fetch_ds","text":"list containing current dataset following format: isgood: Boolean indicating whether dataset found (FALSE) ds: List datasets element names corresponding R object name dataset. following format label: Text label dataset (used display user) DS: Data frame dataset DSMETA: Data frame metadata colunns dataset DS. data frame following columns: col1: column 1 code: Code generate dataset. checksum: Module checksum dataset pulled DSchecksum: Checksum dataframe DS catalog: Dataframe containing tabular catalog datasets found. label: Text label object: Name R Object containing data frame MOD_TYPE: Short name type module id: Module ID checksum: Module checksum DSchecksum: Checksum dataset code: Code generate dataset modules: List entry module. element name short name. list entry shiny module ID. checksum. example access checksum DW module module ID 'my_id', use following: res$modules$DW$my_id.","code":""},{"path":"/reference/FM_fetch_ds.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches Datasets from Modules in the App — FM_fetch_ds","text":"","code":"# We need a module state and a Shiny session variable # to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = sess_res$state ds = FM_fetch_ds(state, session) ds$catalog #> label object MOD_TYPE id checksum #> 1 Original data set myDS UD UD 897d952fecbc804999396a96f9df4b20 #> DSchecksum #> 1 897d952fecbc804999396a96f9df4b20 #> code #> 1 myDS = readxl::read_excel(path=\"TEST_DATA.xlsx\", sheet=\"DATA\")\\nmyDS = janitor::clean_names(myDS, case=\"none\")"},{"path":"/reference/FM_fetch_log_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches the Path to the Log File — FM_fetch_log_path","title":"Fetches the Path to the Log File — FM_fetch_log_path","text":"Use get path formods log file","code":""},{"path":"/reference/FM_fetch_log_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches the Path to the Log File — FM_fetch_log_path","text":"","code":"FM_fetch_log_path(state)"},{"path":"/reference/FM_fetch_log_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches the Path to the Log File — FM_fetch_log_path","text":"state module state yaml read","code":""},{"path":"/reference/FM_fetch_log_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches the Path to the Log File — FM_fetch_log_path","text":"Character string path log file.","code":""},{"path":"/reference/FM_fetch_log_path.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches the Path to the Log File — FM_fetch_log_path","text":"","code":"# Within shiny a session variable will exist, # this creates one here for testing purposes: sess_res = UD_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session # This function assumes that some module state exists: state = UD_init_state( FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"UD.yaml\"), id = \"UD\", session = session) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized FM_fetch_log_path(state) #> [1] \"/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/non_shiny/FM/formods_log.txt\""},{"path":"/reference/FM_fetch_mdl.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches Models from Modules in the App — FM_fetch_mdl","title":"Fetches Models from Modules in the App — FM_fetch_mdl","text":"Loops specified module ID modules ID specified. ID, attempt made extract models available.","code":""},{"path":"/reference/FM_fetch_mdl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches Models from Modules in the App — FM_fetch_mdl","text":"","code":"FM_fetch_mdl(state, session, ids = NULL)"},{"path":"/reference/FM_fetch_mdl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches Models from Modules in the App — FM_fetch_mdl","text":"state Current module state yaml file read session Shiny session variable ids Vector ID strings modules containing models NULL modules models available.","code":""},{"path":"/reference/FM_fetch_mdl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches Models from Modules in the App — FM_fetch_mdl","text":"list containing current dataset following format: isgood: General logical indicator successfully. hasmdl: Logical indicating least one model found. modules: List module checksums. mdl: Result MM_fetch_mdl, see vignette(\"making_modules\", package = \"formods\") catalog: Dataframe containing tabular catalog models found. label: Text label model. object : Name object contains compiled rxode2 model. MOD_TYPE: Type 'formods' module model came . id: Source 'formods' Module ID. checksum: Checksum module model came . MDLchecksum: Checksum model. code: Code generate model.","code":""},{"path":"/reference/FM_fetch_mdl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches Models from Modules in the App — FM_fetch_mdl","text":"","code":"# We need a module state and a Shiny session variable # to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = sess_res$state mdl = FM_fetch_mdl(state, session) mdl$catalog #> NULL"},{"path":"/reference/FM_fetch_mod_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch the Module State — FM_fetch_mod_state","title":"Fetch the Module State — FM_fetch_mod_state","text":"Fetches module state userdata specified id","code":""},{"path":"/reference/FM_fetch_mod_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch the Module State — FM_fetch_mod_state","text":"","code":"FM_fetch_mod_state(session, id)"},{"path":"/reference/FM_fetch_mod_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch the Module State — FM_fetch_mod_state","text":"session Shiny session variable. id ID string module.","code":""},{"path":"/reference/FM_fetch_mod_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch the Module State — FM_fetch_mod_state","text":"module state NULL defined.","code":""},{"path":"/reference/FM_fetch_mod_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch the Module State — FM_fetch_mod_state","text":"","code":"# We need a Shiny session variable to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = FM_fetch_mod_state(session, id)"},{"path":"/reference/FM_fetch_user_files_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetches the Path to the User Files — FM_fetch_user_files_path","title":"Fetches the Path to the User Files — FM_fetch_user_files_path","text":"Use get path temporary directory formods stores user files.","code":""},{"path":"/reference/FM_fetch_user_files_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetches the Path to the User Files — FM_fetch_user_files_path","text":"","code":"FM_fetch_user_files_path(state)"},{"path":"/reference/FM_fetch_user_files_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetches the Path to the User Files — FM_fetch_user_files_path","text":"state module state yaml read","code":""},{"path":"/reference/FM_fetch_user_files_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetches the Path to the User Files — FM_fetch_user_files_path","text":"Character string path log file.","code":""},{"path":"/reference/FM_fetch_user_files_path.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetches the Path to the User Files — FM_fetch_user_files_path","text":"","code":"# We need a state object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 state = sess_res$state user_dir = FM_fetch_user_files_path(state) user_dir #> [1] \"/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/non_shiny/FM\""},{"path":"/reference/FM_generate_report.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Report — FM_generate_report","title":"Generate Report — FM_generate_report","text":"Generates report states different modules. type report based file extension file_name.","code":""},{"path":"/reference/FM_generate_report.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Report — FM_generate_report","text":"","code":"FM_generate_report( state, session, file_dir, file_name, gen_code_only = FALSE, rpterrors = TRUE )"},{"path":"/reference/FM_generate_report.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Report — FM_generate_report","text":"state Module state requesting report generation session Shiny session variable file_dir path location file written. file_name base_filename (acceptable extensions xlsx, docx, pptx). gen_code_only Boolean value indicating code generated (FALSE). rpterrors Boolean variable generate reports errors.","code":""},{"path":"/reference/FM_generate_report.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate Report — FM_generate_report","text":"List following elements","code":""},{"path":"/reference/FM_generate_report.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate Report — FM_generate_report","text":"function look loaded modules find reporting enabbled. reporting enabled look reporting functions module. Reporting functions following format (name arguments): XX_append_report(state, rpt, rpttype) XX module short name. state current state module. rpt contains current content report. vary based report type: xlsx: List two elements. first summary data frame two columns. first column called Sheet_Name second column called Description. catalog sheets added report user can appended using rbind. second element xlsx rpt another list element names corresponding report sheet names values corresponding dataframes exported report. pptx docx: Corresponding onbrand reporting object.","code":""},{"path":"/reference/FM_generate_report.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Report — FM_generate_report","text":"","code":"# Within shiny both session and input variables will exist, # this creates examples here for testing purposes: if(interactive()){ sess_res = FG_test_mksession(session=list(), full_session=FALSE) session = sess_res$session input = sess_res$input # This will create a populated FG state object: state = sess_res$state # This is the directory to write the report: file_dir = tempdir() # This is the file name that determines the type of report to write: file_name = \"my_report.pptx\" rpt_res = FM_generate_report(state = state, session = session, file_dir = file_dir, file_name = file_name, gen_code_only = TRUE, rpterrors = TRUE) # This contains the exit status of the report generation rpt_res$isgood # This is the underlying code that was used to generate the report cat(paste0(rpt_res$code, collapse=\"\\n\")) }"},{"path":"/reference/FM_init_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize a formods State Object — FM_init_state","title":"Initialize a formods State Object — FM_init_state","text":"Initializes formods state object common elements.","code":""},{"path":"/reference/FM_init_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize a formods State Object — FM_init_state","text":"","code":"FM_init_state( FM_yaml_file, MOD_yaml_file, id, dep_mod_ids = c(), MT, button_counters, ui_ids, ui_hold, session )"},{"path":"/reference/FM_init_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize a formods State Object — FM_init_state","text":"FM_yaml_file App configuration file FM main section. MOD_yaml_file Module configuration file MC main section. id Shiny module ID. dep_mod_ids Vector module ids module depends . MT Type module using short name (e.g. \"UD\", \"FG\", etc.). button_counters Vector button UI elements need tracked. ui_ids List UI ids module. ui_hold Vector UI elements require holding. session Shiny session variable","code":""},{"path":"/reference/FM_init_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize a formods State Object — FM_init_state","text":"List state initialized.","code":""},{"path":"/reference/FM_init_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialize a formods State Object — FM_init_state","text":"","code":"# Within shiny a session variable will exist, # this creates examples here for testing purposes: sess_res = UD_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = FM_init_state( FM_yaml_file = system.file(package = \"formods\", \"templates\", \"formods.yaml\"), MOD_yaml_file = system.file(package = \"formods\", \"templates\", \"UD.yaml\"), id = \"UD\", MT = \"UD\", button_counters = NULL, ui_ids = NULL, ui_hold = NULL, session = session) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") state #> $yaml #> $yaml$FM #> $yaml$FM$include #> $yaml$FM$include$files #> $yaml$FM$include$files[[1]] #> $yaml$FM$include$files[[1]]$file #> $yaml$FM$include$files[[1]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.docx\\\")\" #> #> $yaml$FM$include$files[[1]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.docx\\\")\" #> #> #> #> $yaml$FM$include$files[[2]] #> $yaml$FM$include$files[[2]]$file #> $yaml$FM$include$files[[2]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.pptx\\\")\" #> #> $yaml$FM$include$files[[2]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.pptx\\\")\" #> #> #> #> $yaml$FM$include$files[[3]] #> $yaml$FM$include$files[[3]]$file #> $yaml$FM$include$files[[3]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.yaml\\\")\" #> #> $yaml$FM$include$files[[3]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.yaml\\\")\" #> #> #> #> #> #> $yaml$FM$deployed #> [1] FALSE #> #> $yaml$FM$code #> $yaml$FM$code$theme #> [1] \"vibrant_ink\" #> #> $yaml$FM$code$showLineNumbers #> [1] TRUE #> #> $yaml$FM$code$gen_file #> [1] \"run_analysis.R\" #> #> $yaml$FM$code$gen_preamble #> [1] \"# formods automated output ------------------------------------------------\\n# https://formods.ubiquity.tools/\\nrm(list=ls())\" #> #> $yaml$FM$code$packages #> [1] \"onbrand\" \"writexl\" #> #> #> $yaml$FM$notifications #> $yaml$FM$notifications$config #> $yaml$FM$notifications$config$success #> $yaml$FM$notifications$config$success$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$success$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$success$background #> [1] \"#5bb85b\" #> #> #> $yaml$FM$notifications$config$failure #> $yaml$FM$notifications$config$failure$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$failure$background #> [1] \"#d9534f\" #> #> #> $yaml$FM$notifications$config$info #> $yaml$FM$notifications$config$info$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$info$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$info$background #> [1] \"#5bc0de\" #> #> #> $yaml$FM$notifications$config$warning #> $yaml$FM$notifications$config$warning$useFontAwesome #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$useIcon #> [1] FALSE #> #> $yaml$FM$notifications$config$warning$background #> [1] \"#f0ac4d\" #> #> #> #> #> $yaml$FM$reporting #> $yaml$FM$reporting$enabled #> [1] TRUE #> #> $yaml$FM$reporting$content_init #> $yaml$FM$reporting$content_init$xlsx #> [1] \"rpt = list(summary = NULL,\\n sheets = list())\" #> #> $yaml$FM$reporting$content_init$docx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.docx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> $yaml$FM$reporting$content_init$pptx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.pptx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> #> #> $yaml$FM$ui #> $yaml$FM$ui$button_style #> [1] \"fill\" #> #> $yaml$FM$ui$select_size #> [1] 10 #> #> $yaml$FM$ui$color_green #> [1] \"#00BB8A\" #> #> $yaml$FM$ui$color_red #> [1] \"#FF475E\" #> #> $yaml$FM$ui$color_blue #> [1] \"#0088FF\" #> #> $yaml$FM$ui$color_purple #> [1] \"#bd2cf4\" #> #> #> $yaml$FM$data_meta #> $yaml$FM$data_meta$data_header #> [1] \"===NAME===<\/b>
===LABEL===<\/font><\/span>\" #> #> $yaml$FM$data_meta$subtext #> [1] \"===LABEL===: ===RANGE===\" #> #> $yaml$FM$data_meta$many_sep #> [1] \",⋅⋅⋅,\" #> #> $yaml$FM$data_meta$data_types #> $yaml$FM$data_meta$data_types$character #> $yaml$FM$data_meta$data_types$character$color #> [1] \"#DD4B39\" #> #> $yaml$FM$data_meta$data_types$character$label #> [1] \"text\" #> #> #> $yaml$FM$data_meta$data_types$double #> $yaml$FM$data_meta$data_types$double$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$double$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$integer #> $yaml$FM$data_meta$data_types$integer$color #> [1] \"#3C8DBC\" #> #> $yaml$FM$data_meta$data_types$integer$label #> [1] \"num\" #> #> #> $yaml$FM$data_meta$data_types$other #> $yaml$FM$data_meta$data_types$other$color #> [1] \"black\" #> #> $yaml$FM$data_meta$data_types$other$label #> [1] \"other\" #> #> #> #> #> $yaml$FM$labels #> $yaml$FM$labels$default_ds #> [1] \"Original data set\" #> #> #> $yaml$FM$user_files #> $yaml$FM$user_files$use_tmpdir #> [1] TRUE #> #> #> $yaml$FM$logging #> $yaml$FM$logging$enabled #> [1] TRUE #> #> $yaml$FM$logging$timestamp #> [1] TRUE #> #> $yaml$FM$logging$timestamp_fmt #> [1] \"%Y-%m-%d %H:%M:%S\" #> #> $yaml$FM$logging$log_file #> [1] \"formods_log.txt\" #> #> $yaml$FM$logging$console #> [1] TRUE #> #> #> #> #> $MC #> $MC$compact #> $MC$compact$code #> [1] FALSE #> #> $MC$compact$preview #> [1] TRUE #> #> #> $MC$reporting #> $MC$reporting$enabled #> [1] FALSE #> #> $MC$reporting$priority #> [1] 1 #> #> #> $MC$labels #> $MC$labels$default_ds #> [1] \"Original data set\" #> #> $MC$labels$upload_button #> [1] \"Select file\" #> #> $MC$labels$tab_main #> [1] \"Upload file\" #> #> $MC$labels$tab_code #> [1] \"Code\" #> #> $MC$labels$tab_preview #> [1] \"Data preview\" #> #> $MC$labels$switch_clean #> [1] \"Clean column names on upload\" #> #> $MC$labels$msg_bad_extension #> [1] \"Incorrect file extension (===EXT===). Unable to load file ===FILE===.\\nOnly the following extesions are allowed: ===ALLOWEDEXT===.\" #> #> #> $MC$tooltips #> $MC$tooltips$include #> [1] TRUE #> #> $MC$tooltips$show_code #> [1] \"Show data reading code\" #> #> #> $MC$formatting #> $MC$formatting$preview #> $MC$formatting$preview$width #> [1] 800 #> #> $MC$formatting$preview$height #> [1] 500 #> #> #> $MC$formatting$code #> $MC$formatting$code$width #> [1] 500 #> #> $MC$formatting$code$height #> [1] 200 #> #> #> $MC$formatting$switch_clean #> $MC$formatting$switch_clean$tooltip #> [1] \"Strange characters in column names can cause problems. When switched on, this will clean up the column headers and fix those that might break things.\" #> #> $MC$formatting$switch_clean$tooltip_position #> [1] \"bottom\" #> #> #> #> $MC$allowed_extensions #> [1] \"csv\" \"tsv\" \"xls\" \"xlsx\" #> #> $MC$code #> $MC$code$packages #> [1] \"readxl\" \"readr\" \"janitor\" #> #> $MC$code$readOnly #> [1] TRUE #> #> $MC$code$mode #> [1] \"r\" #> #> $MC$code$preamble #> [1] \"# Loading data ------------------------------------------------------------\" #> #> #> $MC$ds_object_name #> [1] \"myDS\" #> #> $MC$clean_data #> $MC$clean_data$enabled #> [1] TRUE #> #> $MC$clean_data$default #> [1] TRUE #> #> $MC$clean_data$code #> [1] \"# Make sure you put whatever packages you use here in the packages section\\n# above.\\n#\\n# contents - data frame containing the loaded dataset.\\n# code - code used to load the dataset you need to append any cleaning\\n# code you generate here.\\n# object_name - Name of the dataset object used in generated code.\\nif(system.file(package=\\\"janitor\\\") != \\\"\\\"){\\n contents = janitor::clean_names(contents, case=\\\"none\\\")\\n code = paste0(code, '\\\\n', object_name, ' = janitor::clean_names(', object_name,', case=\\\"none\\\")')\\n}\" #> #> #> #> $UD #> $UD$button_counters #> list() #> #> $UD$ui_hold #> list() #> #> $UD$isgood #> [1] TRUE #> #> #> $MOD_TYPE #> [1] \"UD\" #> #> $id #> [1] \"UD\" #> #> $FM_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/formods.yaml\" #> #> $MOD_yaml_file #> [1] \"/private/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T/RtmpmmUNHY/temp_libpath1103cc61b6e8/formods/templates/UD.yaml\" #> #> $shiny_token #> [1] \"non_shiny\" #>"},{"path":"/reference/FM_le.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds Message to Log File and Displays it to the Console — FM_le","title":"Adds Message to Log File and Displays it to the Console — FM_le","text":"Add supplied txt module type log file display console.","code":""},{"path":"/reference/FM_le.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds Message to Log File and Displays it to the Console — FM_le","text":"","code":"FM_le(state, entry, escape_braces = TRUE, entry_type = \"alert\")"},{"path":"/reference/FM_le.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds Message to Log File and Displays it to the Console — FM_le","text":"state Module state yaml read entry Text add escape_braces Set TRUE (default) escape curly braces entry, set FALSE values interpreted. entry_type Set either \"alert\"(default), \"danger\", \"info\", \"success\", \"warning\"","code":""},{"path":"/reference/FM_le.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adds Message to Log File and Displays it to the Console — FM_le","text":"Boolean value indicating success (TRUE) failure (FALSE).","code":""},{"path":"/reference/FM_le.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adds Message to Log File and Displays it to the Console — FM_le","text":"","code":"# We need a module state to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 state = sess_res$state FM_le(state, \"This is a normal message\") #> → UD: This is a normal message #> NULL FM_le(state, \"This is a danger message\", entry_type=\"danger\") #> ✖ UD: This is a danger message #> NULL FM_le(state, \"This is a info message\", entry_type=\"info\") #> ℹ UD: This is a info message #> NULL FM_le(state, \"This is a success message\", entry_type=\"success\") #> ✔ UD: This is a success message #> NULL FM_le(state, \"This is a warning message\", entry_type=\"warning\") #> ! UD: This is a warning message #> NULL"},{"path":"/reference/FM_message.html","id":null,"dir":"Reference","previous_headings":"","what":"Show Message to User — FM_message","title":"Show Message to User — FM_message","text":"Writes message console depending whether cli installed .","code":""},{"path":"/reference/FM_message.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show Message to User — FM_message","text":"","code":"FM_message(line, escape_braces = TRUE, entry_type = \"alert\")"},{"path":"/reference/FM_message.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show Message to User — FM_message","text":"line Text display escape_braces Set TRUE (default) escape curly braces entry, set FALSE values interpreted. entry_type Set either \"alert\"(default), \"danger\", \"info\", \"success\", \"warning\", \"h1\", \"h2\", \"h3\"","code":""},{"path":"/reference/FM_message.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show Message to User — FM_message","text":"Returns NULL","code":""},{"path":"/reference/FM_message.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show Message to User — FM_message","text":"","code":"mr = FM_message(\"This is a normal message\") #> → This is a normal message mr = FM_message(\"This is a danger message\", entry_type=\"danger\") #> ✖ This is a danger message mr = FM_message(\"This is a info message\", entry_type=\"info\") #> ℹ This is a info message mr = FM_message(\"This is a success message\", entry_type=\"success\") #> ✔ This is a success message mr = FM_message(\"This is a warning message\", entry_type=\"warning\") #> ! This is a warning message mr = FM_message(\"This is an H1 header\", entry_type=\"h1\") #> #> ── This is an H1 header ──────────────────────────────────────────────────────── mr = FM_message(\"This is an H2 header\", entry_type=\"h2\") #> #> ── This is an H2 header ── #> mr = FM_message(\"This is an H3 header\", entry_type=\"h3\") #> ── This is an H3 header"},{"path":"/reference/FM_mk_error_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates `ggplot` Object with Error Message — FM_mk_error_fig","title":"Generates `ggplot` Object with Error Message — FM_mk_error_fig","text":"Takes vector messages returns ggplot object text figure. can used automated figure generation cascade error message end user.","code":""},{"path":"/reference/FM_mk_error_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates `ggplot` Object with Error Message — FM_mk_error_fig","text":"","code":"FM_mk_error_fig(msgs)"},{"path":"/reference/FM_mk_error_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates `ggplot` Object with Error Message — FM_mk_error_fig","text":"msgs Vector error messages","code":""},{"path":"/reference/FM_mk_error_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates `ggplot` Object with Error Message — FM_mk_error_fig","text":"ggplot object","code":""},{"path":"/reference/FM_mk_error_fig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates `ggplot` Object with Error Message — FM_mk_error_fig","text":"","code":"FM_mk_error_fig(\"Oh nos! You've made a mistake!\")"},{"path":"/reference/FM_notify.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny Notification — FM_notify","title":"Shiny Notification — FM_notify","text":"Generates notification show .","code":""},{"path":"/reference/FM_notify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny Notification — FM_notify","text":"","code":"FM_notify(state, session)"},{"path":"/reference/FM_notify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny Notification — FM_notify","text":"state Module state generating notification session Shiny session variable","code":""},{"path":"/reference/FM_notify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny Notification — FM_notify","text":"Boolean variable indicating notification triggered","code":""},{"path":"/reference/FM_notify.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shiny Notification — FM_notify","text":"","code":"if(interactive()){ library(formods) library(shiny) library(shinydashboard) #https://fontawesome.com/icons?from=io ui <- dashboardPage( skin=\"red\", dashboardHeader(title=\"Test Notifications\"), dashboardSidebar( sidebarMenu( menuItem(\"Notifications\", tabName=\"example\", icon=icon(\"table\")) ) ), dashboardBody( tabItems( tabItem(tabName=\"example\", fluidRow( shiny::actionButton(\"set_notification\", \"Set Notification\"), shiny::textInput(\"user_text\", label=\"Notify Text Here\", value=\"Notify me\"), shiny::actionButton(\"show_notification\", \"Show Notification\") ) ) ) ) ) # Main app server server <- function(input, output, session) { # Need formods state object sess_res = UD_test_mksession(session, id=\"UD\") # Captures input and sets the notification observeEvent(input$set_notification, { state = FM_fetch_mod_state(session, id=\"UD\") state = FM_set_notification(state, notify_text = isolate(input$user_text), notify_id = \"example\") FM_set_mod_state(session, id=\"UD\", state) }) # Displays the notification observeEvent(input$show_notification, { state = FM_fetch_mod_state(session, id=\"UD\") FM_notify(state, session) }) } shinyApp(ui, server) }"},{"path":"/reference/FM_pause_screen.html","id":null,"dir":"Reference","previous_headings":"","what":"Starts Modal Screen Pause — FM_pause_screen","title":"Starts Modal Screen Pause — FM_pause_screen","text":"Start modal screen pause.","code":""},{"path":"/reference/FM_pause_screen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Starts Modal Screen Pause — FM_pause_screen","text":"","code":"FM_pause_screen(state, session, message)"},{"path":"/reference/FM_pause_screen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Starts Modal Screen Pause — FM_pause_screen","text":"state Current module state yaml file read. session Shiny session variable. message Optional message pause.","code":""},{"path":"/reference/FM_pause_screen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Starts Modal Screen Pause — FM_pause_screen","text":"Pauses screen return value.","code":""},{"path":"/reference/FM_pause_screen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Starts Modal Screen Pause — FM_pause_screen","text":"","code":"# We need a module state object and Shiny session objects to use this function: sess_res = UD_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = sess_res$state FM_pause_screen(state, session) #> NULL FM_resume_screen(state, session) #> NULL"},{"path":"/reference/FM_pretty_sort.html","id":null,"dir":"Reference","previous_headings":"","what":"Centralized Sorting Function — FM_pretty_sort","title":"Centralized Sorting Function — FM_pretty_sort","text":"displaying information pull function can used sort options.","code":""},{"path":"/reference/FM_pretty_sort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Centralized Sorting Function — FM_pretty_sort","text":"","code":"FM_pretty_sort(unsrt_data)"},{"path":"/reference/FM_pretty_sort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Centralized Sorting Function — FM_pretty_sort","text":"unsrt_data Unsorted data.","code":""},{"path":"/reference/FM_pretty_sort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Centralized Sorting Function — FM_pretty_sort","text":"sorted data","code":""},{"path":"/reference/FM_pretty_sort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Centralized Sorting Function — FM_pretty_sort","text":"","code":"# This is the full path to a test data file: data_file_local = system.file(package=\"formods\", \"test_data\", \"TEST_DATA.xlsx\") # Excel files need a sheet specification: sheet = \"DATA\" # We will also attach the sheets along with it df = readxl::read_excel(path=data_file_local, sheet=sheet) # Regular sorting: sort(unique(df$Cohort)) #> [1] \"MD 10 mg IV\" \"MD 10 mg SC\" \"MD 100 mg IV\" \"MD 100 mg SC\" \"MD 3 mg IV\" #> [6] \"MD 3 mg SC\" \"MD 30 mg IV\" \"MD 30 mg SC\" \"MD 300 mg IV\" \"MD 300 mg SC\" #> [11] \"MD 500 mg IV\" \"MD 500 mg SC\" \"SD 10 mg IV\" \"SD 100 mg IV\" \"SD 3 mg IV\" #> [16] \"SD 30 mg IV\" \"SD 300 mg IV\" \"SD 500 mg IV\" FM_pretty_sort(unique(df$Cohort)) #> [1] \"MD 3 mg IV\" \"MD 3 mg SC\" \"MD 10 mg IV\" \"MD 10 mg SC\" \"MD 30 mg IV\" #> [6] \"MD 30 mg SC\" \"MD 100 mg IV\" \"MD 100 mg SC\" \"MD 300 mg IV\" \"MD 300 mg SC\" #> [11] \"MD 500 mg IV\" \"MD 500 mg SC\" \"SD 3 mg IV\" \"SD 10 mg IV\" \"SD 30 mg IV\" #> [16] \"SD 100 mg IV\" \"SD 300 mg IV\" \"SD 500 mg IV\""},{"path":"/reference/FM_proc_include.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets Message in State from UI Processing — FM_proc_include","title":"Sets Message in State from UI Processing — FM_proc_include","text":"errors need passed back user can set function.","code":""},{"path":"/reference/FM_proc_include.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets Message in State from UI Processing — FM_proc_include","text":"","code":"FM_proc_include(state, session)"},{"path":"/reference/FM_proc_include.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sets Message in State from UI Processing — FM_proc_include","text":"state formods State object. session Shiny session variable.","code":""},{"path":"/reference/FM_proc_include.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets Message in State from UI Processing — FM_proc_include","text":"return value, sets message supplied session variable.","code":""},{"path":"/reference/FM_proc_include.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sets Message in State from UI Processing — FM_proc_include","text":"","code":"# We need a module state object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 state = sess_res$state session = sess_res$session FM_proc_include(state, session) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\")"},{"path":"/reference/FM_resume_screen.html","id":null,"dir":"Reference","previous_headings":"","what":"Stops Modal Screen Pause — FM_resume_screen","title":"Stops Modal Screen Pause — FM_resume_screen","text":"Stops Modal Screen Pause","code":""},{"path":"/reference/FM_resume_screen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stops Modal Screen Pause — FM_resume_screen","text":"","code":"FM_resume_screen(state, session)"},{"path":"/reference/FM_resume_screen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stops Modal Screen Pause — FM_resume_screen","text":"state Current module state yaml file read. session Shiny session variable.","code":""},{"path":"/reference/FM_resume_screen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stops Modal Screen Pause — FM_resume_screen","text":"return value, called disable screen pause.","code":""},{"path":"/reference/FM_resume_screen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stops Modal Screen Pause — FM_resume_screen","text":"","code":"# We need a module state object and Shiny session objects to use this function: sess_res = UD_test_mksession(session=list()) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = sess_res$state FM_pause_screen(state, session) #> NULL FM_resume_screen(state, session) #> NULL"},{"path":"/reference/FM_set_app_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the App State — FM_set_app_state","title":"Set the App State — FM_set_app_state","text":"Takes loaded app state overwrites current app state","code":""},{"path":"/reference/FM_set_app_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the App State — FM_set_app_state","text":"","code":"FM_set_app_state(session, app_state, set_holds = TRUE)"},{"path":"/reference/FM_set_app_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the App State — FM_set_app_state","text":"session Shiny session variable. app_state Loaded app state. set_holds TRUE (default) holds set modules present app state.","code":""},{"path":"/reference/FM_set_app_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the App State — FM_set_app_state","text":"return value, just updates app state session variable.","code":""},{"path":"/reference/FM_set_app_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set the App State — FM_set_app_state","text":"","code":"# We need a Shiny session object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session app_state = FM_fetch_app_state(session) FM_set_app_state(session, app_state) #> → FM_set_app_state() #> → Unable to find ASM state. #> NULL"},{"path":"/reference/FM_set_mod_state.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the Module State — FM_set_mod_state","title":"Set the Module State — FM_set_mod_state","text":"Sets module state userdata specified id","code":""},{"path":"/reference/FM_set_mod_state.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the Module State — FM_set_mod_state","text":"","code":"FM_set_mod_state(session, id, state)"},{"path":"/reference/FM_set_mod_state.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the Module State — FM_set_mod_state","text":"session Shiny session variable id ID string module. state Module state set.","code":""},{"path":"/reference/FM_set_mod_state.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the Module State — FM_set_mod_state","text":"Session variable module state set.","code":""},{"path":"/reference/FM_set_mod_state.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set the Module State — FM_set_mod_state","text":"","code":"# We need a Shiny session variable and a module state # object to use this function: id=\"UD\" sess_res = UD_test_mksession(session=list(), id=id) #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.docx\") #> → UD: dest: file.path(\"config\",\"report.docx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.pptx\") #> → UD: dest: file.path(\"config\",\"report.pptx\") #> → UD: including file #> → UD: source: file.path(system.file(package=\"onbrand\"), \"templates\", \"report.yaml\") #> → UD: dest: file.path(\"config\",\"report.yaml\") #> → UD: State initialized #> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20 session = sess_res$session state = sess_res$state FM_set_mod_state(session, id, state) #> $userData #> $userData$FM #> $userData$FM$FM_UD #> $userData$FM$FM_UD$yaml #> $userData$FM$FM_UD$yaml$FM #> $userData$FM$FM_UD$yaml$FM$include #> $userData$FM$FM_UD$yaml$FM$include$files #> $userData$FM$FM_UD$yaml$FM$include$files[[1]] #> $userData$FM$FM_UD$yaml$FM$include$files[[1]]$file #> $userData$FM$FM_UD$yaml$FM$include$files[[1]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.docx\\\")\" #> #> $userData$FM$FM_UD$yaml$FM$include$files[[1]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.docx\\\")\" #> #> #> #> $userData$FM$FM_UD$yaml$FM$include$files[[2]] #> $userData$FM$FM_UD$yaml$FM$include$files[[2]]$file #> $userData$FM$FM_UD$yaml$FM$include$files[[2]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.pptx\\\")\" #> #> $userData$FM$FM_UD$yaml$FM$include$files[[2]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.pptx\\\")\" #> #> #> #> $userData$FM$FM_UD$yaml$FM$include$files[[3]] #> $userData$FM$FM_UD$yaml$FM$include$files[[3]]$file #> $userData$FM$FM_UD$yaml$FM$include$files[[3]]$file$source #> [1] \"file.path(system.file(package=\\\"onbrand\\\"), \\\"templates\\\", \\\"report.yaml\\\")\" #> #> $userData$FM$FM_UD$yaml$FM$include$files[[3]]$file$dest #> [1] \"file.path(\\\"config\\\",\\\"report.yaml\\\")\" #> #> #> #> #> #> $userData$FM$FM_UD$yaml$FM$deployed #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$code #> $userData$FM$FM_UD$yaml$FM$code$theme #> [1] \"vibrant_ink\" #> #> $userData$FM$FM_UD$yaml$FM$code$showLineNumbers #> [1] TRUE #> #> $userData$FM$FM_UD$yaml$FM$code$gen_file #> [1] \"run_analysis.R\" #> #> $userData$FM$FM_UD$yaml$FM$code$gen_preamble #> [1] \"# formods automated output ------------------------------------------------\\n# https://formods.ubiquity.tools/\\nrm(list=ls())\" #> #> $userData$FM$FM_UD$yaml$FM$code$packages #> [1] \"onbrand\" \"writexl\" #> #> #> $userData$FM$FM_UD$yaml$FM$notifications #> $userData$FM$FM_UD$yaml$FM$notifications$config #> $userData$FM$FM_UD$yaml$FM$notifications$config$success #> $userData$FM$FM_UD$yaml$FM$notifications$config$success$useFontAwesome #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$success$useIcon #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$success$background #> [1] \"#5bb85b\" #> #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$failure #> $userData$FM$FM_UD$yaml$FM$notifications$config$failure$useFontAwesome #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$failure$useIcon #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$failure$background #> [1] \"#d9534f\" #> #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$info #> $userData$FM$FM_UD$yaml$FM$notifications$config$info$useFontAwesome #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$info$useIcon #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$info$background #> [1] \"#5bc0de\" #> #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$warning #> $userData$FM$FM_UD$yaml$FM$notifications$config$warning$useFontAwesome #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$warning$useIcon #> [1] FALSE #> #> $userData$FM$FM_UD$yaml$FM$notifications$config$warning$background #> [1] \"#f0ac4d\" #> #> #> #> #> $userData$FM$FM_UD$yaml$FM$reporting #> $userData$FM$FM_UD$yaml$FM$reporting$enabled #> [1] TRUE #> #> $userData$FM$FM_UD$yaml$FM$reporting$content_init #> $userData$FM$FM_UD$yaml$FM$reporting$content_init$xlsx #> [1] \"rpt = list(summary = NULL,\\n sheets = list())\" #> #> $userData$FM$FM_UD$yaml$FM$reporting$content_init$docx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.docx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> $userData$FM$FM_UD$yaml$FM$reporting$content_init$pptx #> [1] \"rpt = onbrand::read_template(\\n template = file.path(\\\"config\\\", \\\"report.pptx\\\"),\\n mapping = file.path(\\\"config\\\", \\\"report.yaml\\\"))\" #> #> #> #> $userData$FM$FM_UD$yaml$FM$ui #> $userData$FM$FM_UD$yaml$FM$ui$button_style #> [1] \"fill\" #> #> $userData$FM$FM_UD$yaml$FM$ui$select_size #> [1] 10 #> #> $userData$FM$FM_UD$yaml$FM$ui$color_green #> [1] \"#00BB8A\" #> #> $userData$FM$FM_UD$yaml$FM$ui$color_red #> [1] \"#FF475E\" #> #> $userData$FM$FM_UD$yaml$FM$ui$color_blue #> [1] \"#0088FF\" #> #> $userData$FM$FM_UD$yaml$FM$ui$color_purple #> [1] \"#bd2cf4\" #> #> #> $userData$FM$FM_UD$yaml$FM$data_meta #> $userData$FM$FM_UD$yaml$FM$data_meta$data_header #> [1] \"===NAME===<\/b>
===LABEL===<\/font><\/span>\" #> #> $userData$FM$FM_UD$yaml$FM$data_meta$subtext #> [1] \"===LABEL===: ===RANGE===\" #> #> $userData$FM$FM_UD$yaml$FM$data_meta$many_sep #> [1] \",⋅⋅⋅,\" #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$character #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$character$color #> [1] \"#DD4B39\" #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$character$label #> [1] \"text\" #> #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$double #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$double$color #> [1] \"#3C8DBC\" #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$double$label #> [1] \"num\" #> #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$integer #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$integer$color #> [1] \"#3C8DBC\" #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$integer$label #> [1] \"num\" #> #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$other #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$other$color #> [1] \"black\" #> #> $userData$FM$FM_UD$yaml$FM$data_meta$data_types$other$label #> [1] \"other\" #> #> #> #> #> $userData$FM$FM_UD$yaml$FM$labels #> $userData$FM$FM_UD$yaml$FM$labels$default_ds #> [1] \"Original data set\" #> #> #> $userData$FM$FM_UD$yaml$FM$user_files #> $userData$FM$FM_UD$yaml$FM$user_files$use_tmpdir #> [1] TRUE #> #> #> $userData$FM$FM_UD$yaml$FM$logging #> $userData$FM$FM_UD$yaml$FM$logging$enabled #> [1] TRUE #> #> $userData$FM$FM_UD$yaml$FM$logging$timestamp #> [1] TRUE #> #> $userData$FM$FM_UD$yaml$FM$logging$timestamp_fmt #> [1] \"%Y-%m-%d %H:%M:%S\" #> #> $userData$FM$FM_UD$yaml$FM$logging$log_file #> [1] \"formods_log.txt\" #> #> $userData$FM$FM_UD$yaml$FM$logging$console #> [1] TRUE #> #> #> #> #> $userData$FM$FM_UD$MC #> $userData$FM$FM_UD$MC$compact #> $userData$FM$FM_UD$MC$compact$code #> [1] FALSE #> #> $userData$FM$FM_UD$MC$compact$preview #> [1] TRUE #> #> #> $userData$FM$FM_UD$MC$reporting #> $userData$FM$FM_UD$MC$reporting$enabled #> [1] FALSE #> #> $userData$FM$FM_UD$MC$reporting$priority #> [1] 1 #> #> #> $userData$FM$FM_UD$MC$labels #> $userData$FM$FM_UD$MC$labels$default_ds #> [1] \"Original data set\" #> #> $userData$FM$FM_UD$MC$labels$upload_button #> [1] \"Select file\" #> #> $userData$FM$FM_UD$MC$labels$tab_main #> [1] \"Upload file\" #> #> $userData$FM$FM_UD$MC$labels$tab_code #> [1] \"Code\" #> #> $userData$FM$FM_UD$MC$labels$tab_preview #> [1] \"Data preview\" #> #> $userData$FM$FM_UD$MC$labels$switch_clean #> [1] \"Clean column names on upload\" #> #> $userData$FM$FM_UD$MC$labels$msg_bad_extension #> [1] \"Incorrect file extension (===EXT===). Unable to load file ===FILE===.\\nOnly the following extesions are allowed: ===ALLOWEDEXT===.\" #> #> #> $userData$FM$FM_UD$MC$tooltips #> $userData$FM$FM_UD$MC$tooltips$include #> [1] TRUE #> #> $userData$FM$FM_UD$MC$tooltips$show_code #> [1] \"Show data reading code\" #> #> #> $userData$FM$FM_UD$MC$formatting #> $userData$FM$FM_UD$MC$formatting$preview #> $userData$FM$FM_UD$MC$formatting$preview$width #> [1] 800 #> #> $userData$FM$FM_UD$MC$formatting$preview$height #> [1] 500 #> #> #> $userData$FM$FM_UD$MC$formatting$code #> $userData$FM$FM_UD$MC$formatting$code$width #> [1] 500 #> #> $userData$FM$FM_UD$MC$formatting$code$height #> [1] 200 #> #> #> $userData$FM$FM_UD$MC$formatting$switch_clean #> $userData$FM$FM_UD$MC$formatting$switch_clean$tooltip #> [1] \"Strange characters in column names can cause problems. When switched on, this will clean up the column headers and fix those that might break things.\" #> #> $userData$FM$FM_UD$MC$formatting$switch_clean$tooltip_position #> [1] \"bottom\" #> #> #> #> $userData$FM$FM_UD$MC$allowed_extensions #> [1] \"csv\" \"tsv\" \"xls\" \"xlsx\" #> #> $userData$FM$FM_UD$MC$code #> $userData$FM$FM_UD$MC$code$packages #> [1] \"readxl\" \"readr\" \"janitor\" #> #> $userData$FM$FM_UD$MC$code$readOnly #> [1] TRUE #> #> $userData$FM$FM_UD$MC$code$mode #> [1] \"r\" #> #> $userData$FM$FM_UD$MC$code$preamble #> [1] \"# Loading data ------------------------------------------------------------\" #> #> #> $userData$FM$FM_UD$MC$ds_object_name #> [1] \"myDS\" #> #> $userData$FM$FM_UD$MC$clean_data #> $userData$FM$FM_UD$MC$clean_data$enabled #> [1] TRUE #> #> $userData$FM$FM_UD$MC$clean_data$default #> [1] TRUE #> #> $userData$FM$FM_UD$MC$clean_data$code #> [1] \"# Make sure you put whatever packages you use here in the packages section\\n# above.\\n#\\n# contents - data frame containing the loaded dataset.\\n# code - code used to load the dataset you need to append any cleaning\\n# code you generate here.\\n# object_name - Name of the dataset object used in generated code.\\nif(system.file(package=\\\"janitor\\\") != \\\"\\\"){\\n contents = janitor::clean_names(contents, case=\\\"none\\\")\\n code = paste0(code, '\\\\n', object_name, ' = janitor::clean_names(', object_name,', case=\\\"none\\\")')\\n}\" #> #> #> #> $userData$FM$FM_UD$UD #> $userData$FM$FM_UD$UD$isgood #> [1] TRUE #> #> $userData$FM$FM_UD$UD$clean #> [1] TRUE #> #> $userData$FM$FM_UD$UD$load_msg #> File loaded.<\/em> #> #> $userData$FM$FM_UD$UD$data_file_local #> [1] \"/var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpgHdpAj/non_shiny/FM/TEST_DATA.xlsx\" #> #> $userData$FM$FM_UD$UD$data_file_ext #> [1] \"xlsx\" #> #> $userData$FM$FM_UD$UD$data_file #> [1] \"TEST_DATA.xlsx\" #> #> $userData$FM$FM_UD$UD$sheet #> NULL #> #> $userData$FM$FM_UD$UD$sheets #> [1] \"DATA\" \"DDT\" #> #> $userData$FM$FM_UD$UD$code #> [1] \"myDS = readxl::read_excel(path=\\\"TEST_DATA.xlsx\\\", sheet=\\\"DATA\\\")\\nmyDS = janitor::clean_names(myDS, case=\\\"none\\\")\" #> #> $userData$FM$FM_UD$UD$object_name #> [1] \"myDS\" #> #> $userData$FM$FM_UD$UD$checksum #> [1] \"897d952fecbc804999396a96f9df4b20\" #> #> $userData$FM$FM_UD$UD$contents #> # A tibble: 10,680 × 33 #> ID TIME_DY TIME_HR NTIME_DY NTIME_HR TIME AMT DV RECDESC DOSE #> #> 1 1 0 0 0 0 0 3000000 0 dose 3000000 #> 2 1 0 0 0 0 0 0 1250 BM_ng_ml 3000000 #> 3 1 0 0 0 0 0 0 0 C_ng_ml 3000000 #> 4 1 1 24 1 24 24 0 1647 BM_ng_ml 3000000 #> 5 1 1 24 1 24 24 0 690. C_ng_ml 3000000 #> 6 1 2 48 2 48 48 0 1947 BM_ng_ml 3000000 #> 7 1 2 48 2 48 48 0 588. C_ng_ml 3000000 #> 8 1 3 72 3 72 72 0 2170 BM_ng_ml 3000000 #> 9 1 3 72 3 72 72 0 506. C_ng_ml 3000000 #> 10 1 4 96 4 96 96 0 2332 BM_ng_ml 3000000 #> # ℹ 10,670 more rows #> # ℹ 23 more variables: DOSE_STR , Cohort , ROUTE , WT , #> # SUBTYPE , SEX , F1 , ka , CL , Vc , Vp , #> # Q , BM_IC , kdeg_BM , Emax , EC50 , CMT , #> # DUR