Add Initial data spec

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.0.0.9004
+Version: 0.0.0.9005
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut")),
     person("GCP-Service International Ltd.& Co. KG", role = "fnd")

NEWS.md

@@ -7,12 +7,12 @@
 - Created two renv profiles, one for development and one for production. Goal is 
 to minimize the package dependencies of the production version.
 - Removed development package dependencies (for example devtools) that were not needed to run the application.  
-- Improved data anonimization.
+- Improved data anonymization.
 - Changed license.
-
 - Updated Description file.
 - Improved reading of data files within clinsight::run_app()
 - Improved creating test result report.
+- Added data specification to `run_app()` documentation
 
 ## Bug fixes
 

R/data.R

@@ -42,9 +42,19 @@
 #' 
 "col_palette"
 
+
 #' Clinical Trial test data
 #'
-#' A data frame containing randomly created clinical trial data. Used for
-#' testing purposes.
+#' A data.frame containing randomly created clinical trial data. Used for
+#' testing purposes. It will also be used to run the app with example data when
+#' executing `run_app()` with the default configuration settings, or when
+#' running `golem::run_dev()`.
+#'
+#' @format a data.frame with 6,483 rows and 24 variables.
+#'
 #' @source Created with `data-raw/create_random_data.R`
 "clinsightful_data"
+
+
+
+

R/run_app.R

@@ -1,5 +1,5 @@
 #' Run the Shiny Application
-#'
+#' 
 #' @param data_folder Character string. The folder in which all data resides is
 #'   usually set in the config.yml file. However, this can be overwritten if a
 #'   path is set in this argument. Useful for testing purposes.
@@ -8,6 +8,8 @@
 #' @param ... arguments to pass to golem_opts. See `?golem::get_golem_options`
 #'   for more details.
 #' @inheritParams shiny::shinyApp
+#' 
+#' 
 #'
 #' @export
 #' 

dev/02_dev.R

@@ -11,6 +11,82 @@
 #### CURRENT FILE: DEV SCRIPT #####
 ###################################
 
+# Exploring for insights on data spec
+unique(clinsightful_data[,c("site_code","region")]) |> arrange(site_code)
+unique(clinsightful_data[,c("event_id","event_name")])
+unique(clinsightful_data[,c("form_id","form_repeat")])
+unique(clinsightful_data[,c("event_repeat","event_id","event_name")])
+unique(clinsightful_data[,c("event_repeat","event_id","event_name","form_id","form_repeat")])
+unique(clinsightful_data[,c("event_repeat","event_id","event_name", "day")])
+unique(clinsightful_data[,c("event_repeat","event_id","event_name", "event_label")])
+
+# form exploration
+unique(clinsightful_data[,c("form_id")])
+unique(clinsightful_data[,c("form_id","item_group", "item_type")])
+
+# other
+unique(clinsightful_data[,c("item_group","item_type")])
+other <- clinsightful_data |>
+  filter(item_type == "other")
+unique(other[,c("item_group","item_type","item_name")]) |>
+  print(n=40)
+
+# bds
+unique(clinsightful_data[,c("item_group","item_type")])
+bds <- clinsightful_data |>
+  filter(item_type != "other")
+unique(bds[,c("item_group","item_type","item_name")]) |>
+  print(n=40)
+
+
+unique(clinsightful_data[,c("item_group","item_type")])
+other <- clinsightful_data |>
+  filter(item_group == "Vital signs")
+unique(other[,c("item_group","item_type","item_name")]) |>
+  print(n=40)
+
+# dirty?
+library(clinsight)
+data("clinsightful_data")
+dirty <- clinsightful_data |>
+  filter(item_value %in% c("µg/h","µg/ml"))
+
+str(clinsightful_data$item_value)
+
+# day
+class(clinsightful_data$day)
+
+# exploring events
+data("clinsightful_data")
+d_1pat <- clinsightful_data |>
+  filter(subject_id == "BEL_04_772") |>
+  filter(event_id == "COMMON_CM")
+
+# exploring event_repeat & event_date
+library(dplyr)
+clinsightful_data |>
+  filter(subject_id == "BEL_04_772") |>
+  group_by(subject_id, event_id, event_repeat, event_date) |>
+  summarize(n = n()) |>
+  # filter(event_repeat != form_repeat) |>
+  print(n = 36)
+
+d_1pat <- clinsightful_data |>
+  filter(subject_id == "BEL_04_772") |>
+  filter(event_id == "COMMON_AE")
+
+clinsightful_data |>
+  filter(subject_id == "BEL_04_772") |>
+  group_by(subject_id, event_id, event_repeat, event_date, form_repeat) |>
+  summarize(n = n()) |>
+  filter(event_repeat != form_repeat) |>
+  print(n = 36)
+
+
+# metadata
+
+clinsight::metadata$column_specs$col_type |> unique()
+
 # Engineering
 
 ## Dependencies ----
@@ -47,6 +123,7 @@ usethis::use_test("app")
 
 ## Vignette ----
 usethis::use_vignette("testgolem")
+usethis::use_vignette(name = "data_spec", title = "Input Data Specification")
 #devtools::build_vignettes()
 
 ## Code Coverage----

dev/app.R

@@ -0,0 +1,41 @@
+
+devtools::load_all()
+# pkg_name <- "clinsight"
+# library(pkg_name, character.only = TRUE)
+
+
+# datapath <- "data1pt"
+datapath <- app_sys("tests/testthat/fixtures/csvtestdata") # For interactive use
+
+metadata <- get_metadata(filepath = here::here("data-raw/metadata.xlsx"))
+usethis::use_data(metadata, overwrite = TRUE) # do I need this?
+my_raw_data <- get_raw_data(data_path = datapath, column_specs = metadata$column_specs)
+  # fix_multiple_choice_vars() - metadata not found
+
+merged_data <- merge_meta_with_data(
+  data = my_raw_data,
+  meta = metadata
+  )
+# tempdir not useful for production mode
+data_folder <- "."
+data_path <- file.path(data_folder, 
+                       "merged_data.rds")
+saveRDS(merged_data, data_path)
+db_path <- file.path(data_folder, "user_db.sqlite")
+
+# if test_mode == FALSE, you'll need to setup...
+# DB_SECRET env var to setup credentials db
+usethis::edit_r_environ()
+Sys.getenv("DB_SECRET")
+
+# initiate the user db
+db_create(get_review_data(merged_data),
+          db_path = db_path
+          )
+
+run_app(
+  data = data_path, #merged_data, # or db_path works too
+  # user_db = db_path, # defaults to "user_db.sqlite"
+  test_mode = FALSE#, 
+  # onStart = \(){onStop(\(){unlink(data_folder, recursive = TRUE)})} # be careful here
+)

inst/golem-config.yml

@@ -1,6 +1,6 @@
 default:
   golem_name: clinsight
-  golem_version: 0.0.0.9004
+  golem_version: 0.0.0.9005
   app_prod: no
   user_identification: test_user
   study_data: !expr clinsight::clinsightful_data