Dev (#18)

* dev portfolio performance * continued portf performance * contin port perf * refactoring portolio sims * porf sim started completing tests * portfolio perforamnce checks ok * smooth out portf perf * fixes in progress * portfolio performance finished * fix imports Co-authored-by: bjoern koneswarakantha <[email protected]>
openpharma · Nov 2, 2021 · 1066de0 · 1066de0
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,6 @@
 ^README\.Rmd$
 ^\.github$
 ^.\.sas7bdat$
+^Dockerfile$
+^docker-compose.yml$
+^.dockerignore$
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,2 @@
+.vscode
+.git
diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,11 @@
 *.sas7bdat
 
 vignettes/do_not_commit.Rmd
+vignettes/ae_profile.csv
+vignettes/scen.csv
+vignettes/scen_old.csv
+vignettes/scen_days.csv
+vignettes/*.html
+run_remote.md
+.vscode
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: simaerep
 Title: Simulate adverse event reporting in clinical trials with the goal of detecting under-reporting sites
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: 
     person(given = "Bjoern",
            family = "Koneswarakantha",
@@ -16,9 +16,9 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends:
-    ggplot2,
-    dplyr
+    ggplot2
 Imports:
+    dplyr,
     lintr,
     tidyr,
     magrittr,
@@ -28,18 +28,16 @@ Imports:
     forcats,
     cowplot,
     RColorBrewer,
-    feather,
     furrr (>= 0.2.1),
-    future
+    progressr,
+    knitr,
+    tibble
 Suggests:
     testthat,
     devtools,
     pkgdown,
-    knitr,
-    tibble,
     spelling,
-    haven,
-    sqldf
+    haven
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Language: en-US
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,4 @@
+FROM rocker/verse:4.1
+COPY .  /simaerep
+RUN R -e "devtools::install('/simaerep/.', upgrade = 'never', dependencies = TRUE, repos = 'http://cran.us.r-project.org')" 
+RUN rm /simaerep -r -f
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,8 +6,10 @@ export(check_df_visit)
 export(eval_sites)
 export(eval_sites_deprecated)
 export(exp_implicit_missing_visits)
+export(get_config)
 export(get_ecd_values)
 export(get_pat_pool_config)
+export(get_portf_perf)
 export(lint_package)
 export(pat_aggr)
 export(pat_pool)
@@ -17,30 +19,79 @@ export(plot_sim_examples)
 export(plot_study)
 export(plot_visit_med75)
 export(poiss_test_site_ae_vs_study_ae)
+export(prep_for_sim)
 export(prob_lower_site_ae_vs_study_ae)
+export(purrr_bar)
+export(sim_after_prep)
+export(sim_scenario)
 export(sim_sites)
 export(sim_studies)
 export(sim_test_data_patient)
+export(sim_test_data_portfolio)
 export(sim_test_data_study)
+export(sim_ur_scenarios)
 export(site_aggr)
-import(dplyr)
-import(furrr)
-import(future)
+export(with_progress_cnd)
 import(ggplot2)
-import(purrr)
-import(tidyr)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(cowplot,draw_label)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,ggdraw)
 importFrom(cowplot,plot_grid)
-importFrom(feather,read_feather)
-importFrom(feather,write_feather)
+importFrom(dplyr,arrange)
+importFrom(dplyr,between)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,case_when)
+importFrom(dplyr,dense_rank)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
+importFrom(dplyr,everything)
+importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_at)
+importFrom(dplyr,inner_join)
+importFrom(dplyr,is_grouped_df)
+importFrom(dplyr,lag)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,mutate_all)
+importFrom(dplyr,mutate_at)
+importFrom(dplyr,n)
+importFrom(dplyr,n_distinct)
+importFrom(dplyr,one_of)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(dplyr,right_join)
+importFrom(dplyr,row_number)
+importFrom(dplyr,sample_n)
+importFrom(dplyr,select)
+importFrom(dplyr,summarise)
+importFrom(dplyr,summarise_all)
+importFrom(dplyr,summarise_at)
+importFrom(dplyr,ungroup)
+importFrom(dplyr,vars)
 importFrom(forcats,fct_relevel)
+importFrom(furrr,furrr_options)
+importFrom(furrr,future_map)
+importFrom(furrr,future_pmap)
+importFrom(knitr,kable)
 importFrom(lintr,lint_package)
 importFrom(magrittr,"%>%")
+importFrom(progressr,progressor)
+importFrom(progressr,with_progress)
+importFrom(purrr,map)
+importFrom(purrr,map2)
+importFrom(purrr,map2_dbl)
+importFrom(purrr,map_chr)
+importFrom(purrr,map_dbl)
+importFrom(purrr,map_int)
+importFrom(purrr,pmap)
+importFrom(purrr,pmap_dbl)
+importFrom(purrr,possibly)
 importFrom(purrr,safely)
 importFrom(rlang,":=")
+importFrom(rlang,.data)
 importFrom(stats,ecdf)
 importFrom(stats,median)
 importFrom(stats,p.adjust)
@@ -49,6 +100,12 @@ importFrom(stats,quantile)
 importFrom(stats,rnorm)
 importFrom(stats,rpois)
 importFrom(stats,runif)
+importFrom(stats,sd)
 importFrom(stringr,str_count)
 importFrom(stringr,str_pad)
+importFrom(tibble,tibble)
+importFrom(tidyr,fill)
+importFrom(tidyr,nest)
+importFrom(tidyr,tibble)
+importFrom(tidyr,unnest)
 importFrom(utils,head)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# simaerep 0.3.2
+- added portfolio performance assessment
+
 # simaerep 0.3.1
 - changed MIT License holder from openpharma to F. Hoffmann-La Roche Ltd and simaerep authors
 
@@ -8,4 +11,4 @@
 # simaerep 0.2.0
 - use Benjamin Hochberg procedure for alpha error correction
 - fix warnings around parallel processing
-- improved SAS files vignette
+- improved SAS files vignette
diff --git a/R/0_imports.R b/R/0_imports.R
@@ -0,0 +1,32 @@
+# satisfy lintr
+# lintr falsely flags possibly_ecdf as unused variable
+# using rlang::.data here causes error with furrr in sim_test_data_portfolio
+# patnum, n_ae, visit
+
+if (getRversion() >= "2.15.1") {
+  utils::globalVariables(c("possibly_ecdf", "patnum", "n_ae", "visit"))
+}
+
+#' @importFrom progressr progressor
+#' @importFrom cowplot get_legend plot_grid ggdraw draw_label plot_grid plot_grid
+#' @importFrom cowplot ggdraw draw_label
+#' @importFrom forcats fct_relevel
+#' @importFrom RColorBrewer brewer.pal
+#' @importFrom utils head
+#' @importFrom stats p.adjust quantile median runif poisson.test ecdf rnorm rpois sd
+#' @importFrom purrr safely possibly pmap map map2 pmap_dbl map2_dbl map_dbl
+#' @importFrom purrr map_int map_chr
+#' @importFrom furrr future_map future_pmap furrr_options
+#' @importFrom progressr with_progress
+#' @importFrom stringr str_count str_pad
+#' @importFrom rlang := .data
+#' @importFrom dplyr select mutate filter summarise group_by summarise_all summarise_at
+#' @importFrom dplyr mutate_all mutate_at ungroup vars bind_cols bind_rows pull
+#' @importFrom dplyr n_distinct distinct arrange right_join left_join inner_join
+#' @importFrom dplyr rename sample_n between row_number dense_rank desc case_when
+#' @importFrom dplyr group_by_at n is_grouped_df everything one_of lag
+#' @importFrom tidyr tibble unnest nest fill
+#' @importFrom lintr lint_package
+#' @importFrom knitr kable
+#' @importFrom tibble tibble
+NULL
diff --git a/R/lint.R b/R/lint.R
@@ -11,7 +11,6 @@
 #' @seealso \code{\link[lintr]{lint_package}}
 #' @rdname lint_package
 #' @export
-#' @importFrom lintr lint_package
 lint_package <- function(path = ".", ...) {
 
   lint_results <- lintr::lint_package(path = path,