adress comments (#40)

.Rbuildignore

@@ -14,3 +14,4 @@
 ^\.git
 ^cran-comments\.md$
 ^data-raw$
+^CRAN-SUBMISSION$

DESCRIPTION

@@ -1,16 +1,20 @@
 Package: simaerep
-Title: Simulate Adverse Event Reporting in Clinical Trials with the Goal of Detecting under-Reporting Sites
+Title: Find Clinical Trial Sites Under-Reporting Adverse Events
 Version: 0.4.2
-Authors@R: 
+Authors@R: c(
     person(given = "Bjoern",
            family = "Koneswarakantha",
-           role = c("aut", "cre"),
+           role = c("aut", "cre", "cph"),
            email = "[email protected]",
-           comment = c(ORCID = "0000-0003-4585-7799"))
-Description: This can detect clinical trial sites that are under-reporting adverse events (AE).
-  Bootstrap-based simulations are used to simulate AE reporting and to assign an AE 
-  under-reporting probability to each site in a clinical trial (Koneswarakantha 2021 
-  <doi:10.1007/s40264-020-01011-5>).
+           comment = c(ORCID = "0000-0003-4585-7799")),
+    person("F. Hoffmann-La Roche Ltd",
+           role = c("cph"))
+  )
+Description: Monitoring of Adverse Event (AE) reporting in clinical trials is 
+  important for patient safety. Sites that are under-reporting AEs can be detected 
+  using Bootstrap-based simulations that simulate overall AE reporting. Based on the 
+  simulation an AE under-reporting probability is assigned to each site in a 
+  given trial (Koneswarakantha 2021 <doi:10.1007/s40264-020-01011-5>).
 URL: https://openpharma.github.io/simaerep/, https://github.com/openpharma/simaerep
 License: MIT + file LICENSE
 Encoding: UTF-8

R/S3_simaerep.R

@@ -176,7 +176,7 @@ simaerep <- function(df_visit,
 #' @details see [plot_study()][plot_study] and
 #'   [plot_visit_med75()][plot_visit_med75]
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' df_visit <- sim_test_data_study(
 #'   n_pat = 100,
 #'   n_sites = 5,

R/lint.R

@@ -6,9 +6,10 @@
 #'   cyclocomp_linter = lintr::cyclocomp_linter(25)
 #' @param path character
 #' @inheritParams lintr::lint_package
-#' @return " "
+#' @return No return value, called for side effects
 #' @seealso \code{\link[lintr]{lint_package}}
 #' @rdname lint_package
+#' @noRd
 lint_package <- function(path = ".", ...) {
 
   lint_results <- lintr::lint_package(path = path,
@@ -21,9 +22,9 @@ lint_package <- function(path = ".", ...) {
                                       ...)
 
   if (length(lint_results) > 0) {
-    print(lint_results) # does not work wit cat()
+    message(lint_results) # does not work wit cat()
     stop(paste(lint_results))
   } else {
-    print("no lint violations")
+    message("no lint violations")
   }
 }

R/progress.R

@@ -1,7 +1,7 @@
 #' @title Execute a purrr or furrr function with a progress
 #' bar.
 #' @description Internal utility function.
-#' @details Call still needs to be wrapped in \code{\link[progressr]{with_progress}} 
+#' @details Call still needs to be wrapped in \code{\link[progressr]{with_progress}}
 #' or [with_progress_cnd()][with_progress_cnd()]
 #' @param .purrr purrr or furrr function
 #' @param ... iterable arguments passed to .purrr
@@ -17,7 +17,7 @@
 #'   purrr_bar(rep(0.25, 5), .purrr = purrr::map, .f = Sys.sleep, .steps = 5)
 #' )
 #'
-#'\dontrun{
+#'\donttest{
 #' # purrr::walk
 #' progressr::with_progress(
 #'  purrr_bar(rep(0.25, 5), .purrr = purrr::walk,.f = Sys.sleep, .steps = 5)
@@ -67,10 +67,11 @@
 #'
 #' # with mutate
 #' progressr::with_progress(
-#'  tibble(x = rep(0.25, 5)) %>%
-#'   mutate(x = purrr_bar(x, .purrr = purrr::map, .f = Sys.sleep, .steps = 5))
+#'  tibble::tibble(x = rep(0.25, 5)) %>%
+#'   dplyr::mutate(x = purrr_bar(x, .purrr = purrr::map, .f = Sys.sleep, .steps = 5))
 #' )
 #'}
+#' @return result of function passed to .f
 #' @rdname purrr_bar
 #' @export
 purrr_bar <- function(...,
@@ -116,7 +117,8 @@ purrr_bar <- function(...,
 #'@param ex expression
 #'@param progress logical, Default: TRUE
 #'@details This wrapper adds a progress parameter to \code{\link[progressr]{with_progress}}
-#' so that we can control the progress bar in the user facing functions.
+#' so that we can control the progress bar in the user facing functions. The progressbar
+#' only shows in interactive mode.
 #' @examples
 #' if (interactive()) {
 #'
@@ -155,6 +157,7 @@ purrr_bar <- function(...,
 #'   )
 #' )
 #'}
+#'@return No return value, called for side effects
 #'@seealso \code{\link[progressr]{with_progress}}
 #'@rdname with_progress_cnd
 #'@export

R/simaerep.R

@@ -1030,7 +1030,7 @@ get_pat_pool_config <- function(df_visit, df_site, min_n_pat_with_med75 = 1) {
 #'   are calculated.
 #' @return dataframe
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' df_visit1 <- sim_test_data_study(n_pat = 100, n_sites = 5,
 #'                                       frac_site_with_ur = 0.4, ur_rate = 0.6)
 #'
@@ -1046,7 +1046,8 @@ get_pat_pool_config <- function(df_visit, df_site, min_n_pat_with_med75 = 1) {
 #' df_site <- site_aggr(df_visit)
 #'
 #' sim_studies(df_visit, df_site, r = 3, keep_ae = TRUE)
-#'
+#'}
+#' \dontrun{
 #' # parallel processing -------------------------
 #' library(future)
 #' future::plan(multiprocess)

R/simaerep_plot.R

@@ -138,11 +138,12 @@ plot_dots <- function(df,
 #' @param color_low character, hex color value, Default: '#25A69A'
 #' @param title logical, include title, Default: T
 #' @param legend logical, include legend, Default: T
+#' @param seed pass seed for simulations Default: 5
 #' @return ggplot
 #' @details uses [plot_dots()][plot_dots()] and adds 2 simulation panels, uses made-up
 #' site config with three sites A,B,C simulating site C
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' plot_sim_example(size_dots = 5)
 #' }
 #' @seealso
@@ -158,8 +159,9 @@ plot_sim_example <- function(substract_ae_per_pat = 0,
                              color_high = "#00695C",
                              color_low = "#25A69A",
                              title = TRUE,
-                             legend = TRUE) {
-  set.seed(5)
+                             legend = TRUE,
+                             seed = 5) {
+  set.seed(seed)
 
   study <- tibble(
     site = LETTERS[1:3],
@@ -292,13 +294,14 @@ plot_sim_example <- function(substract_ae_per_pat = 0,
 #' @param ... parameters passed to plot_sim_example()
 #' @details This function is a wrapper for plot_sim_example()
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' plot_sim_examples(size_dot = 3, size_raster_label = 10)
 #' plot_sim_examples()
 #' }
 #' @seealso
 #'  \code{\link[cowplot]{ggdraw}},\code{\link[cowplot]{draw_label}},\code{\link[cowplot]{plot_grid}}
 #' @rdname plot_sim_examples
+#' @return ggplot
 #' @export
 
 plot_sim_examples <- function(substract_ae_per_pat = c(0, 1, 3), ...) {
@@ -403,7 +406,7 @@ plot_sim_examples <- function(substract_ae_per_pat = c(0, 1, 3), ...) {
 #'   number of patients. Patients that have not been on the study long enough to
 #'   reach the evaluation point (visit_med75) will be ignored.
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' df_visit <- sim_test_data_study(n_pat = 1000, n_sites = 10,
 #'     frac_site_with_ur = 0.2, ur_rate = 0.15, max_visit_sd = 8)
 #'
@@ -682,7 +685,7 @@ plot_study <- function(df_visit,
     labs(y = "Mean Cumulative AE Count per Site")
 
   if (length(sites_ordered) == 0) {
-    print("no sites with P/FP ratio > 1")
+    message("no sites with P/FP ratio > 1")
     return(p_study)
   }
 

R/simulate_test_data.R

@@ -186,7 +186,7 @@ sim_scenario <- function(n_ae_site, n_ae_study, frac_pat_with_ur, ur_rate) {
 #'   run. For this to work we need to specify the plan for how the code should
 #'   run, e.g. plan(multisession, workers = 18)
 #' @examples
-#' if (interactive()) {
+#' \donttest{
 #' df_visit1 <- sim_test_data_study(n_pat = 100, n_sites = 10,
 #'                                  frac_site_with_ur = 0.4, ur_rate = 0.6)
 #'
@@ -200,8 +200,8 @@ sim_scenario <- function(n_ae_site, n_ae_study, frac_pat_with_ur, ur_rate) {
 #' df_visit <- dplyr::bind_rows(df_visit1, df_visit2)
 #'
 #' df_site_max <- df_visit %>%
-#'   group_by(study_id, site_number, patnum) %>%
-#'   summarise(max_visit = max(visit),
+#'   dplyr::group_by(study_id, site_number, patnum) %>%
+#'   dplyr::summarise(max_visit = max(visit),
 #'             max_ae = max(n_ae),
 #'             .groups = "drop")
 #'
@@ -406,7 +406,7 @@ sim_ur_scenarios <- function(df_portf,
 #'   run. For this to work we need to specify the plan for how the code should
 #'   run, e.g. `plan(multisession, workers = 3)
 #' @examples
-#' if (interactive()) {
+#' \donttest{
 #' df_visit1 <- sim_test_data_study(n_pat = 100, n_sites = 10,
 #'                                  frac_site_with_ur = 0.4, ur_rate = 0.6)
 #'
@@ -420,8 +420,8 @@ sim_ur_scenarios <- function(df_portf,
 #' df_visit <- dplyr::bind_rows(df_visit1, df_visit2)
 #'
 #' df_site_max <- df_visit %>%
-#'   group_by(study_id, site_number, patnum) %>%
-#'   summarise(max_visit = max(visit),
+#'   dplyr::group_by(study_id, site_number, patnum) %>%
+#'   dplyr::summarise(max_visit = max(visit),
 #'             max_ae = max(n_ae),
 #'             .groups = "drop")
 #'
@@ -559,22 +559,22 @@ sim_test_data_portfolio <- function(df_config, parallel = FALSE, progress = TRUE
 #'  site} \item{**max_visit_mean**}{mean of maximum patient visits per site}
 #'  \item{**n_pat**}{number of patients} }
 #' @examples
-#' if (interactive()) {
+#' \donttest{
 #' df_visit1 <- sim_test_data_study(n_pat = 100, n_sites = 10,
 #'                                  frac_site_with_ur = 0.4, ur_rate = 0.6)
-#'.
+#'
 #' df_visit1$study_id <- "A"
-#'.
+#'
 #' df_visit2 <- sim_test_data_study(n_pat = 100, n_sites = 10,
 #'                                  frac_site_with_ur = 0.2, ur_rate = 0.1)
-#'.
+#'
 #' df_visit2$study_id <- "B"
-#'.
+#'
 #' df_visit <- dplyr::bind_rows(df_visit1, df_visit2)
 #'
 #' df_site_max <- df_visit %>%
-#'   group_by(study_id, site_number, patnum) %>%
-#'   summarise(max_visit = max(visit),
+#'   dplyr::group_by(study_id, site_number, patnum) %>%
+#'   dplyr::summarise(max_visit = max(visit),
 #'             max_ae = max(n_ae),
 #'             .groups = "drop")
 #'
@@ -674,7 +674,7 @@ get_config <- function(df_site,
 #' @return dataframe
 #' @details DETAILS
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' df_visit1 <- sim_test_data_study(n_pat = 100, n_sites = 10,
 #'                                  frac_site_with_ur = 0.4, ur_rate = 0.6)
 #'

R/utils-pipe.R

@@ -8,4 +8,5 @@
 #' @export
 #' @importFrom magrittr %>%
 #' @usage lhs \%>\% rhs
+#' @return returns output of rhs function
 NULL

_pkgdown.yml

@@ -95,6 +95,3 @@ reference:
   - plot_sim_examples
   - plot_sim_example
   - plot_dots
-- title: internal
-  contents:
-  - lint_package

cran-comments.md

@@ -1,3 +1,60 @@
+# Resubmission of simaerep
+
+Thank you for taking the time to review my submission. I have addressed all of your
+comments.
+
+## DESCRIPTION
+
+Please reduce the length of the title to less than 65 characters.
+
+*done*
+
+Please do not start the description with "This package", package name,
+title or similar.
+I would start with: "Detect clinical trial sites..."
+
+*done*
+
+Please always add all authors, contributors and copyright holders in the
+Authors@R field with the appropriate roles.
+
+*I have added Hoffmann La Roche to the Authors@R field and assigned cph*
+*role to the institution and myself. This reflects our internal policy.*
+*as stated in the licence file.*
+*COPYRIGHT HOLDER: F. Hoffmann-La Roche Ltd and simaerep authors*
+*This covers copyright interest of potential future external collaborators.*
+
+## Examples
+
+Please unwrap the examples if they are executable in < 5 sec, or replace
+dontrun{} with \donttest{}.
+*done, with one exception in the sim_studies() example show casing parallel*
+*processing which makes changes to the user's environment.*
+
+Please replace if(interactive()){} with \donttest or unwrap the
+examples.
+*done, with one exception, with_progress_cnd() the progressbar is only visible*
+*in interactive mode*
+
+## Console Messages
+
+R/lint.R
+
+*lint_package() has been declared an internal function, print() calls have been*
+*exchanged for message() calls*
+
+R/simaerep_plot.R
+*print() calls have been exchanged for message() calls that inform user that*
+*certain element of the plot cannot be generated*
+
+## Seed
+R/simaerep_plot.R
+*seed can now be passed as parameter, fixed seed is desired so that the generated*
+*plot always looks the same*
+
+
+
+
 # First Submission of simaerep
 
 ## Test Results