lots of fixes for R CMD CHECK

DESCRIPTION

@@ -72,14 +72,11 @@ Collate:
     'options.R'
     'population_plot.R'
     'project.R'
-    'recist_check.R'
     'sanity_checks.R'
     'sas_format.R'
     'save_to_excel.R'
     'search_for_newer_data.R'
     'split_mixed.R'
     'swimmerplot.R'
-    'todo_base_macro.R'
-    'todo_read_all_csv.R'
     'trialmaster.R'
     'waterfall_plot.R'

NAMESPACE

@@ -76,6 +76,7 @@ importFrom(cli,cli_inform)
 importFrom(cli,cli_vec)
 importFrom(cli,cli_warn)
 importFrom(cli,col_green)
+importFrom(cli,col_red)
 importFrom(cli,format_inline)
 importFrom(cli,qty)
 importFrom(cli,rule)
@@ -112,7 +113,6 @@ importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)
 importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
-importFrom(dplyr,semi_join)
 importFrom(dplyr,setdiff)
 importFrom(dplyr,slice)
 importFrom(dplyr,slice_max)
@@ -212,7 +212,6 @@ importFrom(rlang,current_env)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,ensym)
-importFrom(rlang,env)
 importFrom(rlang,have_name)
 importFrom(rlang,int)
 importFrom(rlang,is_empty)
@@ -254,7 +253,6 @@ importFrom(tibble,deframe)
 importFrom(tibble,lst)
 importFrom(tibble,tibble)
 importFrom(tidyr,build_wider_spec)
-importFrom(tidyr,fill)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider_spec)
 importFrom(tidyr,replace_na)

R/EDCimport-package.R

@@ -1,7 +1,7 @@
 #' @keywords internal
 #' @importFrom dplyr %>% 
 #' @importFrom rlang %||% := 
-#' @importFrom cli qty col_green
+#' @importFrom cli qty col_green col_red
 "_PACKAGE"
 
 ## usethis namespace: start
@@ -27,7 +27,8 @@ edcimport_env = rlang::new_environment()
 edcimport_env$warn_list = list()
 edcimport_env$lookup = NULL
 
-utils::globalVariables(c(".", ":=", "!!", ".data", ".env", "SUBJID", "age", "dataset", "n_id", "name", "value", ".id", "aegr", "aesoc", "best_resp", "case_when", "diff_first", "element_blank", "facet_grid", "first_sum", "grade2", "grade_max", "last_sum", "min_sum", "n_ae", "n_arm", "n_soc", "n_term", "replace_na", "resp", "resp_num", "sae", "scale_fill_steps", "star", "star_txt", "subjid", "variable", "vars", "x", "column", "last_date", "origin", "pct_datasets", "arm_", "grade_", "soc_", "subjid_", "term_", "any_ae", "any_severe", "label", "label_percent_positive", "n_severe", "pct_ae", "pct_severe", "severe_", "unit"))
+utils::globalVariables(c(".", ":=", "!!", ".data", ".env", "SUBJID", "age", "dataset", "n_id", "name", "value", ".id", "aegr", "aesoc", "best_resp", "case_when", "diff_first", "element_blank", "facet_grid", "first_sum", "grade2", "grade_max", "last_sum", "min_sum", "n_ae", "n_arm", "n_soc", "n_term", "replace_na", "resp", "resp_num", "sae", "scale_fill_steps", "star", "star_txt", "subjid", "variable", "vars", "x", "column", "last_date", "origin", "pct_datasets", "arm_", "grade_", "soc_", "subjid_", "term_", "any_ae", "any_severe", "label", "label_percent_positive", "n_severe", "pct_ae", "pct_severe", "severe_", "unit", ".name", "Tot", "any_grade_sup_na", "calc", "col_keys", "crfstat", "datetime_extraction", "first_date", "h1", "h2", "origin_col", "origin_data", "origin_label", "prefered", "resp2", "showNA", "sort_by_count", "title", "weight"))
+
 
 
 

R/ae_table_grade.R

@@ -8,7 +8,6 @@
 
 #' Summary tables for AE
 #' 
-#' @param type one or several of `c("max", "sup", "eq")`. `max` computes the maximum AE grade per patient, `sup` computes the number of patients having experienced at least one AE of grade higher or equal to X, and `eq` computes the number of patients having experienced at least one AE of grade equal to X.
 #' @param percent whether to show percentages with counts. Defaults to TRUE. Can also be "only" to not show counts.
 #' @inheritParams ae_table_soc
 #' @inherit ae_table_soc seealso
@@ -23,10 +22,11 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' tm = edc_example_ae()
 #' load_list(tm)
 #' 
+#' if(require(flextable)){
+#' 
 #' ae_table_grade(df_ae=ae, df_enrol=enrolres, arm=NULL) %>% 
 #'   as_flextable(header_show_n=TRUE)
 #' 
@@ -38,8 +38,9 @@
 #' ae %>% 
 #'   filter(sae=="Yes") %>% 
 #'   ae_table_grade(df_enrol=enrolres, arm="ARM") %>% 
-#'   mutate_all(~str_replace(.x, "AE", "SAE")) %>% 
+#'   dplyr::mutate_all(~stringr::str_replace(.x, "AE", "SAE")) %>% 
 #'   as_flextable(header_show_n=TRUE) 
+#'   
 #' }
 ae_table_grade = function(
     df_ae, ..., df_enrol, 
@@ -94,10 +95,10 @@ ae_table_grade = function(
       any_grade_sup_na   = case_when(!cur_group()$subjid %in% df_ae$subjid ~ lab_no_ae,
                                      any(is.na(grade), na.rm=TRUE) ~ "Any missing grade",
                                      .default="foobar"),,
-      any_grade_sup_1 = ifelse(any(grade >= 1, na.rm=TRUE), "Grade ≥ 1", "foobar"), 
-      any_grade_sup_2 = ifelse(any(grade >= 2, na.rm=TRUE), "Grade ≥ 2", "foobar"), 
-      any_grade_sup_3 = ifelse(any(grade >= 3, na.rm=TRUE), "Grade ≥ 3", "foobar"), 
-      any_grade_sup_4 = ifelse(any(grade >= 4, na.rm=TRUE), "Grade ≥ 4", "foobar"), 
+      any_grade_sup_1 = ifelse(any(grade >= 1, na.rm=TRUE), "Grade \u2265 1", "foobar"), 
+      any_grade_sup_2 = ifelse(any(grade >= 2, na.rm=TRUE), "Grade \u2265 2", "foobar"), 
+      any_grade_sup_3 = ifelse(any(grade >= 3, na.rm=TRUE), "Grade \u2265 3", "foobar"), 
+      any_grade_sup_4 = ifelse(any(grade >= 4, na.rm=TRUE), "Grade \u2265 4", "foobar"), 
       any_grade_sup_5 = ifelse(any(grade >= 5, na.rm=TRUE), "Grade = 5", "foobar"), 
       any_grade_eq_na   = any_grade_sup_na,
       any_grade_eq_1 = ifelse(any(grade == 1, na.rm=TRUE), "Grade 1", "foobar"), 
@@ -472,6 +473,7 @@ ae_table_grade_max = function(
 #' 
 #' @inheritParams ae_table_soc 
 #' @inherit ae_table_soc seealso
+#' @param proportion display proportion instead of count.
 #' @param type the plots to be included. One of `c("stack", "dodge", "fill")`.
 #' @param drop_levels whether to drop unused grade levels.
 #'

R/ae_table_soc.R

@@ -8,27 +8,37 @@
 #' The function `ae_table_soc()` creates a summary table of maximum AE grades for each patient according to term and SOC CTCAE. 
 #' The resulting dataframe can be piped to `as_flextable()` to get a nicely formatted flextable.
 #' 
-#' @param df_ae adverse event dataset, one row per AE, containing subjid, soc, and grade
+#' @param df_ae adverse event dataset, one row per AE, containing subjid, soc, and grade.
 #' @param df_enrol enrollment dataset, one row per patient, containing subjid (and arm if needed). All patients should be in this dataset.
-#' @param subjid name of the patient ID in both `df_ae` and `df_enrol`. Case-insensitive.
-#' @param arm name of the treatment column in `df_enrol`. Case-insensitive. Can be set to `NULL` to not group.
-#' @param grade  name of the AE grade column in `df_ae`. Case-insensitive.
-#' @param soc name of the SOC column in `df_ae`. Case-insensitive. Grade will be considered 0 if missing(e.g. if patient if absent from `df_ae`).
+#' @param variant one or several of `c("max", "sup", "eq")`. `max` computes the maximum AE grade per patient, `sup` computes the number of patients having experienced at least one AE of grade higher or equal to X, and `eq` computes the number of patients having experienced at least one AE of grade equal to X.
+#' @param arm name of the treatment column in `df_enrol`. Case-insensitive. Can be set to `NULL`.
 #' @param term name of the the CTCAE term column in `df_ae`. Case-insensitive. Can be set to `NULL`.
-#' @param sort_by_ae should the table be sorted by number or alphabetically
-#' @param total whether to add a `total` column for each arm
-#' @param digits significant digits for percentages
-#' @param warn_miss whether to warn for missing values
+#' @param sort_by_count should the table be sorted by the number of AE or by SOC alphabetically.
+#' @param total whether to add a `total` column for each arm.
+#' @param showNA whether to display missing grades.
+#' @param digits significant digits for percentages.
+#' @param warn_miss whether to warn for missing values.
+#' @param grade  name of the AE grade column in `df_ae`. Case-insensitive.
+#' @param soc name of the SOC column in `df_ae`. Case-insensitive. Grade will be considered 0 if missing (e.g. if patient if absent from `df_ae`).
+#' @param subjid name of the patient ID in both `df_ae` and `df_enrol`. Case-insensitive.
 #' @param ... unused
 #'
 #' @return a dataframe (`ae_table_soc()`) or a flextable (`as_flextable()`).
 #' 
 #' @seealso [ae_table_grade_max()], [ae_table_grade_n()], [ae_table_soc()], [ae_plot_grade_max()], [ae_plot_grade_n()]
 #' 
+#' @importFrom cli cli_warn
+#' @importFrom dplyr across any_of arrange count cur_group filter full_join if_else mutate pull rename select summarise
+#' @importFrom forcats fct_infreq
+#' @importFrom glue glue
+#' @importFrom purrr iwalk keep map
+#' @importFrom rlang arg_match check_dots_empty ensym is_empty set_names
+#' @importFrom tibble deframe lst
+#' @importFrom tidyr build_wider_spec pivot_wider_spec unnest
+#' @importFrom tidyselect matches
 #' @export
 #'
-#' @examples
-#' 
+#' @examples 
 #' tm = edc_example_ae()
 #' ae_table_soc(df_ae=tm$ae, df_enrol=tm$enrolres, term=NULL)
 #' ae_table_soc(df_ae=tm$ae, df_enrol=tm$enrolres, term=NULL, arm=NULL)
@@ -46,20 +56,12 @@
 #'   as_flextable() %>% 
 #'   highlight(i=~soc=="Hepatobiliary disorders", j="all_patients_Tot")
 #' }
-#' @importFrom cli cli_warn
-#' @importFrom dplyr across any_of arrange count cur_group filter full_join if_else mutate pull rename select summarise
-#' @importFrom forcats fct_infreq
-#' @importFrom glue glue
-#' @importFrom purrr iwalk keep map
-#' @importFrom rlang arg_match check_dots_empty ensym is_empty set_names
-#' @importFrom tibble deframe lst
-#' @importFrom tidyr build_wider_spec pivot_wider_spec unnest
-#' @importFrom tidyselect matches
 ae_table_soc = function(
     df_ae, ..., df_enrol, 
     variant=c("max", "sup", "eq"), 
-    arm=NULL, grade="AEGR", soc="AESOC", term=NULL, subjid="SUBJID",
-    sort_by_count=TRUE, total=TRUE, showNA=TRUE, digits=0, warn_miss=FALSE
+    arm=NULL, term=NULL,
+    sort_by_count=TRUE, total=TRUE, showNA=TRUE, digits=0, warn_miss=FALSE, 
+    grade="AEGR", soc="AESOC", subjid="SUBJID"
 ){
   check_dots_empty()
   default_arm = set_label("All patients", "Treatment arm")
@@ -286,7 +288,7 @@ as_flextable.ae_table_soc = function(x,
 #'   
 #' ae2 %>% 
 #'   butterfly_plot(df_enrol=enrolres, severe="serious") + 
-#'   labs(caption="Darker areas represent Serious Adverse Events")
+#'   ggplot2::labs(caption="Darker areas represent Serious Adverse Events")
 butterfly_plot = function(
     df_ae, ..., df_enrol, severe=NULL, sort_by=c("total", "severe"), range_min=NULL,
     arm="ARM", subjid="SUBJID", soc="AESOC"
@@ -381,7 +383,7 @@ butterfly_plot = function(
 
 
 #' @rdname butterfly_plot
-#' @usage ae_plot_soc(...)
+#' @usage ae_plot_soc(df_ae, ..., df_enrol, severe, sort_by, range_min, arm, subjid, soc)
 #' @export
 ae_plot_soc = butterfly_plot
 

R/crf_status.R

@@ -11,6 +11,7 @@
 #' @param crfstat_lvls the CRF status levels, from "best" to "worst". The plot is ordered by the "worst" level. 
 #' @param x_label a glue pattern determining the tick label in the x axis. Available variables are `c("nrow", "ncol", "n_id", "rows_per_id", "crfname")`, taken from [edc_lookup()].
 #' @param treat_as_worst a regex for levels that should be treated as worst in the ordering
+#' @param ... unused
 #'
 #' @return a ggplot
 #' @export
@@ -83,7 +84,7 @@ crf_status_plot = function(crfstat_col="CRFSTAT",
 
 #' @rdname crf_status_plot
 #' @export
-#' @source ggsci:::ggsci_db$lancet[["lanonc"]] %>% dput()
+#' @source `ggsci:::ggsci_db$lancet[["lanonc"]] %>% dput()`
 edc_pal_crf = function(){
   c("Complete"="#000e8b", 
     "Complete Locked"="#0053a5", 

R/helpers.R

@@ -108,7 +108,7 @@ find_keyword = function(keyword, data=edc_lookup(), ignore_case=TRUE){
 #'  
 #' x          
 #' #y and z are left untouched (or throw an error if fail=TRUE)   
-#' mutate_all(x, fct_yesno, fail=FALSE)
+#' sapply(x, fct_yesno, fail=FALSE)
 #' 
 #' # as "1-Yes" is not in `input`, x$e is untouched/fails if strict=TRUE
 #' fct_yesno(x$e)
@@ -316,11 +316,13 @@ edc_inform_code = function(main="main.R", Rdir="R/"){
 #'
 #' @return nothing
 #' @export
-#'
-#' @examples
-#' save_sessioninfo()
 #' @importFrom fs dir_create path path_dir path_ext path_ext_remove
 #' @importFrom utils capture.output sessionInfo
+#'
+#' @examples
+#' \dontrun{
+#'    save_sessioninfo()
+#' }
 save_sessioninfo = function(path="check/session_info.txt", with_date=TRUE){
   target = path %>% 
     path_ext_remove() %>% 

R/sanity_checks.R

@@ -234,7 +234,7 @@ edc_data_warn = function(df, message, ...,
 }
 
 #' @rdname edc_data_warn
-#' @usage edc_data_stop(...) #same arguments
+#' @usage edc_data_stop(df, message, ..., issue_n, max_subjid, csv_path, col_subjid)
 #' @export
 #' @importFrom rlang check_dots_empty
 edc_data_stop = function(df, message, ..., 

R/search_for_newer_data.R

@@ -4,11 +4,12 @@
 #' 
 #' Search in some folders if a TrialMaster database more recent than the current extration is present. By default, it will search the "data" folder and the OS usual "Downloads" folder. If a newer database is found, user will be asked if they want to move it to the "data" folder.
 #'
-#' @param project archive path, giving the project name
+#' @param archive TM archive path, giving the project name and date
 #' @param source the path vector to be searched, default to both "data" and the usual "Downloads" folder
 #' @param target the path where files should be copied
 #' @param ask whether to ask the user to move the file to "data"
 #' @param advice whether to advice how to move it instead, if `ask==FALSE`
+#' @param ... unused
 #'
 #' @return the path to the newer file, invisibly.
 #' @export
@@ -22,7 +23,9 @@
 #' 
 #' @examples
 #' \dontrun{
-#' 
+#'   archive = "data/MYPROJECT_ExportTemplate_xxx_SAS_XPORT_2024_06_01_12_00.zip"
+#'   #tm = read_trialmaster(archive)
+#'   search_for_newer_data(archive)
 #' }
 search_for_newer_data = function(archive, ..., 
                                  source=path_home("Downloads"), 

R/utils.R

@@ -91,7 +91,7 @@ deprecatedly = function(f, what, when, with=caller_arg(f), details=NULL, type="w
 #' @source https://github.com/r-lib/cli/issues/228#issuecomment-1453614104
 #' @importFrom rlang caller_env
 cli_menu <- function(prompt, not_interactive, choices, quit = integer(), .envir = caller_env()) {
-  if (!cli:::is_interactive()) {
+  if (!interactive()) {
     cli::cli_abort(c(prompt, not_interactive), .envir = .envir)
   }
   choices <- sapply(choices, cli::format_inline, .envir = .envir, USE.NAMES = FALSE)

R/waterfall_plot.R

@@ -34,7 +34,8 @@
 #' rc %>% 
 #'   left_join(enrolres, by="SUBJID") %>% #adds the ARM column
 #'   mutate(new_lesion = ifelse(RCNEW=="1-Yes", "New lesion", NA)) %>% 
-#'   waterfall_plot(rc_date="RCDT", rc_sum="RCTLSUM", rc_resp="RCRESP", arm="ARM", rc_star="new_lesion")
+#'   waterfall_plot(rc_date="RCDT", rc_sum="RCTLSUM", rc_resp="RCRESP", 
+#'                  arm="ARM", rc_star="new_lesion")
 #'}
 waterfall_plot = function(data_recist, rc_sum="RCTLSUM", rc_resp="RCRESP", rc_date="RCDT",
                           type = c("best_resp", "worst_resp"),