Implement subsetting on peak values

Author: luffmark

DESCRIPTION

@@ -1,39 +1,42 @@
 Package: dv.edish
-Type: Package
 Title: eDISH Plot Module for DILI assessment
-Version: 1.3.0
-Authors@R: 
-    c(
-      person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
-      person("Isabel", "Glauss", email = "isabel.glauss@boehringer-ingelheim.com", role = c("aut", "cre")),
-      person("Mark", "Luff", email = "mark.luff.ext@boehringer-ingelheim.com", role = "aut")
-    )
-Description: This DaVinci package contains a module which is meant to support the assessment of drug-induced liver 
-    injury by means of the (modified) evaluation of Drug-Induced Serious Hepatotoxicity plot.
+Version: 1.3.0-9000
+Authors@R: c(
+    person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
+    person("Isabel", "Glauss", , "isabel.glauss@boehringer-ingelheim.com", role = c("aut", "cre")),
+    person("Mark", "Luff", , "mark.luff.ext@boehringer-ingelheim.com", role = "aut")
+  )
+Description: This DaVinci package contains a module which is meant to
+    support the assessment of drug-induced liver injury by means of the
+    (modified) evaluation of Drug-Induced Serious Hepatotoxicity plot.
 License: Apache License (>= 2)
+Depends: 
+    R (>= 4.0)
+Imports:
+    checkmate (>= 2.1.0),
+    dplyr (>= 1.0.5),
+    dv.manager (>= 2.1.4),
+    ggplot2,
+    magrittr (>= 2.0.3),
+    plotly (>= 4.10.1),
+    rlang (>= 1.1.2),
+    shiny (>= 1.8.0),
+    shinyWidgets,
+    stats (>= 4.2.2),
+    tidyr (>= 1.3.0)
+Suggests: 
+    knitr (>= 1.43),
+    pharmaverseadam (>= 0.2.0),
+    rmarkdown (>= 2.25),
+    shinytest2 (>= 0.2.0),
+    testthat (>= 3.0.2),
+    tibble (>= 3.2.1)
+VignetteBuilder: 
+    knitr
+Remotes: 
+    boehringer-ingelheim/dv.manager@main
+Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.0
-Suggests: 
-  knitr (>= 1.43),
-  pharmaverseadam (>= 0.2.0),
-  rmarkdown (>= 2.25),
-  shinytest2 (>= 0.2.0),
-  testthat (>= 3.0.2),
-  tibble (>= 3.2.1)
-Config/testthat/edition: 3
-Imports:
-  checkmate (>= 2.1.0),
-  dplyr (>= 1.0.5),
-  magrittr (>= 2.0.3),
-  plotly (>= 4.10.1),
-  rlang (>= 1.1.2),
-  shiny (>= 1.8.0),
-  stats (>= 4.2.2),
-  tidyr (>= 1.3.0),
-  dv.manager (>= 2.1.4),
-  shinyWidgets
-Depends: R (>= 4.0)
-Remotes: boehringer-ingelheim/dv.manager@main
-VignetteBuilder: knitr

R/check_call_auto.R

@@ -4,9 +4,9 @@
 
 # dv.edish::mod_edish
 check_mod_edish_auto <- function(afmm, datasets, module_id, subject_level_dataset_name, lab_dataset_name,
-    subjectid_var, arm_var, arm_default_vals, visit_var, baseline_visit_val, lb_test_var, lb_test_choices,
-    lb_test_default_x_val, lb_test_default_y_val, lb_result_var, ref_range_upper_lim_var, receiver_id,
-    warn, err) {
+    subjectid_var, arm_var, arm_default_vals, visit_var, baseline_visit_val, lb_test_var, at_choices,
+    tbili_choice, alp_choice, lb_date_var, lb_result_var, ref_range_upper_lim_var, receiver_id, warn,
+    err) {
     OK <- logical(0)
     used_dataset_names <- new.env(parent = emptyenv())
     OK[["module_id"]] <- CM$check_module_id("module_id", module_id, warn, err)
@@ -40,19 +40,20 @@ check_mod_edish_auto <- function(afmm, datasets, module_id, subject_level_datase
     flags <- structure(list(), names = character(0))
     OK[["lb_test_var"]] <- OK[["lab_dataset_name"]] && CM$check_dataset_colum_name("lb_test_var", lb_test_var,
         subkind, flags, lab_dataset_name, datasets[[lab_dataset_name]], warn, err)
-    flags <- list(one_or_more = TRUE, optional = TRUE)
-    OK[["lb_test_choices"]] <- OK[["lb_test_var"]] && CM$check_choice_from_col_contents("lb_test_choices",
-        lb_test_choices, flags, "lab_dataset_name", datasets[[lab_dataset_name]], lb_test_var, warn,
-        err)
-    flags <- list(optional = TRUE)
-    OK[["lb_test_default_x_val"]] <- OK[["lb_test_var"]] && CM$check_choice_from_col_contents("lb_test_default_x_val",
-        lb_test_default_x_val, flags, "lab_dataset_name", datasets[[lab_dataset_name]], lb_test_var,
-        warn, err)
+    flags <- list(one_or_more = TRUE)
+    OK[["at_choices"]] <- OK[["lb_test_var"]] && CM$check_choice_from_col_contents("at_choices", at_choices,
+        flags, "lab_dataset_name", datasets[[lab_dataset_name]], lb_test_var, warn, err)
+    flags <- structure(list(), names = character(0))
+    OK[["tbili_choice"]] <- OK[["lb_test_var"]] && CM$check_choice_from_col_contents("tbili_choice",
+        tbili_choice, flags, "lab_dataset_name", datasets[[lab_dataset_name]], lb_test_var, warn, err)
     flags <- list(optional = TRUE)
-    OK[["lb_test_default_y_val"]] <- OK[["lb_test_var"]] && CM$check_choice_from_col_contents("lb_test_default_y_val",
-        lb_test_default_y_val, flags, "lab_dataset_name", datasets[[lab_dataset_name]], lb_test_var,
-        warn, err)
-    subkind <- list(kind = "or", options = list(list(kind = "numeric", min = NA, max = NA)))
+    OK[["alp_choice"]] <- OK[["lb_test_var"]] && CM$check_choice_from_col_contents("alp_choice", alp_choice,
+        flags, "lab_dataset_name", datasets[[lab_dataset_name]], lb_test_var, warn, err)
+    subkind <- list(kind = "or", options = list(list(kind = "date"), list(kind = "datetime")))
+    flags <- structure(list(), names = character(0))
+    OK[["lb_date_var"]] <- OK[["lab_dataset_name"]] && CM$check_dataset_colum_name("lb_date_var", lb_date_var,
+        subkind, flags, lab_dataset_name, datasets[[lab_dataset_name]], warn, err)
+    subkind <- list(kind = "numeric", min = NA, max = NA)
     flags <- structure(list(), names = character(0))
     OK[["lb_result_var"]] <- OK[["lab_dataset_name"]] && CM$check_dataset_colum_name("lb_result_var",
         lb_result_var, subkind, flags, lab_dataset_name, datasets[[lab_dataset_name]], warn, err)