rerun ADaM templates

DESCRIPTION

@@ -22,7 +22,7 @@ Language: en-US
 LazyData: true
 LazyDataCompression: bzip2
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: R (>= 3.5)
 Imports:
 Suggests:

NEWS.md

@@ -2,7 +2,8 @@
 
 ## New Features
 
- - Variables labels are applied to datasets by `metacore`/`metatools`.
+ - Variables labels are applied to datasets by `metacore`/`metatools`. (#50)
+ - ADPC, ADPPK and ADPP are updated to handle urine records. (#57)
 
 # pharmaverseadam 0.1.1
 

R/adpc.R

@@ -4,7 +4,7 @@
 #'
 #' @name adpc
 #' @docType data
-#' @format A data frame with 122 columns:
+#' @format A data frame with 123 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ USUBJID }{Unique Subject Identifier}
@@ -51,6 +51,7 @@
 #'     \item{ PCRFTDT }{Reference Date of Dose for Analyte}
 #'     \item{ PCRFTTM }{Reference Time of Dose for Analyte}
 #'     \item{ NRRLT }{Nominal Rel. Time from Ref. Dose}
+#'     \item{ PARCAT1 }{undocumented field}
 #'     \item{ ATPTN }{Analysis Timepoint (N)}
 #'     \item{ ATPT }{Analysis Timepoint}
 #'     \item{ ATPTREF }{Analysis Timepoint Reference}

R/adpp.R

@@ -4,7 +4,7 @@
 #'
 #' @name adpp
 #' @docType data
-#' @format A data frame with 74 columns:
+#' @format A data frame with 76 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ USUBJID }{Unique Subject Identifier}
@@ -25,15 +25,17 @@
 #'     \item{ ADT }{Analysis Date}
 #'     \item{ ADY }{Analysis Relative Day}
 #'     \item{ PARAMCD }{Parameter Code}
+#'     \item{ PARCAT1 }{Parameter Category}
 #'     \item{ AVAL }{Numeric Result/Finding in Standard Units}
 #'     \item{ AVALC }{Character Result/Finding in Std Format}
+#'     \item{ AVALU }{Standard Units}
 #'     \item{ SRCDOM }{Domain Abbreviation}
 #'     \item{ SRCVAR }{Source Variable}
 #'     \item{ SRCSEQ }{Sequence Number}
-#'     \item{ VISIT }{Visit Name}
-#'     \item{ VISITNUM }{Visit Number}
-#'     \item{ AVISIT }{Analysis Visit}
 #'     \item{ AVISITN }{Analysis Visit (N)}
+#'     \item{ AVISIT }{Analysis Visit}
+#'     \item{ VISITNUM }{Visit Number}
+#'     \item{ VISIT }{Visit Name}
 #'     \item{ TRTP }{Planned Treatment}
 #'     \item{ TRTA }{Actual Treatment}
 #'     \item{ AVALCA1N }{Analysis Value Category 1 (N)}

R/adppk.R

@@ -4,7 +4,7 @@
 #'
 #' @name adppk
 #' @docType data
-#' @format A data frame with 59 columns:
+#' @format A data frame with 62 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ USUBJID }{Unique Subject Identifier}
@@ -15,6 +15,7 @@
 #'     \item{ NPRLT }{Nominal Rel Time from Previous Dose}
 #'     \item{ DOSEA }{Actual Treatment Dose}
 #'     \item{ DOSEP }{Planned Treatment Dose}
+#'     \item{ PARAMCD }{undocumented field}
 #'     \item{ ALLOQ }{Analysis Lower Limit of Quantitation}
 #'     \item{ CMT }{Compartment}
 #'     \item{ BLQFL }{Below Lower Limit of Quant Flag}
@@ -29,6 +30,8 @@
 #'     \item{ II }{Dosing Interval (unit)}
 #'     \item{ SS }{Steady State}
 #'     \item{ ASEQ }{Analysis Sequence Number}
+#'     \item{ PARAM }{undocumented field}
+#'     \item{ PARAMN }{undocumented field}
 #'     \item{ PROJID }{Project Identifier}
 #'     \item{ PROJIDN }{Project Identifier (N)}
 #'     \item{ STUDYIDN }{Study Identifier (N)}

R/adtte_onco.R

@@ -8,12 +8,12 @@
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ USUBJID }{Unique Subject Identifier}
+#'     \item{ ADT }{Analysis Date}
 #'     \item{ EVNTDESC }{Event or Censoring Description}
 #'     \item{ SRCDOM }{Source Data}
 #'     \item{ SRCVAR }{Source Variable}
 #'     \item{ SRCSEQ }{Source Sequence Number}
 #'     \item{ CNSR }{Censor}
-#'     \item{ ADT }{Analysis Date}
 #'     \item{ CNSDTDSC }{Censor Date Description}
 #'     \item{ STARTDT }{Time-to-Event Origin Date for Subject}
 #'     \item{ PARAMCD }{Parameter Code}

data-raw/create_adams_data.R

@@ -1,6 +1,6 @@
 # ensure every packages are installed
 
-update_pkg <- FALSE
+update_pkg <- TRUE
 ignore_templates <- list(
   "admiralonco" = c("ad_adrs_basic.R")
 )
@@ -123,17 +123,8 @@ run_template <- function(tp) {
 
 if (update_pkg) {
   github_pat <- Sys.getenv("GITHUB_TOKEN") # in case of run through github workflows
-  if (github_pat == "") {
-    token_file <- "data-raw/github_token.R"
-    if (file.exists(token_file)) {
-      source(token_file)
-    } else {
-      "WARNING - you might have issues installing pharmaverse deps -
-            Please follow instructions in the readme.md"
-    }
-  }
   # install pharmaversesdtm dep: TODO: see if we install from github or latest release?
-  install.packages("pharmaverse/pharmaversesdtm")
+  remotes::install_github("pharmaverse/pharmaversesdtm", ref = "main", force = TRUE)
 }
 
 # dict to match admiral xlsx specs suffixes
@@ -152,7 +143,11 @@ for (pkg in packages_list) {
   if (update_pkg) {
     # TODO: replace by main once done
     remotes::install_github(sprintf("pharmaverse/%s", pkg),
-      ref = "workflow_dispatch_templates", auth_token = github_pat,
+      ref = "main", auth_token = if (github_pat == "") {
+        NULL
+      } else {
+        github_pat
+      },
       upgrade = "always", force = TRUE
     )
   }