Add sdtm_terminology dataset and update doc for valid_versions

R/data.R

@@ -2,11 +2,34 @@
 #' combination
 #' 
 #' @format
-#' \itemize{
+#' \describe{
 #'   \item{SDTM}{The SDTM version}
 #'   \item{IG_NAME}{The implementation guide (IG) name being used}
 #'   \item{IG_VERSION}{The implemetation guide (IG) version}
 #'   \item{archived}{The SDTM version/IG pair has been archived (and should not
 #'     be used for current studies)}
 #' }
 "valid_versions"
+
+#' The current SDTM terminology
+#' 
+#' SDTM terminology is used for reserved words and lists of codes that can be
+#' used for values in the SDTM standard.  The version date from the download is
+#' available via \code{attr(sdtm_terminology, "version")}.
+#' 
+#' The description of the columns draw from
+#' \url{https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM CDISC ReadMe.doc}, and
+#' the column names are modified slightly to work better in R.
+#' 
+#' @format
+#' \describe{
+#'   \item{code}{Unique numeric code randomly generated by NCI Thesaurus (NCIt) and assigned to individual CDISC controlled terms.}
+#'   \item{codelist_code}{Unique numeric code randomly generated by NCI Thesaurus (NCIt) and assigned to the SDTM parent codelist names. This code is repeated for each controlled term (aka permissible value) belonging to a codelist. **NOTE - light blue highlighting is used to identify the beginning of a new SDTM codelist and its applicable term set.}
+#'   \item{codelist_extensible_yes_no}{Defines if controlled terms may be added to the codelist. New terms may be added to existing codelist values when the codelist has "Yes" in Column C as long as the terms are not duplicates or synonyms of existing terms. The expectation is that sponsors will use the published controlled terminology as a standard baseline and codelists defined as "extensible" (or "Yes") may have terms added by the sponsor internally.  For codelists with "No" in Column C sponsor organizations may not add to the published lists. Suggestions for new terms may be requested through the New Term Request Page.}
+#'   \item{codelist_name}{Contains the descriptive name of the codelist. As with the Codelist Code, the Codelist Name is repeated for each controlled term belonging to a codelist.}
+#'   \item{CDISC_submission_value}{IMPORTANT COLUMN: Currently this is the specific value expected for submissions. Each value corresponds to a SDTM Codelist Name as indicated by light blue shading.}
+#'   \item{CDISC_synonym}{This identifies the applicable synonyms for the CDISC Submission Value in Column E. These terms should not be submitted, but are included for collection and mapping purposes.**NOTE - this is especially important in instances where a Test name or Parameter Test name contains a corresponding Test Code or Parameter Test Code.}
+#'   \item{CDISC_definition}{This identifies the CDISC definition for a particular term. In many cases an existing NCI definition has been used. The source for a definition is noted in parentheses (e.g. NCI, CDISC glossary).}
+#'   \item{NCI_preferred_term}{This identifies the NCI preferred name for a term as identified in NCIt. **NOTE - This column designates the human readable, fully specified preferred term corresponding to the NCI c-code, and is especially helpful for searching NCIt to get the entire concept with links to all instances of the term.}
+#' }
+"sdtm_terminology"

data-raw/sdtm_terminology.R

@@ -0,0 +1,37 @@
+# Load and save the SDTM terminology data set
+
+library(tidyverse)
+library(janitor)
+library(assertr)
+
+url <- "https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM%20Terminology.xls"
+local_file <- file.path(tempdir(), basename(url))
+download_result <- curl::curl_download(url=url, destfile=local_file, quiet=FALSE)
+
+d_raw <- rio::import_list(local_file)
+names(d_raw)
+sheet_to_use <- names(d_raw)[startsWith(names(d_raw), "SDTM Terminology")]
+if (length(sheet_to_use) != 1) {
+  stop("Could not find correct sheet name")
+} else {
+  sdtm_terminology <-
+    d_raw[[sheet_to_use]] %>%
+    clean_names() %>%
+    verify(is.na(codelist_code) | is.na(codelist_extensible_yes_no)) %>%
+    verify(is.na(codelist_code) | (codelist_code != code)) %>%
+    verify(
+      !is.na(codelist_code) |
+        (is.na(codelist_code) & codelist_name == cdisc_synonym_s)
+    ) %>%
+    #select(-codelist_name) %>%
+    rename_with(
+      .fn=gsub,
+      pattern="^(CDISC|NCI)",
+      replacement="\\U\\1",
+      ignore.case=TRUE,
+      perl=TRUE
+    ) %>%
+    rename(CDISC_synonym=CDISC_synonym_s)
+  attr(sdtm_terminology, "version") <- sheet_to_use
+  usethis::use_data(sdtm_terminology, compress="xz", overwrite=TRUE, version=3)
+}