Merge branch 'devel' into 43_codeowners@devel

R/get_terms.R

@@ -0,0 +1,71 @@
+#' An example function as expected by the `get_terms_fun` parameter of
+#' `admiral::create_query_data()`
+#'
+#' @param basket_select A basket_select object defining the terms
+#'
+#' @param version MedDRA version
+#'
+#' @param keep_id Should `GRPID` be included in the output?
+#'
+#' @param temp_env Temporary environment
+get_terms <- function(basket_select,
+                      version,
+                      keep_id,
+                      temp_env) {
+  if (basket_select$type == "smq") {
+    if (is.null(temp_env$smq_db)) {
+      data("smq_db", envir = temp_env)
+    }
+    if (!is.null(basket_select$name)) {
+      is_in_smq <- temp_env$smq_db$smq_name == basket_select$name
+    } else {
+      is_in_smq <- temp_env$smq_db$smq_id == basket_select$id
+    }
+    if (basket_select$scope == "NARROW") {
+      is_in_scope <- temp_env$smq_db$scope == "narrow"
+    } else {
+      is_in_scope <- rep(TRUE, nrow(temp_env$smq_db))
+    }
+    if (keep_id) {
+      select_id <- c(GRPID = "smq_id")
+    } else {
+      select_id <- NULL
+    }
+    keep_cols <- c(
+      TERMNAME = "termname",
+      SRCVAR = "termvar",
+      GRPNAME = "smq_name",
+      select_id
+    )
+
+    structure(
+      temp_env$smq_db[is_in_smq & is_in_scope, keep_cols],
+      names = names(keep_cols)
+    )
+  } else if (basket_select$type == "sdg") {
+    if (is.null(temp_env$sdg_db)) {
+      data("sdg_db", envir = temp_env)
+    }
+    if (!is.null(basket_select$name)) {
+      is_in_sdq <- temp_env$sdg_db$sdg_name == basket_select$name
+    } else {
+      is_in_sdq <- temp_env$sdg_db$sdg_id == basket_select$id
+    }
+    if (keep_id) {
+      select_id <- c(GRPID = "sdg_id")
+    } else {
+      select_id <- NULL
+    }
+    keep_cols <- c(
+      TERMNAME = "termname",
+      SRCVAR = "termvar",
+      GRPNAME = "sdg_name",
+      select_id
+    )
+
+    structure(
+      temp_env$sdg_db[is_in_sdq, keep_cols],
+      names = names(keep_cols)
+    )
+  }
+}

data-raw/ae.R

@@ -1,14 +1,22 @@
-# from CDISC pilot study ----
+# Datasets: ae, suppae
+# Description: Standard AE, SUPPAE datasets from CDISC pilot study
+
+# Load libraries -----
 library(dplyr)
 library(metatools)
 library(haven)
 library(admiral)
 
+# Create ae, suppae ----
 raw_ae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true") # nolint
 raw_suppae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true") # nolint
 ae <- convert_blanks_to_na(raw_ae)
 suppae <- convert_blanks_to_na(raw_suppae)
 
-# Save dataset ----
-save(ae, file = "data/ae.rda", compress = "bzip2")
+# Label dataset ----
+attr(ae, "label") <- "Adverse Events"
+attr(suppae, "label") <- "Supplemental Qualifiers for AE"
+
+# Save datasets ----
+usethis::use_data(ae, overwrite = TRUE)
 usethis::use_data(suppae, overwrite = TRUE)

data-raw/ae_ophtha.R

@@ -1,18 +1,22 @@
-# Update AE by adding AELAT variable for admiralophtha package
+# Dataset: ae_ophtha
+# Description: Add ophtha-specific AELAT variable to existing AE dataset
+
+# Load libraries -----
 library(dplyr)
 library(admiral)
 library(metatools)
 library(haven)
 
+# Create ae_ophtha ----
 # Start from standard AE dataset from this package - this should be
 # in the environment already if devtools::load_all() has been run
 ae_ophtha <- ae
 
-# create possible AELAT values - as collected on CRF ----
+## Create possible AELAT values - as collected on CRF ----
 lat <- c("LEFT", "RIGHT", "BOTH")
 
-# create AELAT variable ----
-# with random assignment of lat values where AESOC is "EYE DISORDERS"
+## Create AELAT variable ----
+# Use random assignment of lat values where AESOC is "EYE DISORDERS"
 # Set seed so that result stays the same for each run
 set.seed(1)
 
@@ -24,7 +28,8 @@ ae_ophtha$AELAT <- if_else(ae_ophtha$AESOC == "EYE DISORDERS",
 ae_ophtha <- ae_ophtha %>%
   add_labels(AELAT = "Laterality")
 
+# Label dataset ----
 attr(ae_ophtha, "label") <- "Adverse Events"
 
 # Save dataset ----
-save(ae_ophtha, file = "data/ae_ophtha.rda", compress = "bzip2")
+usethis::use_data(ae_ophtha, overwrite = TRUE)

data-raw/cm.R

@@ -1,7 +1,16 @@
-# from CDISC pilot study ----
+# Dataset: cm
+# Description: Standard CM dataset from CDISC pilot study
+
+# Load libraries -----
 library(haven)
 library(admiral)
+
+# Create cm ----
 raw_cm <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true") # nolint
 cm <- convert_blanks_to_na(raw_cm)
 
+# Label dataset ----
+attr(cm, "label") <- "Concomitant Medications"
+
+# Save dataset ----
 usethis::use_data(cm, overwrite = TRUE)

data-raw/dm.R

@@ -1,11 +1,21 @@
-# from CDISC pilot study ----
+# Datasets: dm, suppdm
+# Description: Standard DM, SUPPDM datasets from CDISC pilot study
+
+# Load libraries -----
 library(haven)
 library(admiral)
+
+# Create dm, suppdm ----
 sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint
 raw_dm <- read_xpt(paste0(sdtm_path, "dm", ".xpt?raw=true"))
 raw_suppdm <- read_xpt(paste0(sdtm_path, "suppdm", ".xpt?raw=true"))
 dm <- convert_blanks_to_na(raw_dm)
 suppdm <- convert_blanks_to_na(raw_suppdm)
 
+# Label dataset ----
+attr(dm, "label") <- "Demographics"
+attr(suppdm, "label") <- "Supplemental Qualifiers for DM"
+
+# Save datasets ----
 usethis::use_data(dm, overwrite = TRUE)
 usethis::use_data(suppdm, overwrite = TRUE)

data-raw/ds.R

@@ -1,29 +1,34 @@
-# Update DS by adding DSDECOD=RANDOMIZED rows
+# Datasets: ds, suppds
+# Description: Standard DS, SUPPDS datasets from CDISC pilot study with added DSDECOD = RANDOMIZED rows
 
+# Load libraries -----
 library(dplyr)
 library(tidyselect)
 library(labelled)
 library(admiral)
 library(metatools)
 library(haven)
 
+# Create ds ----
 data("dm")
 sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint
 raw_ds <- read_xpt(paste0(sdtm_path, "ds", ".xpt?raw=true"))
 raw_suppds <- read_xpt(paste0(sdtm_path, "suppds", ".xpt?raw=true"))
 
-# Converting blank to NA
+## Converting blank to NA ----
 dm <- convert_blanks_to_na(dm)
 ds1a <- convert_blanks_to_na(raw_ds)
 suppds1a <- convert_blanks_to_na(raw_suppds)
 
-# Creating full DS data
+## Creating full DS data ----
 ds1a <- ds1a %>%
   mutate(DSSEQ = as.character(DSSEQ))
 ds1 <- combine_supp(ds1a, suppds1a) %>%
   mutate(DSSEQ = as.numeric(DSSEQ))
 
-# Creating RANDOMIZED records
+dsnames <- names(ds1a)
+
+## Creating RANDOMIZED records ----
 dm1 <- select(dm, c(STUDYID, USUBJID, RFSTDTC)) %>%
   filter(!is.na(RFSTDTC)) %>%
   mutate(
@@ -41,7 +46,7 @@ dm1 <- select(dm, c(STUDYID, USUBJID, RFSTDTC)) %>%
 
 ds2 <- bind_rows(ds1, select(dm1, -c(RFSTDTC)))
 
-# Adding labels
+## Adding labels ----
 dslab <- var_label(ds1a)
 var_label(ds2) <- dslab
 
@@ -56,7 +61,15 @@ ds3 <- ds2 %>%
   ) %>%
   ungroup()
 
-# Creating SUPPDS
+ds4 <- ds3 %>%
+  select(all_of(dsnames))
+
+## Label dataset ----
+attr(ds4, "label") <- "Disposition"
+
+ds <- ds4
+
+# Creating SUPPDS ----
 suppds1 <- select(ds3, c("STUDYID", "USUBJID", "DSSEQ", "DOMAIN", "ENTCRIT")) %>%
   filter(!is.na(ENTCRIT))
 
@@ -68,38 +81,28 @@ suppds2 <- rename(suppds1, "RDOMAIN" = "DOMAIN") %>%
     "QNAM" = "ENTCRIT",
     "QLABEL" = "PROTOCOL ENTRY CRITERIA NOT MET",
     "QORIG" = "CRF"
-  )
+  ) %>%
+  select(STUDYID, RDOMAIN, USUBJID, IDVAR, IDVARVAL, QNAM, QLABEL, QVAL, QORIG)
 
-suppds <- select(
-  suppds2,
-  c(
-    STUDYID, RDOMAIN, USUBJID,
-    IDVAR, IDVARVAL, QNAM, QLABEL,
-    QVAL, QORIG
+## Adding labels ----
+suppds3 <- suppds2 %>%
+  add_labels(
+    STUDYID = "Study Identifier",
+    RDOMAIN = "Related Domain Abbreviation",
+    USUBJID = "Unique Subject Identifier",
+    IDVAR = "Identifying Variable",
+    IDVARVAL = "Identifying Variable Value",
+    QNAM = "Qualifier Variable Name",
+    QLABEL = "Qualifier Variable Label",
+    QVAL = "Data Value",
+    QORIG = "Origin"
   )
-)
-
-admiral_suppds <- suppds %>% add_labels(
-  STUDYID = "Study Identifier",
-  RDOMAIN = "Related Domain Abbreviation",
-  USUBJID = "Unique Subject Identifier",
-  IDVAR = "Identifying Variable",
-  IDVARVAL = "Identifying Variable Value",
-  QNAM = "Qualifier Variable Name",
-  QLABEL = "Qualifier Variable Label",
-  QVAL = "Data Value",
-  QORIG = "Origin"
-)
-
-attr(admiral_suppds, "label") <- "Supplemental Disposition"
-
-# Creating DS
-dsnames <- names(ds1a)
-admiral_ds <- select(ds3, all_of(dsnames))
 
-attr(admiral_ds, "label") <- "Disposition"
+## Label dataset ----
+attr(suppds3, "label") <- "Supplemental Qualifiers for DS"
+
+suppds <- suppds3
 
-ds <- admiral_ds
-suppds <- admiral_suppds
-save(ds, file = "data/ds.rda", compress = "bzip2")
-save(suppds, file = "data/suppds.rda", compress = "bzip2")
+# Save datasets ----
+usethis::use_data(ds, overwrite = TRUE)
+usethis::use_data(suppds, overwrite = TRUE)

data-raw/ex.R

@@ -1,7 +1,16 @@
-# from CDISC pilot study ----
+# Dataset: ex
+# Description: Standard EX dataset from CDISC pilot study
+
+# Load libraries -----
 library(haven)
 library(admiral)
+
+# Create ex ----
 raw_ex <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true") # nolint
 ex <- convert_blanks_to_na(raw_ex)
 
+# Label dataset ----
+attr(ex, "label") <- "Exposure"
+
+# Save dataset ----
 usethis::use_data(ex, overwrite = TRUE)

data-raw/ex_ophtha.R

@@ -1,14 +1,20 @@
+# Dataset: ex_ophtha
+# Description: Add ophtha-specific EXLOC, EXLAT variables to existing EX dataset
+# and modify EXROUTE, EXDOSFRM, EXDOSFRQ to something eye-related
+
+# Load libraries -----
 library(dplyr)
 library(tidyselect)
+
+# Make ex_ophtha dataset
 data("dm")
 data("ex")
 
-# Make ex_ophtha dataset
 ex_ophtha <- dm %>%
-  # Start by merging on ophtha_dm to use the SUBJID variable
+  ## Merge on ophtha_dm to use the SUBJID variable ----
   select(USUBJID, SUBJID) %>%
   right_join(ex, by = c("USUBJID"), multiple = "all") %>%
-  # Create EXLOC & EXLAT, change EXROUTE & EXDOSFRM to something eye-related
+  ## Create EXLOC & EXLAT, change EXROUTE & EXDOSFRM ----
   mutate(
     EXLOC = "EYE",
     EXDOSFRM = "INJECTION",
@@ -24,12 +30,15 @@ ex_ophtha <- dm %>%
     "EXENDTC", "EXSTDY", "EXENDY"
   )
 
-# Label new variables
+## Label new variables ----
 attr(ex_ophtha$EXLOC, "label") <- "Location of Dose Administration"
 attr(ex_ophtha$EXLAT, "label") <- "Laterality"
 attr(ex_ophtha$EXROUTE, "label") <- "Route of Administration"
 attr(ex_ophtha$EXDOSFRM, "label") <- "Dose Form"
 attr(ex_ophtha$EXDOSFRQ, "label") <- "Dose Frequency per Interval"
 
-# Save Dataset
-save(ex_ophtha, file = file.path("data", "ex_ophtha.rda"), compress = "bzip2")
+# Label dataset ----
+attr(ex_ophtha, "label") <- "Exposure"
+
+# Save dataset ----
+usethis::use_data(ex_ophtha, overwrite = TRUE)