Closes #5 split ae into ae_ophtha and ae. (#40)

* #5 split ae into `ae_ophtha` and `ae`.

* #5 chore: spelling and code style

R/data.R

@@ -5,6 +5,13 @@
 #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ae.rda}
 "ae"
 
+#' Ophthalmology Adverse Events Dataset
+#'
+#' An example Adverse Events SDTM dataset with ophthalmology-specific variable `AELAT`
+#'
+#' @source Constructed using `ae` from the `{pharmaversesdtm}` package # nolint
+"ae_ophtha"
+
 #' Concomitant Medication Dataset
 #'
 #' A SDTM CM dataset from the CDISC pilot project

data-raw/ae.R

@@ -1,32 +1,14 @@
-# Update AE by adding AELAT variable for admiraloptha package
-
+# from CDISC pilot study ----
 library(dplyr)
-library(admiral)
 library(metatools)
 library(haven)
+library(admiral)
 
 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)
 
-# 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"
-# Set seed so that result stays the same for each run
-set.seed(1)
-ae$AELAT <- if_else(ae$AESOC == "EYE DISORDERS",
-  apply(ae, 1, function(x) sample(lat, 1)),
-  NA_character_
-)
-admiral_ae <- ae %>%
-  add_labels(AELAT = "Laterality")
-
-attr(admiral_ae, "label") <- "Adverse Events"
-
 # Save dataset ----
-ae <- admiral_ae
 save(ae, file = "data/ae.rda", compress = "bzip2")
 usethis::use_data(suppae, overwrite = TRUE)

data-raw/ae_ophtha.R

@@ -0,0 +1,30 @@
+# Update AE by adding AELAT variable for admiralophtha package
+library(dplyr)
+library(admiral)
+library(metatools)
+library(haven)
+
+# 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 ----
+lat <- c("LEFT", "RIGHT", "BOTH")
+
+# create AELAT variable ----
+# with random assignment of lat values where AESOC is "EYE DISORDERS"
+# Set seed so that result stays the same for each run
+set.seed(1)
+
+ae_ophtha$AELAT <- if_else(ae_ophtha$AESOC == "EYE DISORDERS",
+  apply(ae_ophtha, 1, function(x) sample(lat, 1)),
+  NA_character_
+)
+
+ae_ophtha <- ae_ophtha %>%
+  add_labels(AELAT = "Laterality")
+
+attr(ae_ophtha, "label") <- "Adverse Events"
+
+# Save dataset ----
+save(ae_ophtha, file = "data/ae_ophtha.rda", compress = "bzip2")

inst/WORDLIST

@@ -1,6 +1,7 @@
 ADEG
 ADaM
 AE
+AELAT
 Arancibia
 CDISC
 Changelog
@@ -34,6 +35,7 @@ SV
 TAs
 USUBJIDs
 VFQ
+ae
 admiraldata
 admiraltemplate
 admiralxxx