Closes #40 use pharmaversesdtm to host dm_peds and vs_peds (#84)

* need staged dependencies to check everything still works

* demo pharmaversesdtm works, if properly installed

* check if this works

* needs to be in import

* can it be suggests?

* remove pharmaversesdtm:: reference

* can't be removed yet

* does this work?

* typo

* use :: convention

* only use :: formatting

* missed a spot

* missed one

* slight inconsistencies are fixed

* add news entry

* Update NEWS.md

Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com>

* fix error

---------

Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com>

DESCRIPTION

@@ -48,11 +48,12 @@ Imports:
 Suggests:
     knitr,
     lubridate (>= 1.7.4),
-    pharmaversesdtm (>= 0.2.0),
+    pharmaversesdtm,
     rmarkdown,
     stringr (>= 1.4.0),
     testthat (>= 3.0.0),
     tibble
+Remotes: pharmaverse/pharmaversesdtm@admiralpeds_data_migration
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3

NEWS.md

@@ -9,6 +9,7 @@
 ## Documentation
 
 - Added CRAN installation instructions to README (#10).
+- Subject based test data (e.g. DM, VS) has been migrated out of `{admiralpeds}` to `{pharmaversesdtm}` (#40)
 
 ## Various
 

R/data.R

@@ -193,20 +193,6 @@
 #' @source \url{https://www.cdc.gov/growthcharts/percentile_data_files.htm}
 "cdc_bmiage"
 
-#' Demographic Dataset-pediatrics
-#'
-#' An updated SDTM DM dataset with pediatric patients
-#' @keywords datasets
-#' @family datasets
-"dm_peds"
-
-#' Vital signs Dataset-pediatrics
-#'
-#' An updated SDTM VS dataset with anthropometric measurements for pediatric patients
-#' @keywords datasets
-#' @family datasets
-"vs_peds"
-
 #' Subject Level Analysis Dataset-pediatrics
 #'
 #' An updated ADaM ADSL dataset with pediatric patients

R/derive_params_growth_age.R

@@ -116,10 +116,11 @@
 #' library(lubridate, warn.conflicts = FALSE)
 #' library(rlang, warn.conflicts = FALSE)
 #' library(admiral, warn.conflicts = FALSE)
+#' library(pharmaversesdtm, warn.conflicts = FALSE)
 #'
-#' advs <- dm_peds %>%
+#' advs <- pharmaversesdtm::dm_peds %>%
 #'   select(USUBJID, BRTHDTC, SEX) %>%
-#'   right_join(., vs_peds, by = "USUBJID") %>%
+#'   right_join(., pharmaversesdtm::vs_peds, by = "USUBJID") %>%
 #'   mutate(
 #'     VSDT = ymd(VSDTC),
 #'     BRTHDT = ymd(BRTHDTC)

R/derive_params_growth_height.R

@@ -114,12 +114,13 @@
 #' library(lubridate, warn.conflicts = FALSE)
 #' library(rlang, warn.conflicts = FALSE)
 #' library(admiral, warn.conflicts = FALSE)
+#' library(pharmaversesdtm, warn.conflicts = FALSE)
 #'
 #' # derive weight for height/length only for those under 2 years old using WHO
 #' # weight for length reference file
-#' advs <- dm_peds %>%
+#' advs <- pharmaversesdtm::dm_peds %>%
 #'   select(USUBJID, BRTHDTC, SEX) %>%
-#'   right_join(., vs_peds, by = "USUBJID") %>%
+#'   right_join(., pharmaversesdtm::vs_peds, by = "USUBJID") %>%
 #'   mutate(
 #'     VSDT = ymd(VSDTC),
 #'     BRTHDT = ymd(BRTHDTC)
@@ -132,7 +133,7 @@
 #'     out_unit = "days"
 #'   )
 #'
-#' heights <- vs_peds %>%
+#' heights <- pharmaversesdtm::vs_peds %>%
 #'   filter(VSTESTCD == "HEIGHT") %>%
 #'   select(USUBJID, VSSTRESN, VSSTRESU, VSDTC) %>%
 #'   rename(

data-raw/adsl_peds.R

@@ -11,8 +11,8 @@ library(stringr)
 # Create a basic ADSL for pediatrics ----
 
 # Read in input data ----
-data("dm_peds")
-data("ex")
+dm_peds <- pharmaversesdtm::dm_peds
+ex <- pharmaversesdtm::ex
 
 # Derivations ----