Closes #2040 Update admiral.test to pharmaversesdtm (#2057)

* Chore: #2040 Update admiral.test to pharmaversesdtm * Chore: #2040 Update admiraltest to pharmaversesdtm: Update WORDLIST and run styler * #2040 Update admiral.test to pharmaversesdtm: udpate staged_dependencies.yaml * Chore: #2040 Update admiral.test to pharmaversesdtm: rename suppae and admiral_eg. * Chore #2040 Update admiral.test to pharmaversesdtm: Update test-call_derivation.R * Chore: #2040 Update admiral.test to pharmaversesdtm: Update create_query_data.R * Chore: #2040 Update admiral.test to pharmaversesdtm run documentation for create_query_data --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]>
pharmaverse · Aug 22, 2023 · fb92c46 · fb92c46
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -55,7 +55,7 @@ Imports:
     tidyr (>= 1.0.2),
     tidyselect (>= 1.1.0)
 Suggests:
-    admiral.test (>= 0.6.0),
+    pharmaversesdtm,
     DT,
     diffdf,
     knitr,

diff --git a/NEWS.md b/NEWS.md
@@ -18,6 +18,8 @@
 
 - The function `derive_vars_dy()` is updated to avoid potential error when the input `dataset` with columns ending with `temp`. (#2012)
 
+- Templates, vignettes, and other uses of `{admiral.test}` SDTM data are updated to use `{pharmaversesdtm}` instead. (#2040)
+
 
 ## Breaking Changes
 - The following functions, which were deprecated in previous `{admiral}` versions, have been removed: (#1950)

diff --git a/R/create_query_data.R b/R/create_query_data.R
@@ -106,7 +106,7 @@
 #' @examples
 #' library(tibble)
 #' library(dplyr, warn.conflicts = FALSE)
-#' library(admiral.test)
+#' library(pharmaversesdtm)
 #' library(admiral)
 #'
 #' # creating a query dataset for a customized query
@@ -145,11 +145,11 @@
 #'   )
 #' )
 #'
-#' # The get_terms function from admiral.test is used for this example.
+#' # The get_terms function from pharmaversesdtm is used for this example.
 #' # In a real application a company-specific function must be used.
 #' create_query_data(
 #'   queries = list(pregsmq, bilismq),
-#'   get_terms_fun = admiral.test:::get_terms,
+#'   get_terms_fun = pharmaversesdtm:::get_terms,
 #'   version = "20.1"
 #' )
 #'
@@ -164,16 +164,16 @@
 #'   )
 #' )
 #'
-#' # The get_terms function from admiral.test is used for this example.
+#' # The get_terms function from pharmaversesdtm is used for this example.
 #' # In a real application a company-specific function must be used.
 #' create_query_data(
 #'   queries = list(sdg),
-#'   get_terms_fun = admiral.test:::get_terms,
+#'   get_terms_fun = pharmaversesdtm:::get_terms,
 #'   version = "2019-09"
 #' )
 #'
 #' # creating a query dataset for a customized query including SMQs
-#' # The get_terms function from admiral.test is used for this example.
+#' # The get_terms function from pharmaversesdtm is used for this example.
 #' # In a real application a company-specific function must be used.
 #' create_query_data(
 #'   queries = list(
@@ -190,7 +190,7 @@
 #'       )
 #'     )
 #'   ),
-#'   get_terms_fun = admiral.test:::get_terms,
+#'   get_terms_fun = pharmaversesdtm:::get_terms,
 #'   version = "20.1"
 #' )
 create_query_data <- function(queries,

diff --git a/README.md b/README.md
@@ -26,7 +26,7 @@ if (!requireNamespace("remotes", quietly = TRUE)) {
   install.packages("remotes")
 }
 
-remotes::install_github("pharmaverse/admiral.test") # This is a required dependency of {admiral}
+remotes::install_github("pharmaverse/pharmaversesdtm") # This is a required dependency of {admiral}
 remotes::install_github("pharmaverse/admiraldev") # This is a required dependency of {admiral}
 remotes::install_github("pharmaverse/admiral")
 ```
@@ -37,19 +37,19 @@ remotes::install_github("pharmaverse/admiral")
 The {admiral} family has several downstream and upstream dependencies and so this release shall be done in three
 Phases:
 
-* Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/), {admiral.test}, and [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) core 
+* Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/), {pharmaversesdtm}, and [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) core 
 * Phase 2 release is extension packages, e.g. [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/), [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/), [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/main/)
 
 
 |Release Schedule | Phase 1- Date and Packages                                        | Phase 2- Date and Packages                                                    |
 |---------------- | --------------------------                                        | --------------------------                                                    |   
 | Q3-2023         | September 4th                                                     | September 11th                                                                | 
 |                 | [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/)    | [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/)              | 
-|                 | {admiral.test}                                                    | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/)          | 
+|                 | {pharmaversesdtm}                                                    | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/)          | 
 |                 | [{admiral}](https://pharmaverse.github.io/admiral/main/)          | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/main/)        | 
 | Q4-2023         | December 4th                                                      | December 11th                                                                 | 
 |                 | [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/)    | [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/)              |
-|                 | {admiral.test}                                                    | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/)          |  
+|                 | {pharmaversesdtm}                                                    | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/)          |  
 |                 | [{admiral}](https://pharmaverse.github.io/admiral/main/)          | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/main/)        | 
 
 ## Main Goal

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -301,6 +301,7 @@ occds
 onwards
 parttime
 pharmaverse
+pharmaversesdtm
 phosphatase
 poppk
 pre

diff --git a/inst/example_scripts/derive_single_dose.R b/inst/example_scripts/derive_single_dose.R
@@ -1,9 +1,7 @@
-
-library(admiral.test)
+library(pharmaversesdtm)
 library(admiral)
 library(dplyr)
-data(admiral_ex)
-ex <- admiral_ex
+data(ex)
 
 # check that there is only one start/end date of exposure per subject and visit
 check_cond <- ex %>%

diff --git a/inst/templates/ad_adae.R b/inst/templates/ad_adae.R
@@ -4,7 +4,7 @@
 #
 # Input: ae, adsl, ex_single
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 
@@ -14,13 +14,12 @@ library(lubridate)
 # as needed and assign to the variables below.
 # For illustration purposes read in admiral test data
 
-data("admiral_ae")
+data("ae")
 data("admiral_adsl")
 data("ex_single")
+data("suppae")
 
 adsl <- admiral_adsl
-ae <- admiral_ae
-suppae <- admiral_suppae
 
 # When SAS datasets are imported into R using haven::read_sas(), missing
 # character values from SAS appear as "" characters in R, instead of appearing

diff --git a/inst/templates/ad_adcm.R b/inst/templates/ad_adcm.R
@@ -4,7 +4,7 @@
 #
 # Input: cm, adsl
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 
@@ -14,11 +14,10 @@ library(lubridate)
 # as needed and assign to the variables below.
 # For illustration purposes read in admiral test data
 
-data("admiral_cm")
+data("cm")
 data("admiral_adsl")
 
 adsl <- admiral_adsl
-cm <- admiral_cm
 
 # When SAS datasets are imported into R using haven::read_sas(), missing
 # character values from SAS appear as "" characters in R, instead of appearing

diff --git a/inst/templates/ad_adeg.R b/inst/templates/ad_adeg.R
@@ -6,7 +6,7 @@
 #
 # Input: adsl, eg
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 library(stringr)

diff --git a/inst/templates/ad_adex.R b/inst/templates/ad_adex.R
@@ -6,7 +6,7 @@
 #
 
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 library(stringr)
@@ -19,7 +19,6 @@ data("admiral_adsl")
 data("admiral_ex")
 
 adsl <- admiral_adsl
-ex <- admiral_ex
 
 # When SAS datasets are imported into R using haven::read_sas(), missing
 # character values from SAS appear as "" characters in R, instead of appearing

diff --git a/inst/templates/ad_adlb.R b/inst/templates/ad_adlb.R
@@ -4,7 +4,7 @@
 #
 # Input: adsl, lb
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 library(stringr)
@@ -15,10 +15,9 @@ library(stringr)
 # as needed and assign to the variables below.
 # For illustration purposes read in admiral test data
 
-data("admiral_lb")
+data("lb")
 data("admiral_adsl")
 
-lb <- admiral_lb
 adsl <- admiral_adsl
 
 # When SAS datasets are imported into R using haven::read_sas(), missing

diff --git a/inst/templates/ad_adlbhy.R b/inst/templates/ad_adlbhy.R
@@ -4,7 +4,6 @@
 #
 # Input: adlb
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 

diff --git a/inst/templates/ad_admh.R b/inst/templates/ad_admh.R
@@ -4,7 +4,7 @@
 #
 # Input: mh, adsl
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 
@@ -13,12 +13,11 @@ library(lubridate)
 # Use e.g. haven::read_sas to read in .sas7bdat, or other suitable functions
 # as needed and assign to the variables below.
 # For illustration purposes read in admiral test data
-data("admiral_mh")
+data("mh")
 data("admiral_adsl")
 data("queries_mh")
 
 adsl <- admiral_adsl
-mh <- admiral_mh
 
 mh <- convert_blanks_to_na(mh)
 

diff --git a/inst/templates/ad_adpc.R b/inst/templates/ad_adpc.R
@@ -11,7 +11,7 @@ library(dplyr)
 library(lubridate)
 library(stringr)
 
-library(admiral.test) # Contains example datasets from the CDISC pilot project or simulated
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project or simulated
 
 # ---- Load source datasets ----
 
@@ -21,9 +21,9 @@ library(admiral.test) # Contains example datasets from the CDISC pilot project o
 
 
 # Load PC, EX, VS and ADSL
-data("admiral_pc")
-data("admiral_ex")
-data("admiral_vs")
+data("pc")
+data("ex")
+data("vs")
 
 data("admiral_adsl")
 
@@ -36,15 +36,15 @@ adsl <- admiral_adsl
 
 # Load EX
 
-ex <- convert_blanks_to_na(admiral_ex)
+ex <- convert_blanks_to_na(ex)
 
 # Load PC
 
-pc <- convert_blanks_to_na(admiral_pc)
+pc <- convert_blanks_to_na(pc)
 
 # Load VS for baseline height and weight
 
-vs <- convert_blanks_to_na(admiral_vs)
+vs <- convert_blanks_to_na(vs)
 
 # ---- Lookup tables ----
 param_lookup <- tibble::tribble(

diff --git a/inst/templates/ad_adsl.R b/inst/templates/ad_adsl.R
@@ -4,7 +4,7 @@
 #
 # Input: dm, ex, ds
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 library(stringr)
@@ -15,17 +15,11 @@ library(stringr)
 # as needed and assign to the variables below.
 # For illustration purposes read in admiral test data
 
-data("admiral_dm")
-data("admiral_ds")
-data("admiral_ex")
-data("admiral_ae")
-data("admiral_lb")
-
-dm <- admiral_dm
-ds <- admiral_ds
-ex <- admiral_ex
-ae <- admiral_ae
-lb <- admiral_lb
+data("dm")
+data("ds")
+data("ex")
+data("ae")
+data("lb")
 
 # When SAS datasets are imported into R using haven::read_sas(), missing
 # character values from SAS appear as "" characters in R, instead of appearing

diff --git a/inst/templates/ad_advs.R b/inst/templates/ad_advs.R
@@ -4,7 +4,7 @@
 #
 # Input: adsl, vs
 library(admiral)
-library(admiral.test) # Contains example datasets from the CDISC pilot project
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 library(dplyr)
 library(lubridate)
 library(stringr)
@@ -15,11 +15,10 @@ library(stringr)
 # as needed and assign to the variables below.
 # For illustration purposes read in admiral test data
 
-data("admiral_vs")
+data("vs")
 data("admiral_adsl")
 
 adsl <- admiral_adsl
-vs <- admiral_vs
 
 # When SAS datasets are imported into R using haven::read_sas(), missing
 # character values from SAS appear as "" characters in R, instead of appearing

diff --git a/man/create_query_data.Rd b/man/create_query_data.Rd