Chore: #2040 Update admiral.test to pharmaversesdtm

DESCRIPTION

@@ -55,7 +55,7 @@ Imports:
     tidyr (>= 1.0.2),
     tidyselect (>= 1.1.0)
 Suggests:
-    admiral.test (>= 0.6.0),
+    pharmaversesdtm,
     DT,
     diffdf,
     knitr,

NEWS.md

@@ -11,6 +11,8 @@
 
 - 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)

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

inst/example_scripts/derive_single_dose.R

@@ -1,9 +1,8 @@
 
-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 %>%

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)
 
@@ -14,12 +14,11 @@ 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")
 
 adsl <- admiral_adsl
-ae <- admiral_ae
 suppae <- admiral_suppae
 
 # When SAS datasets are imported into R using haven::read_sas(), missing

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

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)
@@ -18,10 +18,9 @@ library(stringr)
 # For illustration purposes read in admiral test data
 
 data("admiral_adsl")
-data("admiral_eg")
+data("eg")
 
 adsl <- admiral_adsl
-eg <- admiral_eg
 
 # When SAS datasets are imported into R using haven::read_sas(), missing
 # character values from SAS appear as "" characters in R, instead of appearing

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

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

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)
 

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)
 

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(

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

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

vignettes/admiral.Rmd

@@ -26,22 +26,22 @@ for example the following script which creates a (very simple) ADSL dataset.
 
 ## Load Packages and Example Datasets
 
-First, we will load our packages and example datasets to help with our `ADSL` creation. The `{dplyr}` and `{lubridate}` packages are `{tidyverse}` packages and used heavily throughout this script.  The `{admiral}` package also leverages the `{admiral.test}` package for example SDTM datasets which are from the CDISC Pilot Study.
+First, we will load our packages and example datasets to help with our `ADSL` creation. The `{dplyr}` and `{lubridate}` packages are `{tidyverse}` packages and used heavily throughout this script.  The `{admiral}` package also leverages the `{pharmaversesdtm}` package for example SDTM datasets which are from the CDISC Pilot Study.
 
 ```{r, message=FALSE, warning=FALSE}
 library(dplyr, warn.conflicts = FALSE)
 library(lubridate)
 library(admiral)
-library(admiral.test)
+library(pharmaversesdtm)
 
 # Read in SDTM datasets
-data("admiral_dm")
-data("admiral_ds")
-data("admiral_ex")
+data("dm")
+data("ds")
+data("ex")
 
-dm <- convert_blanks_to_na(admiral_dm)
-ds <- convert_blanks_to_na(admiral_ds)
-ex <- convert_blanks_to_na(admiral_ex)
+dm <- convert_blanks_to_na(dm)
+ds <- convert_blanks_to_na(ds)
+ex <- convert_blanks_to_na(ex)
 ```
 
 ## Derive Treatment Variables (`TRT0xP`, `TRT0xA`) {#treatmentvargs}

vignettes/adsl.Rmd

@@ -56,26 +56,26 @@ the environment. This will be a company specific process. Some of the
 data frames needed may be `DM`, `EX`, `DS`, `AE`, and `LB`.
 
 For example purpose, the CDISC Pilot SDTM datasets---which are included in 
-`{admiral.test}`---are used.
+`{pharmaversesdtm}`---are used.
 
 ```{r, message=FALSE, warning=FALSE}
 library(admiral)
 library(dplyr, warn.conflicts = FALSE)
-library(admiral.test)
+library(pharmaversesdtm)
 library(lubridate)
 library(stringr)
 
-data("admiral_dm")
-data("admiral_ds")
-data("admiral_ex")
-data("admiral_ae")
-data("admiral_lb")
-
-dm <- convert_blanks_to_na(admiral_dm)
-ds <- convert_blanks_to_na(admiral_ds)
-ex <- convert_blanks_to_na(admiral_ex)
-ae <- convert_blanks_to_na(admiral_ae)
-lb <- convert_blanks_to_na(admiral_lb)
+data("dm")
+data("ds")
+data("ex")
+data("ae")
+data("lb")
+
+dm <- convert_blanks_to_na(dm)
+ds <- convert_blanks_to_na(ds)
+ex <- convert_blanks_to_na(ex)
+ae <- convert_blanks_to_na(ae)
+lb <- convert_blanks_to_na(lb)
 ```
 
 The `DM` domain is used as the basis for `ADSL`:

vignettes/bds_exposure.Rmd

@@ -52,21 +52,21 @@ To start, all data frames needed for the creation of `ADEX` should be read into
 the environment.  This will be a company specific process.  Some of the 
 data frames needed may be `EX` and `ADSL`.
 
-For example purpose, the CDISC Pilot SDTM and ADaM datasets---which are included in `{admiral.test}`---are used.
+For example purpose, the CDISC Pilot SDTM and ADaM datasets---which are included in `{pharmaversesdtm}`---are used.
 
 ```{r message=FALSE}
 library(admiral)
 library(dplyr, warn.conflicts = FALSE)
-library(admiral.test)
+library(pharmaversesdtm)
 library(lubridate)
 library(stringr)
 library(tibble)
 
 data("admiral_adsl")
-data("admiral_ex")
+data("ex")
 
 adsl <- admiral_adsl
-ex <- convert_blanks_to_na(admiral_ex)
+ex <- convert_blanks_to_na(ex)
 ```
 ```{r echo=FALSE}
 ex <- filter(ex, USUBJID %in% c("01-701-1015", "01-701-1023", "01-703-1086", "01-703-1096", "01-707-1037", "01-716-1024"))