Closes #57: adding admiralmetabolic fns (#59)

* #57 adding admiralmetabolic fns * #57 update news and description * #57 update description typo * #57 Add data, wordlist, dependencies * redoc * Update admiraldiscovery-package.R --------- Co-authored-by: Daniel Sjoberg <[email protected]>
pharmaverse · Feb 6, 2025 · 10c67cf · 10c67cf
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commit 10c67cf
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Showing 11 changed files with 14 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,6 +21,7 @@ Imports:
     admiralonco (>= 1.1.0),
     admiralophtha (>= 1.1.0),
     admiralvaccine (>= 0.2.0),
+    admiralmetabolic (>= 0.1.0),
     dplyr (>= 1.1.4),
     glue (>= 1.7.0),
     gt (>= 0.10.1),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # admiraldiscovery (development version)
 
+* Added variables from the {admiralmetabolic} package to the variable listing. (#57, @manciniedoardo)
+
 # admiraldiscovery 0.3.0
 
 * Added variables from the {admiralpeds} package to the variable listing. (#51, @Fanny-Gautier)

diff --git a/R/admiral_pkg_versions.R b/R/admiral_pkg_versions.R
@@ -6,7 +6,7 @@
 #' @examples
 #' admiral_pkg_versions()
 admiral_pkg_versions <- function() {
-  c("admiral", "admiralonco", "admiralophtha", "admiralvaccine") |>
+  c("admiral", "admiralonco", "admiralophtha", "admiralvaccine", "admiralmetabolic") |>
     lapply(\(x) glue::glue("{x} v{packageVersion(x)}")) |>
     unlist() |>
     glue::glue_collapse(sep = ", ", last = ", and ")

diff --git a/R/admiraldiscovery-package.R b/R/admiraldiscovery-package.R
@@ -11,4 +11,5 @@ this_fn_is_not_used <- function() {
   admiralonco::bor_cr
   admiralophtha::admiralophtha_adbcva
   admiralvaccine::derive_vars_params
+  admiralmetabolic::derive_param_waisthgt
 }
diff --git a/R/get_fns_with_keyword.R b/R/get_fns_with_keyword.R
@@ -29,7 +29,7 @@ NULL
 #' @rdname get_keyword_fns
 #' @export
 get_admiral_deprecated <- function() {
-  c("admiral", "admiralonco", "admiralophtha", "admiralvaccine") |>
+  c("admiral", "admiralonco", "admiralophtha", "admiralvaccine", "admiralmetabolic") |>
     lapply(
       function(x) {
         dplyr::tibble(
@@ -45,7 +45,7 @@ get_admiral_deprecated <- function() {
 #' @rdname get_keyword_fns
 #' @export
 get_admiral_superseded <- function() {
-  c("admiral", "admiralonco", "admiralophtha", "admiralvaccine") |>
+  c("admiral", "admiralonco", "admiralophtha", "admiralvaccine", "admiralmetabolic") |>
     lapply(
       function(x) {
         dplyr::tibble(

diff --git a/admiraldiscovery.Rproj b/admiraldiscovery.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 2f5ea07d-9ae2-41e5-b37b-6ff7627974a9
 
 RestoreWorkspace: No
 SaveWorkspace: No

diff --git a/data/discovery.rda b/data/discovery.rda
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -4,6 +4,7 @@ admiralonco
 admiralophtha
 admiralpeds
 admiralvaccine
+admiralmetabolic
 mayn
 reactable
 roxygen

diff --git a/inst/admiral-lookup-book.csv b/inst/admiral-lookup-book.csv
@@ -422,3 +422,5 @@ ADMH,OCCDS,SMQ02SC,Derive scope of Standardized MedDRA Query 2,admiral,derive_va
 ADMH,OCCDS,SMQ02SCN,Derive scope (N) of Standardized MedDRA Query 2,admiral,derive_vars_query,https://pharmaverse.github.io/admiral/reference/derive_vars_query.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_admh.R
 ADMH,OCCDS,CQ04NAM,Derive name of Customized Query 4,admiral,derive_vars_query,https://pharmaverse.github.io/admiral/reference/derive_vars_query.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_admh.R
 ADMH,OCCDS,CQ04CD,Derive code of Customized Query 4,admiral,derive_vars_query,https://pharmaverse.github.io/admiral/reference/derive_vars_query.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_admh.R
+ADVS,BDS,"PARAMCD=""WSTCIR""",Derive Waist to Height Ratio,admiralmetabolic,derive_param_waisthgt,https://pharmaverse.github.io/admiralmetabolic/reference/derive_param_waisthgt.html,Template Example,https://github.com/pharmaverse/admiralmetabolic/blob/main/vignettes/advs.Rmd
+ADVS,BDS,"PARAMCD=""WSTHIP""",Derive Waist to Hip Ratio,admiralmetabolic,derive_param_waisthip,https://pharmaverse.github.io/admiralmetabolic/reference/derive_param_waisthip.html,Template Example,https://github.com/pharmaverse/admiralmetabolic/blob/main/vignettes/advs.Rmd
diff --git a/man/discovery.Rd b/man/discovery.Rd
diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml
@@ -10,6 +10,8 @@ upstream_repos:
   host: https://github.com
 - repo: pharmaverse/admiralvaccine
   host: https://github.com
+- repo: pharmaverse/admiralmetabolic
+  host: https://github.com
 
 downstream_repos: