diff --git a/DESCRIPTION b/DESCRIPTION index a8c5d8e..e564d57 100644 --- 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 index 3d33c40..3e17f11 100644 --- 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 index 9e46fbf..ee20768 100644 --- 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 index cca014f..2997d62 100644 --- 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 index fcf3c98..19db239 100644 --- 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 index 69fafd4..30647ef 100644 --- 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 index d3bdacb..be4f008 100644 Binary files a/data/discovery.rda and b/data/discovery.rda differ diff --git a/inst/WORDLIST b/inst/WORDLIST index 45eb5b4..339a28a 100644 --- 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 index 8e8656f..a822e89 100644 --- 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 index 8e1be4a..06eafe3 100644 --- a/man/discovery.Rd +++ b/man/discovery.Rd @@ -5,7 +5,7 @@ \alias{discovery} \title{Admiral Function Discovery} \format{ -An object of class \code{spec_tbl_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 422 rows and 9 columns. +An object of class \code{spec_tbl_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 424 rows and 9 columns. } \usage{ discovery diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml index 408f109..e720d61 100644 --- 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: