Closes #51 Update admiral-lookup-book.csv by adding admiralpeds varia…

…bles (#53) * Update admiral-lookup-book.csv by adding admiralpeds variables * #51 update WORDLIST * #51 add admiralpeds dependency * #51 update discovery.rda (run DATASET.R) * #51 documentation * Corrected grammar * bumped into dev version and updated NEWS --------- Co-authored-by: Daniel Sjoberg <[email protected]>
pharmaverse · Oct 2, 2024 · ad22677 · ad22677
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diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,6 @@
-# admiraldiscovery 0.3.0
+# admiraldiscovery (development version)
+
+* Added variables from the {admiralpeds} package to the variable listing. (#51, @Fanny-Gautier)
 
 # admiraldiscovery 0.2.1
 

diff --git a/data/discovery.rda b/data/discovery.rda
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -2,6 +2,7 @@ ADaM
 ORCID
 admiralonco
 admiralophtha
+admiralpeds
 admiralvaccine
 mayn
 reactable

diff --git a/inst/admiral-lookup-book.csv b/inst/admiral-lookup-book.csv
@@ -406,6 +406,16 @@ ADVS,BDS,PCHG,Derive percent change from baseline,admiral,derive_var_pchg,https:
 ADVS,BDS,ANL01FL,Flag last result within an analysis visit and analysis timepoint for post-baseline records,admiral,restrict_derivation,https://pharmaverse.github.io/admiral/reference/restrict_derivation.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_advs.R
 ADVS,BDS,ASEQ,Derive sequential number for observations within each by group,admiral,derive_var_obs_number,https://pharmaverse.github.io/admiral/reference/derive_var_obs_number.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_advs.R
 ADVS,BDS,"DTYPE=""LOV""",Derive LOV value,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""WGTASDS""",Derive Weight-for-age z-score,admiralpeds,derive_params_growth_age,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_age.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""WGTAPCTL""",Derive Weight-for-age percentile,admiralpeds,derive_params_growth_age,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_age.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""HGTSDS""",Derive Height-for-age z-score,admiralpeds,derive_params_growth_age,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_age.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""HGTPCTL""",Derive Height-for-age percentile,admiralpeds,derive_params_growth_age,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_age.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""BMISDS""",Derive BMI-for-age z-score,admiralpeds,derive_params_growth_age,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_age.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""BMIPCTL""",Derive BMI-for-age percentile,admiralpeds,derive_params_growth_age,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_age.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""HDCSDS""",Derive Head Circumference-for-age z-score,admiralpeds,derive_params_growth_height,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_height.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""HDCPCTL""",Derive Head Circumference-for-age percentile,admiralpeds,derive_params_growth_height,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_height.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""WGTHSDS""",Derive Weight-for-length/height Z-Score,admiralpeds,derive_params_growth_height,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_height.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
+ADVS,BDS,"PARAMCD=""WGTHPCTL""",Derive Weight-for-length/height Percentile,admiralpeds,derive_params_growth_height,https://pharmaverse.github.io/admiralpeds/reference/derive_params_growth_height.html,Template Example,https://github.com/pharmaverse/admiralpeds/blob/main/inst/templates/ad_advs.R
 ADMH,OCCDS,SMQ02NAM,Derive name 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,SMQ02CD,Derive code 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,SMQ02SC,Derive scope 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

diff --git a/man/discovery.Rd b/man/discovery.Rd
diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml
@@ -6,6 +6,8 @@ upstream_repos:
   host: https://github.com
 - repo: pharmaverse/admiralophtha
   host: https://github.com
+- repo: pharmaverse/admiralpeds
+  host: https://github.com
 - repo: pharmaverse/admiralvaccine
   host: https://github.com
 

diff --git a/vignettes/gt.Rmd b/vignettes/gt.Rmd
@@ -24,7 +24,7 @@ admiraldiscovery::interactive_discovery("gt")
 
 #### Missing Variables
 
-If you notice a ADaM variable that is missing, please take a moment to [file an issue on GitHub](https://github.com/pharmaverse/admiraldiscovery/issues) to have it added to the listing.
+If you notice an ADaM variable that is missing, please [file an issue on GitHub](https://github.com/pharmaverse/admiraldiscovery/issues) to have it added.
 
 #### Deprecated/Superseded
 

diff --git a/vignettes/reactable.Rmd b/vignettes/reactable.Rmd
@@ -24,7 +24,7 @@ admiraldiscovery::interactive_discovery("reactable")
 
 #### Missing Variables
 
-If you notice a ADaM variable that is missing, please take a moment to [file an issue on GitHub](https://github.com/pharmaverse/admiraldiscovery/issues) to have it added to the listing.
+If you notice an ADaM variable that is missing, please [file an issue on GitHub](https://github.com/pharmaverse/admiraldiscovery/issues) to have it added.
 
 #### Deprecated/Superseded