Merge branch 'main' into 2138_Implement_derive_vars_extreme_event

pharmaverse · Nov 27, 2023 · 69c15b6 · 69c15b6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 0.12.3.9013
+Version: 0.12.3.9014
 Authors@R: c(
     person("Ben", "Straub", , "ben.x.straub@gsk.com", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -161,6 +161,8 @@ the imputation functions, e.g., `derive_vars_dtm()`. (#2222)
 - Moved Development Process from `admiraldev` to Contribution Model in the 
 `admiral` website, updated GitHub strategy. (#2196)
 
+- All "Example Script(s)" sections in the User Guide vignettes were updated to point the user towards using `use_ad_template("ADaM")` rather than linking to the template in the code repository. (#2239)
+
 ## Various
 
 - Website now has button/links to Slack channel and GitHub Issues (#2127)

diff --git a/vignettes/adsl.Rmd b/vignettes/adsl.Rmd
@@ -804,6 +804,6 @@ and perform associated checks can be found at the [pharmaverse E2E example](http
 
 # Example Script 
 
-ADaM | Sample Code
+ADaM | Sourcing Command
 ---- | --------------
-ADSL | [ad_adsl.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R){target="_blank"} 
+ADSL | `use_ad_template("ADSL")`
diff --git a/vignettes/bds_exposure.Rmd b/vignettes/bds_exposure.Rmd
@@ -613,8 +613,8 @@ have them associated with an End to End pipeline under the umbrella of the
 [pharmaverse](https://github.com/pharmaverse). An example of applying metadata 
 and perform associated checks can be found at the [pharmaverse E2E example](https://examples.pharmaverse.org/data/adsl/).
 
-# Example Scripts {#example}
+# Example Script {#example}
 
-ADaM | Sample Code
+ADaM | Sourcing Command
 ---- | --------------
-ADEX | [ad_adex.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adex.R){target="_blank"}
+ADEX | `use_ad_template("ADEX")`
diff --git a/vignettes/bds_finding.Rmd b/vignettes/bds_finding.Rmd
@@ -1062,8 +1062,8 @@ and perform associated checks can be found at the [pharmaverse E2E example](http
 
 # Example Scripts {#example}
 
-ADaM | Sample Code 
+ADaM | Sourcing Command
 ---- | --------------
-ADEG | [ad_adeg.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adeg.R){target="_blank"}
-ADVS | [ad_advs.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_advs.R){target="_blank"}
-ADLB | [ad_adlb.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adlb.R){target="_blank"}
+ADEG | `use_ad_template("ADEG")`
+ADVS | `use_ad_template("ADVS")`
+ADLB | `use_ad_template("ADLB")`
diff --git a/vignettes/hys_law.Rmd b/vignettes/hys_law.Rmd
@@ -195,7 +195,7 @@ We hope by demonstrating the flexibility of `admiral` functions and using a gene
 
 # Example Script 
 
-ADaM   | Sample Code
--------| --------------
-ADLBHY | [ad_adlbhy.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adlbhy.R){target="_blank"} 
+ADaM   | Sourcing Command
+------ | --------------
+ADLBHY | `use_ad_template("ADLBHY")`
 
diff --git a/vignettes/occds.Rmd b/vignettes/occds.Rmd
@@ -552,7 +552,7 @@ and perform associated checks can be found at the [pharmaverse E2E example](http
 
 # Example Scripts
 
-ADaM | Sample Code
+ADaM | Sourcing Command
 ---- | --------------
-ADAE | [`ad_adae.R`](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adae.R){target="_blank"}
-ADCM | [`ad_adcm.R`](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adcm.R){target="_blank"}
+ADAE | `use_ad_template("ADAE")`
+ADCM | `use_ad_template("ADCM")`
diff --git a/vignettes/pk_adnca.Rmd b/vignettes/pk_adnca.Rmd
@@ -1454,7 +1454,7 @@ example](https://examples.pharmaverse.org/data/adsl/).
 
 # Example Scripts {#example}
 
-| ADaM  | Sample Code                                                                                               |
-|------------|------------------------------------------------------------|
-| ADPC  | [ad_adpc.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adpc.R){target="_blank"}   |
-| ADPPK | [ad_adppk.R](https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adppk.R){target="_blank"} |
+ADaM  | Sourcing Command
+----- | --------------
+ADPC  | `use_ad_template("ADPC")`
+ADPPK | `use_ad_template("ADPPK")`