Merge branch 'main' into 2130_cheatsheet

.github/CONTRIBUTING.md

@@ -1,13 +1,13 @@
 # Contribution to {admiral} 
 
-This outlines how to propose a change to the admiral package. For more detailed info about contributing to {admiral}, and other [pharmaverse packages](https://pharmaverse.org/), please see the [development process guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) as well as other Developer Guides in the Articles section of the [{admiral} website](https://pharmaverse.github.io/admiral/cran-release/index.html)
+This outlines how to propose a change to the admiral package. For more detailed info about contributing to {admiral}, and other [pharmaverse packages](https://pharmaverse.org/), please see the [development process guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html) as well as other Developer Guides in the Articles section of the [{admiral} website](https://pharmaverse.github.io/admiral/cran-release/index.html)
 
 # Basics
  * For each new contribution, the user creates an issue on the issue tab on [GitHub](https://github.com/pharmaverse/admiral/issues) to put it in our backlog. The issues can range from bug identification and/or fixes, enhancements to functions, documentation, tests or new features.   
 
  * We advise you to contact us when an [issue](https://github.com/pharmaverse/admiral/issues) is created via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) (If you don't have access, use this [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A) to join).  We can discuss details or align expectations if you are not familiar with the `{admiral}` philosophy and programming strategy. The team will try to review the issues within the next backlog meeting and give some initial feedback. Since we are not a 100% fully resourced software development team it might be that some issues will take longer to respond to depending on the amount of overall issues. 
 
- * Familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/main/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html).
+ * Familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html).
 
  * All newly [created issues](https://github.com/pharmaverse/admiral/issues) will be reviewed within the next backlog meeting and the creator will receive an initial feedback via a comment. Someone from the core development team will then triage new issues by assigning the appropriate labels (such as “user request” so we can easily identify new requests).
 

.github/pull_request_template.md

@@ -1,4 +1,4 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.   
+Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.   
 
 Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task.
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: admiral
 Title: ADaM in R Asset Library
-Version: 0.12.3.9006
+Version: 0.12.3.9007
 Authors@R: c(
     person("Ben", "Straub", , "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),

NEWS.md

@@ -1108,9 +1108,9 @@ this case the day is imputed as `15` (#592)
 
 - README and site homepage has been updated with important new section around expectations of {admiral}, as well as other useful references such as links to conference talks (#868 & #802)
 
-- New vignette [Development Process](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) and improvements made to contribution vignettes (#765 & #758)
+- New vignette [Development Process](https://pharmaverse.github.io/admiraldev/articles/development_process.html) and improvements made to contribution vignettes (#765 & #758)
 
-- Updated [Pull Request Review Guidance](https://pharmaverse.github.io/admiraldev/main/articles/pr_review_guidance.html) on using `task-list-completed` workflow (#817)
+- Updated [Pull Request Review Guidance](https://pharmaverse.github.io/admiraldev/articles/pr_review_guidance.html) on using `task-list-completed` workflow (#817)
 
 ## Various
 
@@ -1124,7 +1124,7 @@ this case the day is imputed as `15` (#592)
 
 - New vignette [Contributing to admiral](https://pharmaverse.github.io/admiral/articles/contribution_model.html) (#679)
 
-- New vignette [Unit Test Guidance](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html) (#679)
+- New vignette [Unit Test Guidance](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html) (#679)
 
 - Broken links in README have been fixed (#564)
 
@@ -1183,9 +1183,9 @@ to specify the unit of the input age (#569)
 
 - New vignette [Queries Dataset Documentation](https://pharmaverse.github.io/admiral/articles/queries_dataset.html) (#561)
 
-- New vignette [Writing Vignettes](https://pharmaverse.github.io/admiraldev/main/articles/writing_vignettes.html) (#334)
+- New vignette [Writing Vignettes](https://pharmaverse.github.io/admiraldev/articles/writing_vignettes.html) (#334)
 
-- New vignette [Pull Request Review Guidance](https://pharmaverse.github.io/admiraldev/main/articles/pr_review_guidance.html) (#554)
+- New vignette [Pull Request Review Guidance](https://pharmaverse.github.io/admiraldev/articles/pr_review_guidance.html) (#554)
 
 - A section on handling missing values when working with {admiral} has been added to the "Get Started" vignette (#577)
 

R/derive_expected_records.R

@@ -6,7 +6,7 @@
 #' @param dataset
 #' `r roxygen_param_dataset(expected_vars = c("dataset_ref", "by_vars"))`
 #'
-#' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
+#' @param dataset_expected_obs `r lifecycle::badge("deprecated")` Please use `dataset_ref` instead.
 #'
 #' @param dataset_ref Expected observations dataset
 #'

R/derive_locf_records.R

@@ -6,7 +6,7 @@
 #' @param dataset
 #' `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var", "order", "keep_vars"))`
 #'
-#' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
+#' @param dataset_expected_obs `r lifecycle::badge("deprecated")` Please use `dataset_ref` instead.
 #'
 #' @param dataset_ref Expected observations dataset
 #'

R/derive_vars_aage.R

@@ -35,7 +35,7 @@
 #'
 #'   Permitted Values: 'years', 'months', 'weeks', 'days', 'hours', 'minutes', 'seconds'
 #'
-#' @param unit *Deprecated*, please use `age_unit` instead.
+#' @param unit `r lifecycle::badge("deprecated")` Please use `age_unit` instead.
 #'
 #' @details The duration is derived as time from start to end date in the
 #'   specified output unit. If the end date is before the start date, the duration

README.md

@@ -47,7 +47,7 @@ Phases:
 | ---------------- | ------------------------------------------------------------------------ | -------------------------------------------------------------------- |
 | Q4-2023          | December 4th                                                             | December 11th                                                        |
 |                  | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/main/) | [{admiralonco}](https://pharmaverse.github.io/admiralonco/)     |
-|                  | [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/)           | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/) |
+|                  | [{admiraldev}](https://pharmaverse.github.io/admiraldev/)           | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/) |
 |                  | [{admiral}](https://pharmaverse.github.io/admiral/)                 |                                                                      |
 
 The `{admiral}` Q4-2023 release will officially be `{admiral}`'s version 1.0.0 release, where we commit to increased package maturity and pivot towards focusing on maintenance rather than new content. This does not mean that there will never be any new content in `{admiral}`, rather it means we will be more mindful about introducing new functionality and/or breaking changes. The release schedule in 2024 and onward will also shift to twice-yearly, rather than quarterly, so that our users have ample time to react to any new content and changes that do make it onto `{admiral}`.
@@ -148,7 +148,7 @@ All `{admiral}` functions are easily findable.
 
 ### Readability
 
-All `{admiral}` functions follow the [Programming Strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html)
+All `{admiral}` functions follow the [Programming Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html)
 that all our developers and contributors must follow, so that all our code has a high degree of consistency and readability.
 
 * We mandate use of tidyverse (e.g. dplyr) over similar functionality existing in base R.
@@ -161,7 +161,7 @@ that all our developers and contributors must follow, so that all our code has a
 
 * Please go to [Get Started](https://pharmaverse.github.io/admiral/articles/admiral.html) section to start using `{admiral}`
 * Please see the [pharmaverse YouTube channel](https://www.youtube.com/channel/UCxQFEv8HNqM01DXzdQLCy6Q) for videos related to `{admiral}`.
-* Please see the [Programming Strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html) to understand how functions are created
+* Please see the [Programming Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html) to understand how functions are created
 * Please see the [FAQ](https://pharmaverse.github.io/admiral/articles/faq.html) for the most frequent questions
 * Please see the [Contribution Model](https://pharmaverse.github.io/admiral/articles/contribution_model.html) for how to get involved with making contributions
 * Please see [FAQ: R and Package Versions](https://pharmaverse.github.io/admiral/articles/faq.html#why-do-we-use-a-certain-r-version-and-package-versions-for-development) for why we develop with certain R and package versions.

vignettes/admiral.Rmd

@@ -299,4 +299,4 @@ channel](https://app.slack.com/client/T028PB489D3/C02M8KN8269).
 
 - [Template scripts](https://github.com/pharmaverse/admiral/tree/main/inst/templates)
 
-- [Programming Strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html)
+- [Programming Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html)

vignettes/contribution_model.Rmd

@@ -28,11 +28,11 @@ Our contribution model is still in a testing phase so we advise you to contact u
  * For each new contribution, the user creates an issue on the issue tab on [GitHub](https://github.com/pharmaverse/admiral/issues) to put it in our backlog. 
 
  * Familiarize yourself with our [programming
- strategy](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html),
+ strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html),
  guidance for [GitHub
- usage](https://pharmaverse.github.io/admiraldev/devel/articles/git_usage.html)
+ usage](https://pharmaverse.github.io/admiraldev/articles/git_usage.html)
  and [unit
- testing](https://pharmaverse.github.io/admiraldev/devel/articles/unit_test_guidance.html).
+ testing](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html).
 
  * All [created issues](https://github.com/pharmaverse/admiral/issues) will be reviewed within the next sprint and the creator will receive an initial feedback via a comment. Someone from the core development team will then triage new issues by assigning the appropriate labels (such as “user request” so we can easily identify new requests).
 
@@ -50,7 +50,7 @@ Type 1 Contribution with Code:
  * First, the user creates an issue or comments on an existing issue to notify that they’d like to contribute code.
 
  * Follow our [development
- process](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html)
+ process](https://pharmaverse.github.io/admiraldev/articles/development_process.html)
  step-by-step guide.
 
  * We advise to contact an `{admiral}` core development team directly via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) before submitting code for complex functionality.

vignettes/faq.Rmd

@@ -95,7 +95,7 @@ knitr::opts_chunk$set(
  * Guidance for testing and documentation expectations of community contribution functions. Then it is for each company to cover the following:
    * validation to be able to use the package on company-specific SCE for GxP purposes and associated audit evidence 
    * strategy of how the use of `{admiral}` fits into company-specific quality assurance process (double programming comparison versus your company-specific legacy ADaM solution could be appropriate until confidence builds)
-   * see our guidance on [unit testing](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html)
+   * see our guidance on [unit testing](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html)
 
 ##### Will **admiral provide harmonized define.xml** or submittable specifications for functions?
 
@@ -116,7 +116,7 @@ knitr::opts_chunk$set(
 
 ##### Will there be a user/**contribution** guide?
 
- * Our [programming strategy](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html) serves as a framework
+ * Our [programming strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html) serves as a framework
  for users how to create their own functions. 
  * Please see the [contribution model website](contribution_model.html) for a detailed description how to contribute