Merge pull request #79 from pharmaverse/71_updates_from_admiralpeds

closes #71 closes #74 closes #78 updates from admiralpeds experience

.Rbuildignore

@@ -1,5 +1,3 @@
-^renv$
-^renv\.lock$
 ^.*\.Rproj$
 ^.*\.lycheeignore$
 ^\.Rproj\.user$

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
-Package: admiraltemplate
-Title: ADaM in R Asset Library - Extension
-Version: 0.0.3
+Package: `<<INSERT PACKAGE EXT NAME>>'
+Title: ADaM in R Asset Library - Extension Package for `<<INSERT TA>>`
+Version: 0.1.0
 Authors@R: 
     person("Open", "Source", , "[email protected]", role = c("aut", "cre"))
 Description: A toolbox for programming Clinical Data Standards Interchange
@@ -11,16 +11,17 @@ Description: A toolbox for programming Clinical Data Standards Interchange
     Administration (FDA). Analysis derivations are implemented in
     accordance with the "Analysis Data Model Implementation Guide" (CDISC
     Analysis Data Model Team, 2021,
-    <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
+    <https://www.cdisc.org/standards/foundational/adam>).  The package is
+    an extension package of the 'admiral' package.
 License: Apache License (>= 2)
 URL: https://pharmaverse.github.io/admiraltemplate,
     https://github.com/pharmaverse/admiraltemplate
 Depends: 
-    R (>= 3.5)
+    R (>= 4.1)
 Imports:
-    admiral (>= 0.10.0),
-    admiraldev (>= 0.5.0),
-    dplyr (>= 0.8.4),
+    admiral (>= 1.0.0),
+    admiraldev (>= 1.0.0),
+    dplyr (>= 1.0.5),
     hms (>= 0.5.3),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),
@@ -31,22 +32,17 @@ Imports:
     tidyr (>= 1.0.2),
     tidyselect (>= 1.1.0)
 Suggests:
-    covr,
-    devtools,
     diffdf,
     DT,
+    htmltools,
     knitr,
-    lintr,
     methods,
-    miniUI,
-    pharmaversesdtm,
-    pkgdown,
+    pharmaversesdtm (>= 0.2.0),
+    reactable,
+    readxl,
     rmarkdown,
-    roxygen2,
-    spelling,
     testthat (>= 3.0.0),
-    tibble,
-    usethis
+    tibble
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3

LICENSE.md

@@ -179,7 +179,7 @@ recommend that a file or class name and description of purpose be included on
 the same “printed page” as the copyright notice for easier identification within
 third-party archives.
 
-    Copyright 2021 F. Hoffmann-La Roche AG and GlaxoSmithKline LLC
+    Copyright `<<INSERT YEAR>>` `<<INSERT CO-DEVELOPMENT PARTNER COMPANIES AS LICENSE HOLDERS>>`
 
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.

NEWS.md

@@ -1,62 +1,8 @@
-# admiraltemplate 0.0.3
+# admiraltemplate 0.1.0
 
-- Removed renv and related files (#70)
-
-## Updates to site
-
- - Package Extension guidance on the front page was updated and moved to [this location](https://pharmaverse.github.io/admiraldev/articles/package_extensions.html) in `{admiraldev}`, and a link was added to point to the new location (#61).
-
-## CI workflows
-
-- [`admiralci` workflows](https://github.com/pharmaverse/admiralci) has been updated. Indeed, workflows are not anymore based on `renv` framework to manage dependencies (`devtools` is used instead). Moreover, we now use latest version of `R` for all workflows, and run `R CMD CHECKS` for following R release version (R latest stable version), R devel version (in development version), and R previous release. More details are available in [admiralci doc](https://pharmaverse.github.io/admiralci/index.html).
-As a result, `.github/workflows/common.yml` file has been updated, and all `renv` configurations has been removed.
-
-## admiral.test removed
-
-- `admiral.test` package has been replaced by [`pharmaversesdtm`](https://github.com/pharmaverse/pharmaversesdtm)
-
-# admiraltemplate 0.0.2
-
-## New Features
-
- - New `renv` lock files were setup (#48)
-
-## Updates of Existing Functions
-
-## Breaking Changes
-
-## Documentation
-
- - Many updates across documentation made to match v0.10.0 of `admiral` [PR #51](https://github.com/pharmaverse/admiraltemplate/pull/51), including: 
- - Links were fixed on the website 
- - Templates were aligned to current `admiral` standards
- - Package dependencies were updated
- - Explanation on how to use family/keywords have been provided
-
-## Various
-
- - Renamed from `admiralext` to `admiraltemplate`
-
-# admiraltemplate 0.0.1
-
-## New Features
-
- - You can link the GitHub Issue to Changelog by using (#ISSUE-NUMBER)
-
-## Updates of Existing Functions
-
- - Updates that you have made for this version (#ISSUE-NUMBER)
-
-## Breaking Changes
-
- - Deprecated functions. (#ISSUE-NUMBER)
- - Bug Fixes (#ISSUE-NUMBER)
-
-## Documentation
-
- - Stuff that you did (#ISSUE-NUMBER)
-
-## Various
-
- - Stuff that you did (#ISSUE-NUMBER)
+- Initial package release focused on `<<ADD INITIAL SCOPE>>`
 
+Note that after first release you should then start maintaining this `NEWS.md` file for every user-facing update.
+You should categorise the updates under title sections for New Features, Updates of Existing Functions,
+Breaking Changes, Documentation, Various.
+Each update should also reference the original issue by adding at the end: (#ISSUE-NUMBER)

R/data.R

@@ -0,0 +1,6 @@
+#' xx Dataset
+#'
+#' An xx test dataset for xx
+#' @keywords datasets
+#' @family datasets
+"xx"

README.md

@@ -47,8 +47,8 @@ The repository template includes the following:
 
 -   License file (Apache 2.0 - but company co-developers need to be
     added to copyright section)
--   Required folders (R; test; templates; vignettes; renv; etc)
--   Set-up files (DESCRIPTION; NAMESPACE; renv.lock; etc)
+-   Required folders (R; test; templates; vignettes; etc)
+-   Set-up files (DESCRIPTION; NAMESPACE; etc)
 -   Issue Templates (Bug Template; Feature Request; Documentation
     Request/Update; Onboarding)
 -   Pull Request Template

_pkgdown.yml

@@ -12,6 +12,10 @@ repo:
     user: https://github.com/
 news:
   cran_dates: true
+
+development:
+  mode: auto
+
 reference:
 
 - title: Derivations for Adding Variables
@@ -53,6 +57,7 @@ reference:
 navbar:
   structure:
     left: [getstarted, reference, articles, news]
+    right: [search, slack, history, newissue, github]
   components:
     getstarted:
       text: Get Started
@@ -65,3 +70,15 @@ navbar:
       menu:
       - text: Creating ADXX
         href: articles/adxx.html
+    history:
+      icon: fa-history
+      href: articles/website-versions.html
+      aria-label: Previous Release Websites
+    slack:
+      icon: fa-slack
+      href: https://pharmaverse.slack.com/
+      aria-label: Slack
+    newissue:
+      icon: fa-bug
+      href: https://github.com/pharmaverse/admiraltemplate/issues/new/choose
+      aria-label: New Issue

data-raw/xx.R

@@ -0,0 +1,7 @@
+# Dataset: xx
+# Description: xx test SDTM dataset for xx
+
+Add code to create test dataset xx and update this in `R/data.R`
+
+# Save dataset ----
+usethis::use_data(xx, overwrite = TRUE)

data/xx.rda

@@ -0,0 +1 @@
+

inst/templates/ad_adxx.R

@@ -3,7 +3,18 @@
 # Label: XXX
 #
 # Input: xx, xx, xx
+
 library(admiral)
 library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
 
 # Add your template ADaM script code
+
+# Save output ----
+
+# Change to whichever directory you want to save the dataset in
+dir <- tools::R_user_dir("admiraltemplate_templates_data", which = "cache")
+if (!file.exists(dir)) {
+  # Create the folder
+  dir.create(dir, recursive = TRUE, showWarnings = FALSE)
+}
+save(adxx, file = file.path(dir, "adxx.rda"), compress = "bzip2")

vignettes/admiraltemplate.Rmd

@@ -19,3 +19,7 @@ library(admiraltemplate)
 ```
 
 Introduction to how to use the package extension...
+
+# Support
+
+Support is provided via [pharmaverse Slack](https://pharmaverse.slack.com/).

vignettes/adxx.Rmd

@@ -18,3 +18,13 @@ knitr::opts_chunk$set(
 # Introduction
 
 This article describes creating an `ADXX` ADaM.
+
+# Programming Workflow
+
+Steps involved to create an `ADXX` ADaM.
+
+# Example Scripts
+
+ADaM | Sourcing Command
+---- | --------------
+ADXX | `admiral::use_ad_template("ADXX", package = "admiraltemplate")`