diff --git a/.Rbuildignore b/.Rbuildignore index 409b610..7e8e3a5 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,3 @@ -^renv$ -^renv\.lock$ ^.*\.Rproj$ ^.*\.lycheeignore$ ^\.Rproj\.user$ diff --git a/DESCRIPTION b/DESCRIPTION index 821ca55..9bfbbd9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package -Package: admiraltemplate -Title: ADaM in R Asset Library - Extension -Version: 0.0.3 +Package: `<>' +Title: ADaM in R Asset Library - Extension Package for `<>` +Version: 0.1.0 Authors@R: person("Open", "Source", , "admiraltemplate@pharmaverse.com", 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, - ). + ). 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 diff --git a/LICENSE.md b/LICENSE.md index 37d7bd9..b92cefd 100644 --- a/LICENSE.md +++ b/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 `<>` `<>` Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/NEWS.md b/NEWS.md index 23bb9e6..6231a62 100644 --- a/NEWS.md +++ b/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 `<>` +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) diff --git a/R/data.R b/R/data.R new file mode 100644 index 0000000..e0c31be --- /dev/null +++ b/R/data.R @@ -0,0 +1,6 @@ +#' xx Dataset +#' +#' An xx test dataset for xx +#' @keywords datasets +#' @family datasets +"xx" diff --git a/README.md b/README.md index 7b47836..e72af7a 100644 --- a/README.md +++ b/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 diff --git a/_pkgdown.yml b/_pkgdown.yml index 035a488..379b934 100644 --- a/_pkgdown.yml +++ b/_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 diff --git a/data-raw/xx.R b/data-raw/xx.R new file mode 100644 index 0000000..b981e62 --- /dev/null +++ b/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) diff --git a/data/xx.rda b/data/xx.rda new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/data/xx.rda @@ -0,0 +1 @@ + diff --git a/inst/templates/ad_adxx.R b/inst/templates/ad_adxx.R index 297c40d..ca371f8 100644 --- a/inst/templates/ad_adxx.R +++ b/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") diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml deleted file mode 100644 index 6cebdb1..0000000 --- a/staged_dependencies.yaml +++ /dev/null @@ -1,12 +0,0 @@ ---- -current_repo: - repo: pharmaverse/admiraltemplate - host: https://github.com -upstream_repos: - - repo: pharmaverse/admiral - host: https://github.com - - repo: pharmaverse/pharmaversesdtm - host: https://github.com - - repo: pharmaverse/admiraldev - host: https://github.com -downstream_repos: diff --git a/vignettes/admiraltemplate.Rmd b/vignettes/admiraltemplate.Rmd index 5e61078..0bea69b 100644 --- a/vignettes/admiraltemplate.Rmd +++ b/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/). diff --git a/vignettes/adxx.Rmd b/vignettes/adxx.Rmd index e9f700f..b847846 100644 --- a/vignettes/adxx.Rmd +++ b/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")`