Closes #1 replace admiraltemplate placeholders (#2)

* #1 replacing admiraltemplate files

* #1 update more files

* #1 chore: amend failed checks

* #1 chore: failed checks

* #1 fix styler check

* Update inst/templates/ad_adxx.R

Co-authored-by: Stefan Bundfuss <[email protected]>

* #1 updates following review

* #1 updated imported packages

* #1 updated namespace

* #1 updates to packages in description

* #1 updated wordlist order

* #1 updated namespace

* Update _pkgdown.yml

---------

Co-authored-by: Stefan Bundfuss <[email protected]>

.Rbuildignore

@@ -11,9 +11,9 @@
 ^man/dev_util_.+\.Rd$
 ^LICENSE\.md$
 ^\.github$
-^admiraltemplate\.Rcheck$
-^admiraltemplate.*\.tar\.gz$
-^admiraltemplate.*\.tgz$
+^admiralmetabolic\.Rcheck$
+^admiralmetabolic.*\.tar\.gz$
+^admiralmetabolic.*\.tgz$
 ^staged_dependencies.yaml$
 ^README.Rmd$
 ^\.devcontainer$

.lycheeignore

@@ -2,8 +2,9 @@
 # Validate Links
 
 https://packagemanager.rstudio.com/cran/linux/focal/latest
-https://github.com/pharmaverse/admiraltemplate/blob/main/
+https://github.com/pharmaverse/admiralmetabolic/blob/main/
 irongut/[email protected]
 insightsengineering/[email protected]
 https://packagemanager.rstudio.com/cran/__linux__/focal/latest
 tj-actions/[email protected]
+https://pharmaverse.github.io/admiralmetabolic

DESCRIPTION

@@ -1,9 +1,9 @@
 Type: Package
-Package: `<<INSERT PACKAGE EXT NAME>>'
-Title: ADaM in R Asset Library - Extension Package for `<<INSERT TA>>`
-Version: 0.1.0
+Package: admiralmetabolic
+Title: Metabolism Extension Package for ADaM in 'R' Asset Library
+Version: 0.0.0
 Authors@R: 
-    person("Open", "Source", , "admiraltemplate@pharmaverse.com", role = c("aut", "cre"))
+    person("Edoardo", "Mancini", , "edoardo.mancini@roche.com", role = c("aut", "cre"))
 Description: A toolbox for programming Clinical Data Standards Interchange
     Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
     ADaM datasets are a mandatory part of any New Drug or Biologics
@@ -12,7 +12,8 @@ Description: A toolbox for programming Clinical Data Standards Interchange
     accordance with the "Analysis Data Model Implementation Guide" (CDISC
     Analysis Data Model Team, 2021,
     <https://www.cdisc.org/standards/foundational/adam>).  The package is
-    an extension package of the 'admiral' package.
+    an extension package of the 'admiral' package focusing on the 
+    metabolism therapeutic area.
 License: Apache License (>= 2)
 URL: https://pharmaverse.github.io/admiraltemplate,
     https://github.com/pharmaverse/admiraltemplate
@@ -21,25 +22,20 @@ Depends:
 Imports:
     admiral (>= 1.0.0),
     admiraldev (>= 1.0.0),
-    dplyr (>= 1.0.5),
-    hms (>= 0.5.3),
+    dplyr (>= 0.8.4),
+    stringr (>= 1.4.0),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),
     magrittr (>= 1.5),
-    purrr (>= 0.3.3),
     rlang (>= 0.4.4),
-    stringr (>= 1.4.0),
-    tidyr (>= 1.0.2),
-    tidyselect (>= 1.1.0)
+    tidyselect (>= 1.0.0)
 Suggests:
     diffdf,
     DT,
     htmltools,
     knitr,
     methods,
-    pharmaversesdtm (>= 0.2.0),
-    reactable,
-    readxl,
+    pharmaversesdtm (>= 1.0.0),
     rmarkdown,
     testthat (>= 3.0.0),
     tibble

NAMESPACE

@@ -1,15 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export(hello_admiral)
-importFrom(admiral,derive_vars_dy)
-importFrom(admiraldev,assert_character_scalar)
-importFrom(admiraldev,assert_character_vector)
-importFrom(admiraldev,assert_data_frame)
-importFrom(admiraldev,assert_filter_cond)
-importFrom(admiraldev,assert_logical_scalar)
-importFrom(admiraldev,assert_numeric_vector)
-importFrom(admiraldev,assert_symbol)
-importFrom(admiraldev,assert_vars)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
@@ -42,7 +33,6 @@ importFrom(dplyr,transmute)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,union)
 importFrom(dplyr,vars)
-importFrom(hms,as_hms)
 importFrom(lifecycle,deprecate_stop)
 importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,deprecated)
@@ -63,20 +53,6 @@ importFrom(lubridate,years)
 importFrom(lubridate,ymd)
 importFrom(lubridate,ymd_hms)
 importFrom(magrittr,"%>%")
-importFrom(purrr,compose)
-importFrom(purrr,every)
-importFrom(purrr,flatten)
-importFrom(purrr,keep)
-importFrom(purrr,map)
-importFrom(purrr,map2)
-importFrom(purrr,map_chr)
-importFrom(purrr,map_if)
-importFrom(purrr,map_lgl)
-importFrom(purrr,modify_at)
-importFrom(purrr,modify_if)
-importFrom(purrr,reduce)
-importFrom(purrr,transpose)
-importFrom(purrr,walk)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,abort)
@@ -136,11 +112,6 @@ importFrom(stringr,str_to_lower)
 importFrom(stringr,str_to_title)
 importFrom(stringr,str_to_upper)
 importFrom(stringr,str_trim)
-importFrom(tidyr,drop_na)
-importFrom(tidyr,nest)
-importFrom(tidyr,pivot_longer)
-importFrom(tidyr,pivot_wider)
-importFrom(tidyr,unnest)
 importFrom(tidyselect,all_of)
 importFrom(tidyselect,contains)
 importFrom(tidyselect,vars_select)

NEWS.md

@@ -1,4 +1,4 @@
-# admiraltemplate 0.1.0
+# admiralmetabolic 0.1.0
 
 - Initial package release focused on `<<ADD INITIAL SCOPE>>`
 

R/admiraltemplate-package.R → R/admiralmetabolic-package.R

@@ -14,18 +14,10 @@
 #'             quo_is_missing quo_is_null quo_is_symbol quos quo_squash quo_text
 #'             set_names sym syms type_of warn quo_set_env quo_get_env
 #' @importFrom utils capture.output str
-#' @importFrom purrr map map2 map_chr map_lgl reduce walk keep map_if transpose
-#'             flatten every modify_at modify_if reduce compose
 #' @importFrom stringr str_c str_detect str_extract str_remove str_remove_all
 #'             str_replace str_trim str_to_lower str_to_title str_to_upper str_glue
 #' @importFrom lubridate as_datetime ceiling_date date days duration floor_date is.Date is.instant
 #'             time_length %--% ymd ymd_hms weeks years hours minutes
-#' @importFrom tidyr drop_na nest pivot_longer pivot_wider unnest
 #' @importFrom tidyselect all_of contains vars_select
-#' @importFrom hms as_hms
 #' @importFrom lifecycle deprecate_warn deprecated deprecate_stop
-#' @importFrom admiral derive_vars_dy
-#' @importFrom admiraldev assert_logical_scalar assert_character_vector assert_vars
-#'             assert_data_frame assert_character_scalar assert_numeric_vector assert_filter_cond
-#'             assert_symbol
 "_PACKAGE"

R/data.R

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

README.md

@@ -1,67 +1,74 @@
-<!-- Please do not edit the README.md file as it is auto-generated after PR merges. Only edit the README.Rmd file -->
-<!-- The purpose of this is to enable dynamic links using dyn_link function above to access devel/main admiral homepage respectively -->
-<!-- To test this in your feature branch use code: rmarkdown::render("README.Rmd", output_format ="md_document") -->
-
-# admiral package extension Template <img src="man/figures/logo.png" align="right" width="200" style="margin-left:50px;"/>
-
-<!-- badges: start -->
-
-[<img src="http://pharmaverse.org/shields/admiral.svg">](https://pharmaverse.org)
-[![CRAN
-status](https://www.r-pkg.org/badges/version/admiral)](https://CRAN.R-project.org/package=admiral)
-[![Test
-Coverage](https://raw.githubusercontent.com/pharmaverse/admiraltemplate/badges/main/test-coverage.svg)](https://github.com/pharmaverse/admiraltemplate/actions/workflows/code-coverage.yml)
-<!-- badges: end -->
-
-## Table of Contents
-
--   [Extension Expectations](#extension-expectations)
--   [What is included in the
-    template](#what-is-included-in-the-template)
--   [Package Extension Guidance](#package-extension-guidance)
--   [Quick Start Guide for Template](#quick-start-guide-for-template)
-
-## Extension Expectations
-
-To be included as an `{admiral}` package extension we expect developers
-to adhere to the following standards:
-
--   [Code of
-    Conduct](https://pharmaverse.github.io/admiral/CODE_OF_CONDUCT.html)
--   [Manifesto](https://pharmaverse.github.io/admiral/index.html?q=manifest#admiral-manifesto)
--   [Programming
-    Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html)
--   Follow consistent workflow checks
--   A CRAN Release means 90% or greater test coverage
-
-We have developed this repository template in order to reduce the burden
-on developers to follow these standards. This template will also help to
-harmonize the `{admiral}` family of R packages, to ensure a consistent
-user experience and ease of installing and adopting all the packages.
-With this in mind, we expect the same core package dependencies and
-versions as used for `{admiral}`.
-
-## What is included in the template
-
-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; etc)
--   Set-up files (DESCRIPTION; NAMESPACE; etc)
--   Issue Templates (Bug Template; Feature Request; Documentation
-    Request/Update; Onboarding)
--   Pull Request Template
--   Workflow actions (a selection of generic and specific CI/CD
-    auto-checks)
--   Package badges (Test coverage; etc)
--   Branch protection rules
-
-## Package Extension Guidance
-
-For detailed information regarding the ethos of `{admiral}` package
-extensions and how to decide if you should set your own one up, please
-see our [Package Extension
-Guidance](https://pharmaverse.github.io/admiraldev/articles/package_extensions.html).
-You will also find details about team setup, suggested workflow and
-lessons learned from past package extensions.
+# admiralmetabolic <img src="man/figures/logo.png" align="right" width="200" style="margin-left:50px;"/>
+
+Metabolism extension package for ADaM in R Asset Library `{admiral}`
+
+## Purpose
+
+To provide a complementary (to `{admiral}`) toolbox that enables users
+to develop specifics for metabolic clinical trials.
+
+## Installation
+
+To install the latest development version of the package directly from
+GitHub use the following code:
+
+```r
+if (!requireNamespace("remotes", quietly = TRUE)) {
+  install.packages("remotes")
+}
+
+remotes::install_github("pharmaverse/admiraldev") # This is a required dependency of {admiralmetabolic}
+remotes::install_github("pharmaverse/admiral") # This is a required dependency of {admiralmetabolic}
+remotes::install_github("pharmaverse/admiralmetabolic")
+```
+
+### Dependencies
+
+The latest version of the package works with the latest versions of the
+packages stated in `DESCRIPTION`.
+
+If a previous version of the package should be used, it is recommended
+to use latest version of the dependencies at the point of time when the
+previous version of `{admiralmetabolic}` was released.
+
+## Scope
+
+-   Build a toolbox of re-usable functions and utilities to create
+    metabolism-specific ADaM datasets in R in a modular manner.
+-   All functions are created based upon the ADaM Implementation Guide
+    and aim to facilitate the programming of ADaM dataset standards.
+-   Initially the package will focus on <insert focus>.
+
+## Expectations
+
+`{admiralmetabolic}` is expected to complement `{admiral}` and provide
+functions to help with the creation of analyses required
+for metabolic trial ADaMs.
+
+## References and Documentation
+
+-   Please refer to the [References and
+    Documentation](https://pharmaverse.github.io/admiral/index.html#references-and-documentation)
+
+## R Versions
+
+Here’s a summary of our strategy for this package related to R versions:
+
+-   R versions for developers and users will follow the same as
+    `{admiral}` core package.
+-   For development the `main` branch of `{admiral}` core is used as a
+    dependency. For releasing a new `{admiralmetabolic}` version it must run
+    using the latest released `{admiral}` core version.
+
+## Contact
+
+We use the following for support and communications between user and
+developer community:
+
+-   [Slack](https://pharmaverse.slack.com/) - for
+    informal discussions, Q&A and building our user community. If you
+    don't have access, use this
+    [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A)
+    to join the pharmaverse Slack workspace
+-   [GitHub Issues](https://github.com/pharmaverse/admiralmetabolic/issues) -
+    for direct feedback, enhancement requests or raising bugs

_pkgdown.yml

@@ -1,14 +1,14 @@
-url: https://pharmaverse.github.io/admiraltemplate
+url: https://pharmaverse.github.io/admiralmetabolic
 
 template:
   bootstrap: 5
   params:
     bootswatch: flatly
 repo:
   url:
-    home: https://github.com/pharmaverse/admiraltemplate
-    source: https://github.com/pharmaverse/admiraltemplate/blob/main/
-    issue: https://github.com/pharmaverse/admiraltemplate/issues/
+    home: https://github.com/pharmaverse/admiralmetabolic
+    source: https://github.com/pharmaverse/admiralmetabolic/blob/main/
+    issue: https://github.com/pharmaverse/admiralmetabolic/issues/
     user: https://github.com/
 news:
   cran_dates: true
@@ -32,7 +32,7 @@ reference:
 
 - title: Advanced Functions
 - subtitle: Pre-Defined Source Objects
-  desc: Source objects defined by {admiraltemplate}
+  desc: Source objects defined by {admiralmetabolic}
 - contents:
   - has_keyword("source_specifications")
 
@@ -61,7 +61,7 @@ navbar:
   components:
     getstarted:
       text: Get Started
-      href: articles/admiraltemplate.html
+      href: articles/admiralmetabolic.html
     reference:
       text: Reference
       href: reference/index.html
@@ -80,5 +80,5 @@ navbar:
       aria-label: Slack
     newissue:
       icon: fa-bug
-      href: https://github.com/pharmaverse/admiraltemplate/issues/new/choose
+      href: https://github.com/pharmaverse/admiralmetabolic/issues/new/choose
       aria-label: New Issue

inst/WORDLIST

@@ -13,9 +13,10 @@ Onboarding
 README
 SDTM
 TAs
+Template
 USUBJIDs
 admiralxxx
-admiraltemplate
+admiralmetabolic
 adxx
 anonymized
 der
@@ -27,4 +28,4 @@ pharmaverse
 renv
 repo
 roxygen
-Template
+

inst/templates/ad_adxx.R

@@ -12,9 +12,9 @@ library(pharmaversesdtm) # Contains example datasets from the CDISC pilot projec
 # Save output ----
 
 # Change to whichever directory you want to save the dataset in
-dir <- tools::R_user_dir("admiraltemplate_templates_data", which = "cache")
+dir <- tools::R_user_dir("admiralmetabolic_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")
+# save(adxx, file = file.path(dir, "adxx.rda"), compress = "bzip2")