Merge branch 'devel' into 39_cleanup@devel

.github/CODEOWNERS.txt

@@ -0,0 +1,7 @@
+# This a CODEOWNERS file, where you can establish code owners.
+# Code owners are automatically requested for review when someone opens a pull request
+# that modifies code that they own.
+#
+#
+data/ts.rda @kaz462
+R/ts.R @kaz462

R/data.R

@@ -93,13 +93,6 @@
 #' @author Antonio Rodríguez Contestí
 "pp"
 
-#' Questionnaire Dataset
-#'
-#' A SDTM QS dataset from the CDISC pilot project & Ophthalmology test data
-#'
-#' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_qs.rda} # nolint
-"qs"
-
 #' Ophthalmology Questionnaire Dataset
 #'
 #' An example Questionnaires SDTM dataset with ophthalmology-specific questionnaire of NEI VFQ-25

README.md

@@ -2,23 +2,21 @@
 
 <!-- badges: start -->
 
-[<img src="http://pharmaverse.org/shields/admiral.svg">](https://pharmaverse.org)
-[![Test Coverage](https://raw.githubusercontent.com/pharmaverse/pharmaversesdtm/badges/main/test-coverage.svg)](https://github.com/pharmaverse/pharmaversesdtm/actions/workflows/code-coverage.yml)
+[<img src="http://pharmaverse.org/shields/admiral.svg"/>](https://pharmaverse.org) [![Test Coverage](https://raw.githubusercontent.com/pharmaverse/pharmaversesdtm/badges/main/test-coverage.svg)](https://github.com/pharmaverse/pharmaversesdtm/actions/workflows/code-coverage.yml)
 
 <!-- badges: end -->
 
-Test data (SDTM) for the pharmaverse family of packages 
+Test data (SDTM) for the pharmaverse family of packages
 
 # Purpose
 
-To provide a one-stop-shop for SDTM test data in the pharmaverse family of packages. This includes  datasets that are therapeutic area (TA)-agnostic (`DM`, `VS`, `EG`, etc.) as well TA-specific ones (`RS`, `TR`, `OE`, etc.).
+To provide a one-stop-shop for SDTM test data in the pharmaverse family of packages. This includes datasets that are therapeutic area (TA)-agnostic (`DM`, `VS`, `EG`, etc.) as well TA-specific ones (`RS`, `TR`, `OE`, etc.).
 
 # Installation
 
-The package is available from CRAN and can be installed by running `install.packages("pharmaversesdtm")`.
-To install the latest development version of the package directly from GitHub use the following code:
+The package is available from CRAN and can be installed by running `install.packages("pharmaversesdtm")`. To install the latest development version of the package directly from GitHub use the following code:
 
-```r
+``` r
 if (!requireNamespace("remotes", quietly = TRUE)) {
   install.packages("remotes")
 }
@@ -28,39 +26,45 @@ remotes::install_github("pharmaverse/pharmaversesdtm", ref = "devel")
 
 # Data Sources
 
-Some of the test datasets has been sourced from the [CDISC pilot project](https://github.com/cdisc-org/sdtm-adam-pilot-project), while other datasets have been constructed ad-hoc by the admiral team. Please check the [Github repository](https://github.com/pharmaverse/admiral.test/tree/main/data) for detailed information regarding the source of specific datasets.
+Some of the test datasets has been sourced from the [CDISC pilot project](https://github.com/cdisc-org/sdtm-adam-pilot-project), while other datasets have been constructed ad-hoc by the admiral team. Please check the [Reference page](https://pharmaverse.github.io/pharmaversesdtm/cran-release/reference/index.html) for detailed information regarding the source of specific datasets.
+
+# Naming Conventions {#naming}
 
-# Naming Conventions
 * Datasets that are TA-agnostic: same as SDTM domain name (e.g., `dm`, `rs`).
-* Datasets that are TA-specific: prefix the domain name with the TA (e.g., `onco_rs`, `ophtha_oe`).
+* Datasets that are TA-specific: domain_TA_others, others go from broader categories to more specific ones (e.g., `oe_ophtha`, `rs_onco`, `rs_onco_irecist`).
 
-**Note**: *If an SDTM domain is used by multiple TAs, `{pharmaversesdtm}` may provide multiple versions of the corresponding test dataset. For instance, the package contains `ex` and `ophtha_ex` as the latter contains ophthalmology-specific variables such as `EXLAT` and `EXLOC`, and `EXROUTE` is exchanged for a plausible ophthalmology value.*
+**Note**: *If an SDTM domain is used by multiple TAs, `{pharmaversesdtm}` may provide multiple versions of the corresponding test dataset. For instance, the package contains `ex` and `ex_ophtha` as the latter contains ophthalmology-specific variables such as `EXLAT` and `EXLOC`, and `EXROUTE` is exchanged for a plausible ophthalmology value.*
 
 # How To Update
 
-Firstly, make a GitHub issue in this repo with the planned updates and tag `@pharmaverse/admiral` so that one of the development core team can sanity check the request.
+Firstly, make a GitHub issue in [`{pharmaversesdtm}`](https://github.com/pharmaverse/pharmaversesdtm) with the planned updates and tag `@pharmaverse/admiral` so that one of the development core team can sanity check the request. 
 Then there are two main ways to extend the test data: either by adding new datasets or extending existing datasets with new records/variables. Whichever method you choose, it is worth noting the following:
 
-* Programs that generate test data are stored in the `dev/` folder.
-* Each of these programs is written as a standalone R script: if any packages need to be loaded for a given program, then call `library()` at the start of the program (but please do __not__ call `library(pharmaversesdtm)`).
-* Most of the packages that you are likely to need will already be specified in the `renv.lock` file, so they will already be installed if you have been keeping in sync--you can check this by entering `renv::status()` in the Console. However, you may also wish to install `{metatools}` and `{ggplot2}`, which are currently not specified in the `renv.lock` file. If you feel that you need to install any other packages in addition to those just mentioned, then please tag `@pharmaverse/admiral` to discuss with the development core team.
-* When you have created a program in the `dev/` folder, you need to run it as a standalone R script, in order to generate a test dataset that will become part of the `{pharmaversesdtm}` package, but you do not need to build the package.
-* Following [best practice](https://r-pkgs.org/data.html#sec-data-data), each dataset is stored as a `.rda` file whose name is consistent with the name of the dataset: for example, the dataset `dm` should be renamed to `raw_dm` before saving it as `raw_dm.rda`; if you save `dm` as `raw_dm.rda` and subsequently load the `.rda` file, then `dm` (not `raw_dm`) will be loaded into the global environment.
-* The programs in `dev/` are stored within the `{pharmaversesdtm}` GitHub repository, but they are __not__ part of the `{pharmaversesdtm}` package--the `dev/` folder is specified in `.Rbuildignore`.
-* When you run a program that is in the `dev/` folder, you generate a dataset that is written to the `data/` folder, which will become part of the `{pharmaversesdtm}` package.
-* The names of test datasets are specified in `R/data.R`, for the purpose of generating documentation in the `man/` folder.
+* Programs that generate test data are stored in the `data-raw/` folder.
+* Each of these programs is written as a standalone R script: if any packages need to be loaded for a given program, then call `library()` at the start of the program (but please do **not** call `library(pharmaversesdtm)`).
+* Most of the packages that you are likely to need will already be specified in the `renv.lock` file, so they will already be installed if you have been keeping in sync--you can check this by entering `renv::status()` in the Console. However, you may also wish to install `{metatools}`, which is currently not specified in the `renv.lock` file. If you feel that you need to install any other packages in addition to those just mentioned, then please tag `@pharmaverse/admiral` to discuss with the development core team.
+* When you have created a program in the `data-raw/` folder, you need to run it as a standalone R script, in order to generate a test dataset that will become part of the `{pharmaversesdtm}` package, but you do not need to build the package.
+* Following [best practice](https://r-pkgs.org/data.html#sec-data-data), each dataset is stored as a `.rda` file whose name is consistent with the name of the dataset, e.g., dataset `xx` is stored as `xx.rda`. The easiest way to achieve this is to use `usethis::use_data(xx)`
+* The programs in `data-raw/` are stored within the `{pharmaversesdtm}` GitHub repository, but they are **not** part of the `{pharmaversesdtm}` package--the `data-raw/` folder is specified in `.Rbuildignore`.
+* When you run a program that is in the `data-raw/` folder, you generate a dataset that is written to the `data/` folder, which will become part of the `{pharmaversesdtm}` package.
+* The names and sources of test datasets are specified in `R/data.R`, for the purpose of generating documentation in the `man/` folder.
 
 ## Adding New SDTM Datasets
 
-* Create a program in the `dev/` folder, named `<name>.R`, where `<name>` is the SDTM domain name, (e.g. `rs.R`), to generate the test data and output `<name>.rda` to the `data/` folder. Use CDISC pilot data such as `dm` as input in this program in order to create realistic synthetic data that remains consistent with other domains. Note that __no personal data should be used__ as part of this package, even if anonymized.
+* Create a program in the `data-raw/` folder, named `<name>.R`, where `<name>` should follow the [naming convention](#naming), to generate the test data and output `<name>.rda` to the `data/` folder.
+    * Use CDISC pilot data such as `dm` as input in this program in order to create realistic synthetic data that remains consistent with other domains (not mandatory).
+    * Note that **no personal data should be used** as part of this package, even if anonymized.
 * Run the program.
 * Reflect this update, by specifying `<name>` in `R/data.R`.
 * Run `devtools::document()` in order to update `NAMESPACE` and update the `.Rd` files in `man/`.
+* Add your GitHub handle to `.github/CODEOWNERS`.
+* Update `NEWS.md`.
 
 ## Updating Existing SDTM Datasets
 
-* Rename the source dataset as `raw_<name>`, where `<name>` is the SDTM domain name (e.g. rename `ds` to `raw_ds`), and then save it to the `data/` folder as `raw_<name>.rda` (e.g. `save(raw_ds, file = "data/raw_ds.rda")`).
-* Create a program in the `dev/` folder, named `update_<name>.R`, to load `raw_<name>.rda`, make the updates, and output `<name>.rda` to the `data/` folder.
-* Run the program.
-* Reflect this update, by specifying both `raw_<name>` and `<name>` in `R/data.R`.
+* Locate the existing program `<name>.R` in the `data-raw/` folder, update it accordingly. 
+* Run the program, and output updated `<name>.rda` to the `data/` folder.
 * Run `devtools::document()` in order to update `NAMESPACE` and update the `.Rd` files in `man/`.
+* Add your GitHub handle to `.github/CODEOWNERS`.
+* Update `NEWS.md`.
+

_pkgdown.yml

@@ -12,56 +12,14 @@ repo:
     user: https://github.com/
 news:
   cran_dates: true
-reference:
 
-- title: Derivations for Adding Variables
-- subtitle: ADXX-specific
-  desc: Derivation Functions helpful for building the ADXX dataset
-- contents:
-  - has_keyword("der_adxx")
-
-- title: Derivations for Adding Parameters
-- subtitle: ADXX-specific
-  desc: Parameter Derivation Functions helpful for building the ADXX dataset
-- contents:
-  - has_keyword("der_prm_adxx")
-
-- title: Advanced Functions
-- subtitle: Pre-Defined Source Objects
-  desc: Source objects defined by {pharmaversesdtm}
-- contents:
-  - has_keyword("source_specifications")
-
-- title: Utility Functions
-- subtitle: Utilities for Formatting Observations
-- contents:
-  - has_keyword('utils_fmt')
-
-- subtitle: Utilities for Dataset Checking
-- contents:
-  - has_keyword('utils_ds_chk')
-
-- subtitle: Utilities for Filtering Observations
-- contents:
-  - has_keyword('utils_fil')
-
-- title: Example Datasets
-  desc: You can run `admiral::use_ad_template()` to produce additional datasets
-- contents:
-  - has_keyword('datasets')
 
 navbar:
   structure:
-    left: [getstarted, reference, articles, news]
+    left: [reference, news]
   components:
-    getstarted:
-      text: Get Started
-      href: articles/pharmaversesdtm.html
     reference:
-      text: Reference
-      href: reference/index.html
-    articles:
-      text: User Guides
-      menu:
-      - text: Creating ADXX
-        href: articles/adxx.html
+       text: Reference
+       href: reference/index.html
+
+

data-raw/pc.R

@@ -6,7 +6,6 @@ library(haven)
 library(plyr)
 library(dplyr)
 library(lubridate)
-library(ggplot2)
 library(labelled)
 library(admiral)
 

data-raw/pp.R

@@ -5,7 +5,6 @@
 library(haven)
 library(dplyr)
 library(lubridate)
-library(ggplot2)
 library(labelled)
 library(admiral)
 

staged_dependencies.yaml

@@ -1,12 +1,15 @@
 ---
 current_repo:
-  repo: pharmaverse/admiraltemplate
+  repo: pharmaverse/pharmaversesdtm
   host: https://github.com
 upstream_repos:
+downstream_repos:
   - repo: pharmaverse/admiral
     host: https://github.com
-  - repo: pharmaverse/admiral.test
+  - repo: pharmaverse/admiralonco
     host: https://github.com
-  - repo: pharmaverse/admiraldev
+  - repo: pharmaverse/admiralvaccine
     host: https://github.com
-downstream_repos:
+  - repo: pharmaverse/admiralophtha
+    host: https://github.com
+