diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index d61b89e99..79e4be23d 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -130,7 +130,7 @@ The package maintainer also reserves the right to adjust the criteria to recogni If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer. -[docs]: https://insightsengineering.github.io/teal.data/latest-tag/index.html -[articles]: https://insightsengineering.github.io/teal.data/latest-tag/articles/index.html -[license]: https://insightsengineering.github.io/teal.data/latest-tag/LICENSE-text.html -[insights]: https://github.com/insightsengineering/teal.data/pulse +[docs]: https://pharmaverse.github.io/teal.data/latest-tag/index.html +[articles]: https://pharmaverse.github.io/teal.data/latest-tag/articles/index.html +[license]: https://pharmaverse.github.io/teal.data/latest-tag/LICENSE-text.html +[insights]: https://github.com/pharmaverse/teal.data/pulse diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml index edb432034..91815af73 100644 --- a/.github/ISSUE_TEMPLATE/bug.yml +++ b/.github/ISSUE_TEMPLATE/bug.yml @@ -33,7 +33,7 @@ body: id: code-of-conduct attributes: label: Code of Conduct - description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.data/latest-tag/CODE_OF_CONDUCT.html) + description: By submitting this issue, you agree to follow our [Code of Conduct.](https://pharmaverse.github.io/teal.data/latest-tag/CODE_OF_CONDUCT.html) options: - label: I agree to follow this project's Code of Conduct. required: true @@ -41,7 +41,7 @@ body: id: contributor-guidelines attributes: label: Contribution Guidelines - description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.data/latest-tag/CONTRIBUTING.html) + description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://pharmaverse.github.io/teal.data/latest-tag/CONTRIBUTING.html) options: - label: I agree to follow this project's Contribution Guidelines. required: true @@ -49,7 +49,7 @@ body: id: security-policy attributes: label: Security Policy - description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/insightsengineering/teal.data/security/policy) + description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/pharmaverse/teal.data/security/policy) options: - label: I agree to follow this project's Security Policy. required: true diff --git a/.github/ISSUE_TEMPLATE/feature.yml b/.github/ISSUE_TEMPLATE/feature.yml index 347e00129..dc364891d 100644 --- a/.github/ISSUE_TEMPLATE/feature.yml +++ b/.github/ISSUE_TEMPLATE/feature.yml @@ -13,7 +13,7 @@ body: id: code-of-conduct attributes: label: Code of Conduct - description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.data/latest-tag/CODE_OF_CONDUCT.html) + description: By submitting this issue, you agree to follow our [Code of Conduct.](https://pharmaverse.github.io/teal.data/latest-tag/CODE_OF_CONDUCT.html) options: - label: I agree to follow this project's Code of Conduct. required: true @@ -21,7 +21,7 @@ body: id: contributor-guidelines attributes: label: Contribution Guidelines - description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.data/latest-tag/CONTRIBUTING.html) + description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://pharmaverse.github.io/teal.data/latest-tag/CONTRIBUTING.html) options: - label: I agree to follow this project's Contribution Guidelines. required: true @@ -29,7 +29,7 @@ body: id: security-policy attributes: label: Security Policy - description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/insightsengineering/teal.data/security/policy) + description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/pharmaverse/teal.data/security/policy) options: - label: I agree to follow this project's Security Policy. required: true diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml index 3446f43eb..2bf0f62f8 100644 --- a/.github/ISSUE_TEMPLATE/question.yml +++ b/.github/ISSUE_TEMPLATE/question.yml @@ -13,7 +13,7 @@ body: id: code-of-conduct attributes: label: Code of Conduct - description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.data/latest-tag/CODE_OF_CONDUCT.html) + description: By submitting this issue, you agree to follow our [Code of Conduct.](https://pharmaverse.github.io/teal.data/latest-tag/CODE_OF_CONDUCT.html) options: - label: I agree to follow this project's Code of Conduct. required: true @@ -21,7 +21,7 @@ body: id: contributor-guidelines attributes: label: Contribution Guidelines - description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.data/latest-tag/CONTRIBUTING.html) + description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://pharmaverse.github.io/teal.data/latest-tag/CONTRIBUTING.html) options: - label: I agree to follow this project's Contribution Guidelines. required: true @@ -29,7 +29,7 @@ body: id: security-policy attributes: label: Security Policy - description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/insightsengineering/teal.data/security/policy) + description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/pharmaverse/teal.data/security/policy) options: - label: I agree to follow this project's Security Policy. required: true diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d00674175..1ff0bdcff 100755 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,7 @@ repos: - methods - rlang - stats - - insightsengineering/teal.code + - pharmaverse/teal.code - utils - yaml - id: spell-check diff --git a/DESCRIPTION b/DESCRIPTION index a8f0bc44b..6b3bdda45 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,9 +24,9 @@ Authors@R: c( Description: Provides a 'teal_data' class as a unified data model for 'teal' applications focusing on reproducibility and relational data. License: Apache License 2.0 -URL: https://insightsengineering.github.io/teal.data/, - https://github.com/insightsengineering/teal.data/ -BugReports: https://github.com/insightsengineering/teal.data/issues +URL: https://pharmaverse.github.io/teal.data/, + https://github.com/pharmaverse/teal.data/ +BugReports: https://github.com/pharmaverse/teal.data/issues Depends: R (>= 4.0), teal.code (>= 0.7.0) @@ -48,11 +48,11 @@ VignetteBuilder: rmarkdown RdMacros: lifecycle -Config/Needs/verdepcheck: insightsengineering/teal.code, mllg/checkmate, +Config/Needs/verdepcheck: pharmaverse/teal.code, mllg/checkmate, r-lib/lifecycle, r-lib/rlang, yihui/knitr, rstudio/rmarkdown, insightsengineering/random.cdisc.data, r-lib/testthat, r-lib/withr Config/Needs/website: insightsengineering/nesttemplate -Config/roxygen2/version: 8.0.0 +Config/roxygen2/version: 8.1.0 Encoding: UTF-8 Language: en-US LazyData: true diff --git a/R/join_keys-names.R b/R/join_keys-names.R index ae029a76f..c9676f80d 100644 --- a/R/join_keys-names.R +++ b/R/join_keys-names.R @@ -1,6 +1,6 @@ #' The names of a `join_keys` object #' -#' @inheritParams base::`names<-` +#' @inheritParams base::names #' @export `names<-.join_keys` <- function(x, value) { new_x <- unclass(x) diff --git a/R/teal_data-class.R b/R/teal_data-class.R index d571dc321..5475ba4d2 100644 --- a/R/teal_data-class.R +++ b/R/teal_data-class.R @@ -27,8 +27,15 @@ setOldClass("join_keys") #' @slot verified (`logical(1)`) flag signifying that code in `@code` has been #' proven to yield contents of `@.xData`. #' Used internally. See [`teal.data::verify()`] for more details. +# FIXME https://github.com/r-lib/roxygen2/issues/1918 @inheritSection teal.code::`qenv-class` Code +#' @section Code: #' -#' @inheritSection teal.code::`qenv-class` Code +#' Each code element is a character representing one call. Each element is named with the random +#' identifier to make sure uniqueness when joining. Each element has possible attributes: +#' - `warnings` (`character`) the warnings output when evaluating the code element. +#' - `messages` (`character`) the messages output when evaluating the code element. +#' - `dependency` (`character`) names of objects that appear in this call and gets affected by this call, +#' separated by `<-` (objects on LHS of `<-` are affected by this line, and objects on RHS are affecting this line). #' #' @import teal.code #' @keywords internal diff --git a/README.md b/README.md index 5fd809b1d..726b62b82 100644 --- a/README.md +++ b/README.md @@ -6,22 +6,22 @@ [![Last Month Downloads](http://cranlogs.r-pkg.org/badges/last-month/teal.data?color=green)](https://cran.r-project.org/package=teal.data) [![Last Week Downloads](http://cranlogs.r-pkg.org/badges/last-week/teal.data?color=green)](https://cran.r-project.org/package=teal.data) -[![Check 🛠](https://github.com/insightsengineering/teal.data/actions/workflows/check.yaml/badge.svg)](https://insightsengineering.github.io/teal.data/main/unit-test-report/) -[![Docs 📚](https://github.com/insightsengineering/teal.data/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/teal.data/) -[![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/teal.data/_xml_coverage_reports/data/main/badge.svg)](https://insightsengineering.github.io/teal.data/main/coverage-report/) - -![GitHub forks](https://img.shields.io/github/forks/insightsengineering/teal.data?style=social) -![GitHub repo stars](https://img.shields.io/github/stars/insightsengineering/teal.data?style=social) - -![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/teal.data) -![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/teal.data) -![GitHub last commit](https://img.shields.io/github/last-commit/insightsengineering/teal.data) -![GitHub pull requests](https://img.shields.io/github/issues-pr/insightsengineering/teal.data) -![GitHub repo size](https://img.shields.io/github/repo-size/insightsengineering/teal.data) -![GitHub language count](https://img.shields.io/github/languages/count/insightsengineering/teal.data) +[![Check 🛠](https://github.com/pharmaverse/teal.data/actions/workflows/check.yaml/badge.svg)](https://pharmaverse.github.io/teal.data/main/unit-test-report/) +[![Docs 📚](https://github.com/pharmaverse/teal.data/actions/workflows/docs.yaml/badge.svg)](https://pharmaverse.github.io/teal.data/) +[![Code Coverage 📔](https://raw.githubusercontent.com/pharmaverse/teal.data/_xml_coverage_reports/data/main/badge.svg)](https://pharmaverse.github.io/teal.data/main/coverage-report/) + +![GitHub forks](https://img.shields.io/github/forks/pharmaverse/teal.data?style=social) +![GitHub repo stars](https://img.shields.io/github/stars/pharmaverse/teal.data?style=social) + +![GitHub commit activity](https://img.shields.io/github/commit-activity/m/pharmaverse/teal.data) +![GitHub contributors](https://img.shields.io/github/contributors/pharmaverse/teal.data) +![GitHub last commit](https://img.shields.io/github/last-commit/pharmaverse/teal.data) +![GitHub pull requests](https://img.shields.io/github/issues-pr/pharmaverse/teal.data) +![GitHub repo size](https://img.shields.io/github/repo-size/pharmaverse/teal.data) +![GitHub language count](https://img.shields.io/github/languages/count/pharmaverse/teal.data) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![Current Version](https://img.shields.io/github/r-package/v/insightsengineering/teal.data/main?color=purple\&label=package%20version)](https://github.com/insightsengineering/teal.data/tree/main) -[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/teal.data?color=red\&label=open%20issues)](https://github.com/insightsengineering/teal.data/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc) +[![Current Version](https://img.shields.io/github/r-package/v/pharmaverse/teal.data/main?color=purple\&label=package%20version)](https://github.com/pharmaverse/teal.data/tree/main) +[![Open Issues](https://img.shields.io/github/issues-raw/pharmaverse/teal.data?color=red\&label=open%20issues)](https://github.com/pharmaverse/teal.data/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc) This package is used to create the data needed for `teal` applications. This data can be: @@ -47,12 +47,12 @@ Alternatively, you might want to use the development version. ```r # install.packages("pak") -pak::pak("insightsengineering/teal.data") +pak::pak("pharmaverse/teal.data") ``` ## Usage -To understand how to use this package, please refer to the [Introduction to `teal.data`](https://insightsengineering.github.io/teal.data/latest-tag/articles/teal-data.html) article, which provides multiple examples of code implementation. +To understand how to use this package, please refer to the [Introduction to `teal.data`](https://pharmaverse.github.io/teal.data/latest-tag/articles/teal-data.html) article, which provides multiple examples of code implementation. Below is the showcase of the example usage. diff --git a/_pkgdown.yml b/_pkgdown.yml index 6cb81eb9c..0065ccb0d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,5 +1,5 @@ --- -url: https://insightsengineering.github.io/teal.data +url: https://pharmaverse.github.io/teal.data template: package: nesttemplate @@ -21,7 +21,7 @@ navbar: github: icon: fa-github aria-label: View on Github - href: https://github.com/insightsengineering/teal.data + href: https://github.com/pharmaverse/teal.data articles: - title: Get started diff --git a/man/teal.data-package.Rd b/man/teal.data-package.Rd index 0dc5a86b6..3c3983f04 100644 --- a/man/teal.data-package.Rd +++ b/man/teal.data-package.Rd @@ -14,9 +14,9 @@ it's easily extendable by another data sources. \seealso{ Useful links: \itemize{ - \item \url{https://insightsengineering.github.io/teal.data/} - \item \url{https://github.com/insightsengineering/teal.data/} - \item Report bugs at \url{https://github.com/insightsengineering/teal.data/issues} + \item \url{https://pharmaverse.github.io/teal.data/} + \item \url{https://github.com/pharmaverse/teal.data/} + \item Report bugs at \url{https://github.com/pharmaverse/teal.data/issues} } } diff --git a/man/teal_data-class.Rd b/man/teal_data-class.Rd index d046b4bd3..336f340fd 100644 --- a/man/teal_data-class.Rd +++ b/man/teal_data-class.Rd @@ -39,7 +39,6 @@ Used internally. See \code{\link[=verify]{verify()}} for more details.} \section{Code}{ - Each code element is a character representing one call. Each element is named with the random identifier to make sure uniqueness when joining. Each element has possible attributes: \itemize{ @@ -48,7 +47,6 @@ identifier to make sure uniqueness when joining. Each element has possible attri \item \code{dependency} (\code{character}) names of objects that appear in this call and gets affected by this call, separated by \verb{<-} (objects on LHS of \verb{<-} are affected by this line, and objects on RHS are affecting this line). } - } \keyword{internal} diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml index 4cf2873be..5af0d59b0 100644 --- a/staged_dependencies.yaml +++ b/staged_dependencies.yaml @@ -1,33 +1,33 @@ --- current_repo: - repo: insightsengineering/teal.data + repo: pharmaverse/teal.data host: https://github.com upstream_repos: - insightsengineering/teal.code: - repo: insightsengineering/teal.code + pharmaverse/teal.code: + repo: pharmaverse/teal.code host: https://github.com downstream_repos: - insightsengineering/teal.slice: - repo: insightsengineering/teal.slice + pharmaverse/teal.slice: + repo: pharmaverse/teal.slice host: https://github.com - insightsengineering/teal: - repo: insightsengineering/teal + pharmaverse/teal: + repo: pharmaverse/teal host: https://github.com - insightsengineering/teal.modules.general: - repo: insightsengineering/teal.modules.general + pharmaverse/teal.modules.general: + repo: pharmaverse/teal.modules.general host: https://github.com - insightsengineering/teal.modules.clinical: - repo: insightsengineering/teal.modules.clinical + pharmaverse/teal.modules.clinical: + repo: pharmaverse/teal.modules.clinical host: https://github.com - insightsengineering/teal.transform: - repo: insightsengineering/teal.transform + pharmaverse/teal.transform: + repo: pharmaverse/teal.transform host: https://github.com - insightsengineering/teal.osprey: - repo: insightsengineering/teal.osprey + pharmaverse/teal.osprey: + repo: pharmaverse/teal.osprey host: https://github.com - insightsengineering/teal.modules.hermes: - repo: insightsengineering/teal.modules.hermes + pharmaverse/teal.modules.hermes: + repo: pharmaverse/teal.modules.hermes host: https://github.com - insightsengineering/teal.modules.helios: - repo: insightsengineering/teal.modules.helios + pharmaverse/teal.modules.helios: + repo: pharmaverse/teal.modules.helios host: https://github.com diff --git a/vignettes/join-keys.Rmd b/vignettes/join-keys.Rmd index 9ead04820..7f8974711 100644 --- a/vignettes/join-keys.Rmd +++ b/vignettes/join-keys.Rmd @@ -25,9 +25,9 @@ Refer to the section ["Joining Keys with ADaM Datasets"](#join-keys-in-adam-data ##### Uses of `join_keys` class in _teal_ applications -The primary function of the `join_keys` class in `teal` applications is to facilitate the seamless [merging of datasets](https://insightsengineering.github.io/teal.transform/latest-tag/articles/data-merge.html) using `teal.transform`. +The primary function of the `join_keys` class in `teal` applications is to facilitate the seamless [merging of datasets](https://pharmaverse.github.io/teal.transform/latest-tag/articles/data-merge.html) using `teal.transform`. -Additionally, it plays a role in the data filtering using the _[Filter Panel](https://insightsengineering.github.io/teal/latest-tag/articles/filter-panel.html)_ in a `teal` application. +Additionally, it plays a role in the data filtering using the _[Filter Panel](https://pharmaverse.github.io/teal/latest-tag/articles/filter-panel.html)_ in a `teal` application. The filters applied to a (parent) dataset are also applied to their children. ## Anatomy of `join_keys` diff --git a/vignettes/teal-data.Rmd b/vignettes/teal-data.Rmd index 174bb2633..59a8c9214 100644 --- a/vignettes/teal-data.Rmd +++ b/vignettes/teal-data.Rmd @@ -13,7 +13,7 @@ vignette: > The `teal.data` package specifies the data format used in `teal` applications. -A `teal_data` is meant to be used for reproducibility purposes. The class inherits from [`qenv`](https://insightsengineering.github.io/teal.code/latest-tag/articles/qenv.html) and we encourage to get familiar with [`teal.code`](https://insightsengineering.github.io/teal.code/latest-tag/) first. `teal_data` has following characteristics: +A `teal_data` is meant to be used for reproducibility purposes. The class inherits from [`qenv`](https://pharmaverse.github.io/teal.code/latest-tag/articles/qenv.html) and we encourage to get familiar with [`teal.code`](https://pharmaverse.github.io/teal.code/latest-tag/) first. `teal_data` has following characteristics: - It inherits from the environment and methods such as `$`, `get()`, `ls()`, `as.list()` work out of the box. - `teal_data` is a locked environment, and data modification is only possible through the `teal.code::eval_code()` and `within.qenv()` functions.