diff --git a/.Rbuildignore b/.Rbuildignore index 2057bf122..d74a07861 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,4 @@ +LICENSE ^renv$ ^renv\.lock$ CODE_OF_CONDUCT.md diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 217e7a9f6..ac91f0e80 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -94,17 +94,17 @@ This repository follows the standard [`tidyverse` style guide](https://style.tid ### Dependency management -Lightweight is the right weight. This repository follows [tinyverse](https://www.tinyverse.org/) recommedations of limiting dependencies to minimum. +Lightweight is the right weight. This repository follows [tinyverse](https://www.tinyverse.org/) recommendations of limiting dependencies to minimum. ### Dependency version management -If the code is not compatible with all (!) historical versions of a given dependenct package, it is required to specify minimal version in the `DESCRIPTION` file. In particular: if the development version requires (imports) the development version of another package - it is required to put `abc (>= 1.2.3.9000)`. +If the code is not compatible with all (!) historical versions of a given dependency package, it is required to specify minimal version in the `DESCRIPTION` file. In particular: if the development version requires (imports) the development version of another package - it is required to put `abc (>= 1.2.3.9000)`. ### Recommended development environment & tools #### R & package versions -We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the `R CMD check` GitHub Action execution log - there is a step that prints out the R `sessionInfo()`. +We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and `BioConductor`. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the `R CMD check` GitHub Action execution log - there is a step that prints out the R `sessionInfo()`. If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports. @@ -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.slice/index.html -[articles]: https://insightsengineering.github.io/teal.slice/main/articles/index.html -[license]: https://insightsengineering.github.io/teal.slice/main/LICENSE-text.html +[docs]: https://insightsengineering.github.io/teal.slice/latest-tag/index.html +[articles]: https://insightsengineering.github.io/teal.slice/latest-tag/articles/index.html +[license]: https://insightsengineering.github.io/teal.slice/latest-tag/LICENSE-text.html [insights]: https://github.com/insightsengineering/teal.slice/pulse diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml index bb27ac26f..040a1c931 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.slice/CODE_OF_CONDUCT.html) + description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/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.slice/CONTRIBUTING.html) + description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/latest-tag/CONTRIBUTING.html) options: - label: I agree to follow this project's Contribution Guidelines. required: true diff --git a/.github/ISSUE_TEMPLATE/feature.yml b/.github/ISSUE_TEMPLATE/feature.yml index 1273cde72..87a57ba6f 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.slice/CODE_OF_CONDUCT.html) + description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/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.slice/CONTRIBUTING.html) + description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/latest-tag/CONTRIBUTING.html) options: - label: I agree to follow this project's Contribution Guidelines. required: true diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml index a66c26255..3be20b7ae 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.slice/CODE_OF_CONDUCT.html) + description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/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.slice/CONTRIBUTING.html) + description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/latest-tag/CONTRIBUTING.html) options: - label: I agree to follow this project's Contribution Guidelines. required: true diff --git a/DESCRIPTION b/DESCRIPTION index 1309dc719..69498e730 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Type: Package Package: teal.slice -Title: Filter Module for `teal` Applications +Title: Filter Module for 'teal' Applications Version: 0.4.0.9012 Date: 2023-09-08 Authors@R: c( @@ -19,8 +19,13 @@ Authors@R: c( person("Junlue", "Zhao", role = "aut"), person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")) ) -Description: Filter module for teal applications. -License: Apache License 2.0 | file LICENSE +Description: + Module containing filter panel for 'teal' applications. Allows for interactive filtering of data stored in + 'data.frame' and 'MultiAssayExperiment' objects. Also displays filtered and unfiltered observation counts. +License: Apache License 2.0 +URL: https://insightsengineering.github.io/teal.slice/, + https://github.com/insightsengineering/teal.slice/ +BugReports: https://github.com/insightsengineering/teal.slice/issues Depends: R (>= 4.0), shiny diff --git a/README.md b/README.md index 75280bed2..2bc460ec1 100644 --- a/README.md +++ b/README.md @@ -27,17 +27,31 @@ ## Installation -From July 2023 `insightsengineering` packages are available on [r-universe](https://r-universe.dev/). - ```r # stable versions install.packages('teal.slice', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org')) +# install.packages("pak") +pak::pak("insightsengineering/teal.slice@*release") +``` + +Alternatively, you might want to use the development version available on [r-universe](https://r-universe.dev/). + +```r # beta versions install.packages('teal.slice', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org')) + +# install.packages("pak") +pak::pak("insightsengineering/teal.slice") ``` -See package vignettes `browseVignettes(package = "teal.slice")` for usage of this package. +## Usage + +To understand how to use this package, please refer to the [Introduction to teal.slice](https://insightsengineering.github.io/teal.slice/latest-tag/articles/teal-slice.html) article, which provides multiple examples of code implementation. + +## Getting help + +If you encounter a bug or you have a feature request - please file an issue. For questions, discussions and staying up to date, please use the "teal" channel in the [`pharmaverse` slack workspace](https://pharmaverse.slack.com). ## Stargazers and Forkers diff --git a/inst/WORDLIST b/inst/WORDLIST index a7fc5fd14..247ee210e 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,10 +1,20 @@ -Forkers -Hoffmann -UI cloneable +Forkers funder +github +Hoffmann +https +insightsengineering +io +Pre programmatically repo reproducibility +sessionInfo subclasses subtype +textarea +tinyverse +UI +upvote +sessionInfo diff --git a/vignettes/filter-panel-for-developers.Rmd b/vignettes/filter-panel-for-developers.Rmd index e5b8dd5d8..e7aca5023 100644 --- a/vignettes/filter-panel-for-developers.Rmd +++ b/vignettes/filter-panel-for-developers.Rmd @@ -1,7 +1,6 @@ --- title: "Filter panel for developers" author: "NEST Core Dev Team" -date: "10/07/2023" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Filter panel for developers} diff --git a/vignettes/teal-slice-classes.Rmd b/vignettes/teal-slice-classes.Rmd index c69657ea6..af0604ff6 100644 --- a/vignettes/teal-slice-classes.Rmd +++ b/vignettes/teal-slice-classes.Rmd @@ -1,7 +1,6 @@ --- title: "teal.slice classes" author: "NEST Core Dev Team" -date: "10/07/2023" output: rmarkdown::html_vignette: toc: true diff --git a/vignettes/teal-slice.Rmd b/vignettes/teal-slice.Rmd index 1c117d98b..c814127e0 100644 --- a/vignettes/teal-slice.Rmd +++ b/vignettes/teal-slice.Rmd @@ -1,7 +1,6 @@ --- title: "Introduction to teal.slice" author: "NEST Core Dev Team" -date: "01/07/2022" output: rmarkdown::html_vignette: toc: true