Replace insightsengineering with pharmaverse

.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.
 
 <!-- urls -->
-[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

.github/ISSUE_TEMPLATE/bug.yml

@@ -33,23 +33,23 @@ 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
   - type: checkboxes
     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
   - type: checkboxes
     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

.github/ISSUE_TEMPLATE/feature.yml

@@ -13,23 +13,23 @@ 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
   - type: checkboxes
     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
   - type: checkboxes
     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

.github/ISSUE_TEMPLATE/question.yml

@@ -13,23 +13,23 @@ 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
   - type: checkboxes
     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
   - type: checkboxes
     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

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
           - methods
           - rlang
           - stats
-          - insightsengineering/teal.code
+          - pharmaverse/teal.code
           - utils
           - yaml
       - id: spell-check

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

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)

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

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)
 <!-- end badges -->
 
 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.
 

_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

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

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`

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.