Merge branch 'main' into refactor

.Rbuildignore

@@ -1,3 +1,4 @@
+LICENSE
 ^renv$
 ^renv\.lock$
 CODE_OF_CONDUCT.md

.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/index.html
-[articles]: https://insightsengineering.github.io/teal/main/articles/index.html
-[license]: https://insightsengineering.github.io/teal/main/LICENSE-text.html
+[docs]: https://insightsengineering.github.io/teal/latest-tag/index.html
+[articles]: https://insightsengineering.github.io/teal/latest-tag/articles/index.html
+[license]: https://insightsengineering.github.io/teal/latest-tag/LICENSE-text.html
 [insights]: https://github.com/insightsengineering/teal/pulse

.github/ISSUE_TEMPLATE/bug.yml

@@ -33,15 +33,15 @@ 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/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal/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/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal/latest-tag/CONTRIBUTING.html)
       options:
         - label: I agree to follow this project's Contribution Guidelines.
           required: true

.github/ISSUE_TEMPLATE/feature.yml

@@ -13,15 +13,15 @@ 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/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal/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/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal/latest-tag/CONTRIBUTING.html)
       options:
         - label: I agree to follow this project's Contribution Guidelines.
           required: true

.github/ISSUE_TEMPLATE/question.yml

@@ -13,15 +13,15 @@ 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/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal/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/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal/latest-tag/CONTRIBUTING.html)
       options:
         - label: I agree to follow this project's Contribution Guidelines.
           required: true

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal
 Title: Exploratory Web Apps for Analyzing Clinical Trials Data
-Version: 0.14.0.9004
-Date: 2023-08-24
+Version: 0.14.0.9007
+Date: 2023-09-13
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -20,11 +20,14 @@ Authors@R: c(
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
     person("Maximilian", "Mordig", role = "ctb")
   )
-Description: A shiny based interactive exploration framework for analyzing
-    clinical trials data. teal currently provides a dynamic filtering
-    facility and different data viewers. teal shiny applications are built
-    using standard shiny modules.
-License: Apache License 2.0 | file LICENSE
+Description: A 'shiny' based interactive exploration framework for
+    analyzing clinical trials data. 'teal' currently provides a dynamic
+    filtering facility and different data viewers. 'teal' 'shiny'
+    applications are built using standard 'shiny' modules.
+License: Apache License 2.0
+URL: https://insightsengineering.github.io/teal/,
+    https://github.com/insightsengineering/teal/
+BugReports: https://github.com/insightsengineering/teal/issues
 Depends:
     R (>= 4.0),
     shiny (>= 1.7.0),

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(c,teal_slices)
 S3method(get_code,tdata)
 S3method(get_join_keys,default)
 S3method(get_join_keys,tdata)

NEWS.md

@@ -1,4 +1,4 @@
-# teal 0.14.0.9004
+# teal 0.14.0.9007
 
 ### Miscellaneous
 

R/teal_slices.R

@@ -110,6 +110,28 @@ as.teal_slices <- function(x) { # nolint
 }
 
 
+#' @rdname teal_slices
+#' @export
+#' @keywords internal
+#'
+c.teal_slices <- function(...) {
+  x <- list(...)
+  checkmate::assert_true(all(vapply(x, is.teal_slices, logical(1L))), .var.name = "all arguments are teal_slices")
+
+  all_attributes <- lapply(x, attributes)
+  all_attributes <- coalesce_r(all_attributes)
+  all_attributes <- all_attributes[names(all_attributes) != "class"]
+
+  do.call(
+    teal_slices,
+    c(
+      unique(unlist(x, recursive = FALSE)),
+      all_attributes
+    )
+  )
+}
+
+
 #' Deep copy `teal_slices`
 #'
 #' it's important to create a new copy of `teal_slices` when

R/zzz.R

@@ -25,8 +25,10 @@
 
 # Use non-exported function(s) from teal.slice.
 # This is a temporary measure and will be removed two release cycles from now (now meaning 0.13.0).
-list_to_teal_slices <- getFromNamespace("list_to_teal_slices", "teal.slice") # nolint
+list_to_teal_slices <- getFromNamespace("list_to_teal_slices", "teal.slice")
 # This one is here because setdiff_teal_slice should not be exported from teal.slice.
 setdiff_teal_slices <- getFromNamespace("setdiff_teal_slices", "teal.slice")
+# This one is here because it is needed by c.teal_slices but we don't want it exported from teal.slice.
+coalesce_r <- getFromNamespace("coalesce_r", "teal.slice")
 # all *Block objects are private in teal.reporter
 RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") # nolint

README.md

@@ -28,7 +28,7 @@
     -    Related datasets, for example a set of `data.frames` with key columns to enable data joins
     -    `MultiAssayExperiment` objects which are R data structures for representing and analyzing multi-omics experiments
 -   `teal` modules:
-    -   `teal modules` are shiny modules built within the `teal` framework that specify analysis to be performed. For example, it can be a module for exploring outliers in the data, or a module for visualizing the data in line plots. Although these can be created from scratch, lost of `teal` modules have been released and we recommend starting with modules found in the following packages:
+    -   `teal modules` are shiny modules built within the `teal` framework that specify analysis to be performed. For example, it can be a module for exploring outliers in the data, or a module for visualizing the data in line plots. Although these can be created from scratch, many `teal` modules have been released and we recommend starting with modules found in the following packages:
         -   [`teal.modules.general`](https://insightsengineering.github.io/teal.modules.general/): general modules for exploring relational/independent/`CDISC` data
         -   [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical/): modules specific to `CDISC` data and clinical trial reporting
         -   [`teal.modules.hermes`](https://insightsengineering.github.io/teal.modules.hermes/): modules for analyzing `MultiAssayExperiment` objects
@@ -103,9 +103,9 @@ shinyApp(app$ui, app$server)
 
 ![App recording](man/figures/readme_app.gif)
 
-Please see [`teal` gallery](https://insightsengineering.github.io/teal.gallery) and [TLG Catalog](https://insightsengineering.github.io/tlg-catalog) to see examples of `teal` apps.
+Please see [`teal.gallery`](https://insightsengineering.github.io/teal.gallery) and [TLG Catalog](https://insightsengineering.github.io/tlg-catalog) to see examples of `teal` apps.
 
-Please start with the ["Getting Started" article](https://insightsengineering.github.io/teal/articles/teal.html) and then other [package vignettes](https://insightsengineering.github.io/teal/articles/index.html) for more detailed guide.
+Please start with the ["Getting Started" article](https://insightsengineering.github.io/teal/latest-tag/articles/teal.html) and then other [package vignettes](https://insightsengineering.github.io/teal/articles/index.html) for more detailed guide.
 
 ## Getting help
 

_pkgdown.yml

@@ -21,49 +21,58 @@ navbar:
       href: https://github.com/insightsengineering/teal
 
 articles:
-  - title: Articles
+  - title: Get Started
     navbar: ~
     contents:
       - teal
+  - title: Articles
+    navbar: Using teal
+    contents:
       - filter-panel
-      - including-general-data-in-teal
+      - teal-options
+      - teal-bs-themes
+  - title: Articles
+    navbar: Data in teal Apps
+    contents:
       - including-adam-data-in-teal
+      - including-general-data-in-teal
       - including-mae-data-in-teal
       - preprocessing-data
+  - title: Articles
+    navbar: Extending teal
+    contents:
       - creating-custom-modules
       - adding-support-for-reporting
-      - teal-options
-      - teal-bs-themes
 
 reference:
-  - title: teal Core Functions
-    desc: These are the main functions needed to build a teal app.
+  - title: Core `teal` Functions
+    desc: Main functions needed to build a `teal` app
     contents:
       - init
       - module
       - modules
       - srv_teal_with_splash
       - ui_teal_with_splash
       - teal_slices
-  - title: Example module
-    desc: A simple example teal module
+  - title: Example Module
+    desc: A simple `teal` module
     contents:
       - example_module
-  - title: Creating reports
+  - title: Creating Reports
     contents:
       - reporter_previewer_module
       - TealReportCard
-  - title: Functions for module developers
+  - title: Functions for Module Developers
     contents:
       - tdata
       - get_code_tdata
       - get_join_keys
       - get_metadata
       - tdata2env
       - show_rcode_modal
-  # - title: Functions moved to other packages
-    # desc: These functions have been moved from teal and will be deprecated.
+  # - title: Functions Moved to Other Packages
+    # desc: These functions have been moved from teal and will be deprecated
     # contents:
-  - title: Validation functions
+  - title: Validation Functions
     contents:
       - starts_with("validate_")

inst/WORDLIST

@@ -1,18 +1,20 @@
+ADaM
 Forkers
 Hoffmann
+MultiAssayExperiment
 TLG
+Theming
 UI
 UIs
 UX
 cloneable
 funder
 omics
 pharmaverse
-preselected
+preprocessed
 programmatically
 repo
 reproducibility
 tabsetted
 themer
-theming
 uncheck

vignettes/adding-support-for-reporting.Rmd

@@ -1,12 +1,11 @@
 ---
-title: "Adding support for Reporting to custom modules"
+title: "Adding Support for Reporting to Custom Modules"
 author: "NEST CoreDev"
-date: "2022-05-23"
 output: 
   rmarkdown::html_vignette:
     toc: true
 vignette: >
-  %\VignetteIndexEntry{Adding support for Reporting to custom modules}
+  %\VignetteIndexEntry{Adding Support for Reporting to Custom Modules}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -15,7 +14,7 @@ vignette: >
 
 The `teal` package offers an integrated reporting feature utilizing the `teal.reporter` package. For a comprehensive explanation of the reporting functionality itself, please refer to the documentation therein.
 
-This article is intended for module developers and aims to provide guidance on enriching a custom `teal` module with an automatic reporting feature. This enhancement enables users to incorporate snapshots of the module outputs into a report which can then be reviewed in another module automatically provided by `teal`. Thus the app user can interact with the report.
+This article is intended for module developers and aims to provide guidance on enhancing a custom `teal` module with an automatic reporting feature. This enhancement enables users to incorporate snapshots of the module outputs into a report which can then be reviewed in another module automatically provided by `teal`. Thus the app user can interact with the report.
 
 The responsibilities of a module developer include:
 

vignettes/creating-custom-modules.Rmd

@@ -1,7 +1,6 @@
 ---
 title: "Creating Custom Modules"
 author: "Nikolas Burkoff"
-date: "2022-03-24"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Creating Custom Modules}
@@ -11,8 +10,7 @@ vignette: >
 
 ## Introduction
 
-The `teal` framework provides a large number of analysis modules to be incorporated into `teal` applications.
-However, it is also possible to create your own modules using the `module()` function.
+The `teal` framework provides a large number of analysis modules to be incorporated into `teal` applications. However, it is also possible to create your own modules using the `module` function.
 
 Here is an implementation of a simple module:
 
@@ -46,11 +44,9 @@ which can be added into `teal` apps using `example_module(label = "Label for tab
 
 ### UI function
 
-This function contains the UI required for the module. It should be a function with at least the arguments `id`.
-It can also contain the argument `data` for access to the application data. See the server section below for more details.
+This function contains the UI required for the module. It should be a function with at least the arguments `id`. It can also contain the argument `data` for access to the application data. See the server section below for more details.
 
-The UI function can contain standard UI components alongside additional widgets provided by the `teal.widgets` package.
-In the example above we are using the `standard_layout` function of `teal.widgets` which generates a layout
+The UI function can contain standard UI components alongside additional widgets provided by the `teal.widgets` package. In the example above we are using the `standard_layout` function of `teal.widgets` which generates a layout
 including an encoding panel on the left and main output covering the rest of the module's UI.
 
 ### Server function
@@ -70,18 +66,14 @@ function(id,
 
 ```
 
-When used inside a teal application called with `teal::init`, the `data` argument is a named list of reactive data.frames
-containing the data after having been filtered through the filter panel. It is of the `tdata` type and can be created using
-the `new_tdata` function.
+When used inside a `teal` application called with `init`, the `data` argument is a named list of reactive `data.frame`s containing the data after having been filtered through the filter panel.  It is of the `tdata` type and can be created using the `new_tdata` function.
 
 ## A More Complicated Example
 
 The `teal` framework also provides:
 
-- A way to create modules which then generate the R code needed to reproduce their outputs;
-these modules use the [`teal.code`](https://insightsengineering.github.io/teal.code/) package.
-- A way extract from and merge related datasets using the
-[`teal.transform`](https://insightsengineering.github.io/teal.transform/) package.
+- A way to create modules which then generate the R code needed to reproduce their outputs; these modules use the [`teal.code`](https://insightsengineering.github.io/teal.code/) package.
+- A way extract from and merge related datasets using the [`teal.transform`](https://insightsengineering.github.io/teal.transform/) package.
 - A way to allow app creators to customize your modules also using `teal.transform`.
 
 The annotated example below demonstrates these features within a simple histogram module, allowing app developers to choose the data and columns that their app users can select for display in a histogram.
@@ -207,9 +199,7 @@ if (interactive()) {
 
 ## `shiny` input cycle
 
-When teal modules are run inside the `teal::init` the initial shiny input cycle is empty for each of them.
-In practice, this means that some inputs might be initialized with `NULL` value, unnecessary triggering some
-observers. A developer has to be aware of this situation as often It will require `shiny::req` or `ignoreInit` argument in observers or `reactive` expressions. This side effect is caused by the `shiny::insertUI` function. We are aware of this inconvenience and have already started to look for a solution.
+When `teal` modules are run inside the `init` the initial shiny input cycle is empty for each of them. In practice, this means that some inputs might be initialized with `NULL` value, unnecessary triggering some observers. A developer has to be aware of this situation as often it will require `shiny::req` or `ignoreInit` argument in observers or `reactive` expressions. This side effect is caused by the `shiny::insertUI` function. We are aware of this inconvenience and have already started to look for a solution.
 
 ## Adding reporting to a module
 Refer to `vignette("adding_support_for_reporting")` to read about adding support for reporting in your `teal` module.