624 PACKAGE LEVEL pre-release activities (#639)

Part of #624 

* [x] Review and update README.md 
    * [x] check example code
    * [x] add CRAN BADGES
    * [x] update installation guidelines
    * [x] add Getting Help Section
* [x]  Review and update DESCRIPTION
* [x] Package `Title` is not duplicated in Package `Description` in
DESCRIPTION file (e.g. this happens in teal.slice currently)
* [x] All package names in `Title` and `Description` fields of
DESCRIPTION file are quoted with `'`
* [x] LICENSE file is not mentioned in License field and LICENSE is add
to `.Rbuildignore`
* [x] Run urlchecker::url_check() to identify broken links and fix
* [x] Run R CMD check --as-cran make sure everything pass
* [x] You have checked the Package Release Template
https://github.com/insightsengineering/teal.reporter/pull/205/files
* [x] Make sure all `teal.*` mentions are lower-cased and quoted
* [x] Make Sure inst/WORDLIST is minimalized
* [x] Make sure each link to our documentation hosted with pkgdown on
github pages do not have `/main/` in the address but it has `/latest/`
instead, so we always expose the documentation of the latest release and
not what's currently on main branch but not yet released
* [x] Remove exception in `.lintr: indentation_linter = NULL`
* [x] `@noMd` (in favor of `Roxygen: list(markdown = TRUE)` in
`DESCRIPTION`)

---------

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
Signed-off-by: Aleksander Chlebowski <114988527+chlebowa@users.noreply.github.com>
Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Signed-off-by: kartikeya kirar <kirar.kartikeya1@gmail.com>
Signed-off-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Co-authored-by: kartikeya kirar <kirar.kartikeya1@gmail.com>
Co-authored-by: Aleksander Chlebowski <114988527+chlebowa@users.noreply.github.com>
Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Co-authored-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Co-authored-by: go_gonzo <dawid.kaledkowski@gmail.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: kartikeya <kartikeya.kirar@unicle.life>
Co-authored-by: Aleksander Chlebowski <aleksander.chlebowski@contractors.roche.com>
Co-authored-by: Dawid Kałędkowski <6959016+gogonzo@users.noreply.github.com>

.Rbuildignore

@@ -28,6 +28,7 @@ SECURITY.md
 ^Jenkinsfile$
 ^logs$
 ^Makefile$
+^man/roxygen$
 ^man-roxygen$
 ^Meta$
 ^outputdir$
@@ -40,6 +41,7 @@ SECURITY.md
 ^staged_dependencies\.yaml$
 ^\.gitlab-ci\.yml$
 ^LICENSE\.md$
+LICENSE
 coverage.*
 ^sample_files$
 ^\.pre-commit-config\.yaml

.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.modules.general/index.html
-[articles]: https://insightsengineering.github.io/teal.modules.general/main/articles/index.html
-[license]: https://insightsengineering.github.io/teal.modules.general/main/LICENSE-text.html
+[docs]: https://insightsengineering.github.io/teal.modules.general/latest-tag/
+[articles]: https://insightsengineering.github.io/teal.modules.general/latest-tag/articles/index.html
+[license]: https://insightsengineering.github.io/teal.modules.general/latest-tag/LICENSE-text.html
 [insights]: https://github.com/insightsengineering/teal.modules.general/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.modules.general/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.modules.general/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.modules.general/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.modules.general/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.modules.general/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.modules.general/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.modules.general/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.modules.general/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.modules.general/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.modules.general/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.modules.general/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.modules.general/latest-tag/CONTRIBUTING.html)
       options:
         - label: I agree to follow this project's Contribution Guidelines.
           required: true

.lintr

@@ -2,5 +2,5 @@ linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
   cyclocomp_linter = NULL,
   object_usage_linter = NULL,
-  indentation_linter = NULL
+  object_name_linter = object_name_linter(styles = c("snake_case", "symbols"), regexes = c(ANL = "^ANL_?[0-9A-Z_]*$", ADaM = "^r?AD[A-Z]{2,3}_?[0-9]*$"))
   )

.pre-commit-config.yaml

@@ -18,18 +18,18 @@ repos:
           - ggmosaic
           - ggplot2
           - shiny
-          - shinyTree
-          - insightsengineering/teal
+          - teal
+          - teal.transform
           - checkmate
           - dplyr
           - DT
           - forcats
           - ggrepel
           - grid
           - logger
-          - magrittr
           - scales
           - shinyjs
+          - shinyTree
           - shinyvalidate
           - shinyWidgets
           - stats
@@ -39,12 +39,10 @@ repos:
           - insightsengineering/teal.logger
           - insightsengineering/teal.reporter
           - insightsengineering/teal.slice
-          - insightsengineering/teal.transform
           - insightsengineering/teal.widgets
           - tern
           - tibble
           - tidyr
-          - tidyselect
           - utils
 
       - id: spell-check

DESCRIPTION

@@ -1,6 +1,6 @@
 Type: Package
 Package: teal.modules.general
-Title: General Modules to Add to a `teal` Application
+Title: General Modules for 'teal' Applications
 Version: 0.2.16.9029
 Date: 2024-02-28
 Authors@R: c(
@@ -13,8 +13,11 @@ Authors@R: c(
     person("Nikolas", "Burkoff", role = "aut"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
-Description: General Purpose Teal Modules.
-License: Apache License 2.0 | file LICENSE
+Description: Prebuilt 'shiny' modules containing tools for viewing data,
+    visualizing data, understanding missing and outlier values within your
+    data and performing simple data analysis.  This extends 'teal'
+    framework that supports reproducible research and analysis.
+License: Apache License 2.0
 URL: https://insightsengineering.github.io/teal.modules.general/,
     https://github.com/insightsengineering/teal.modules.general/
 BugReports: 
@@ -24,7 +27,6 @@ Depends:
     ggplot2 (>= 3.4.0),
     R (>= 3.6),
     shiny (>= 1.6.0),
-    shinyTree,
     teal (>= 0.14.0.9027),
     teal.transform (>= 0.4.0.9011)
 Imports:
@@ -34,21 +36,22 @@ Imports:
     forcats (>= 1.0.0),
     grid,
     logger (>= 0.2.0),
-    magrittr (>= 1.5),
     scales,
     shinyjs,
+    shinyTree (>= 0.2.8),
     shinyvalidate,
     shinyWidgets (>= 0.5.1),
     stats,
     stringr (>= 1.4.1),
     teal.code (>= 0.4.1.9009),
+    teal.data (>= 0.3.0.9018),
     teal.logger (>= 0.1.1),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),
     tern (>= 0.7.10),
     tibble (>= 2.0.0),
     tidyr (>= 0.8.3),
-    tidyselect,
+    tools,
     utils
 Suggests:
     broom (>= 0.7.10),
@@ -64,24 +67,23 @@ Suggests:
     knitr (>= 1.42),
     lattice (>= 0.18-4),
     MASS,
-    methods,
     nestcolor (>= 0.1.0),
     rlang (>= 1.0.0),
     rtables (>= 0.5.1),
     sparkline,
-    teal.data (>= 0.3.0.9018),
     testthat (>= 3.0.4)
 VignetteBuilder:
     knitr
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
-    rstudio/shiny, shinyTree/shinyTree, insightsengineering/teal,
+    rstudio/shiny, insightsengineering/teal, insightsengineering/teal.transform,
     mllg/checkmate, tidyverse/dplyr, rstudio/DT, tidyverse/forcats,
-    daroczig/logger, tidyverse/magrittr, r-lib/scales, daattali/shinyjs,
+    daroczig/logger, r-lib/scales, daattali/shinyjs,
+    shinyTree/shinyTree,
     rstudio/shinyvalidate, dreamRs/shinyWidgets, tidyverse/stringr,
-    insightsengineering/teal.code, insightsengineering/teal.logger,
-    insightsengineering/teal.reporter, insightsengineering/teal.transform,
+    insightsengineering/teal.code, insightsengineering/teal.data,
+    insightsengineering/teal.logger, insightsengineering/teal.reporter,
     insightsengineering/teal.widgets, insightsengineering/tern,
-    tidyverse/tibble, tidyverse/tidyr, r-lib/tidyselect, tidymodels/broom,
+    tidyverse/tibble, tidyverse/tidyr, tidymodels/broom,
     daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
     slowkow/ggrepel, baddstats/goftest, gridExtra, ramnathv/htmlwidgets,
     jeroen/jsonlite, yihui/knitr, deepayan/lattice, MASS,

NAMESPACE

@@ -28,7 +28,6 @@ export(tm_variable_browser)
 import(ggmosaic)
 import(ggplot2)
 import(shiny)
-import(shinyTree)
 import(teal)
 import(teal.transform)
-importFrom(magrittr,"%>%")
+importFrom(dplyr,"%>%")

R/data.R

@@ -1,64 +1,39 @@
 #' Random adverse events
-#'
-#' @description Random adverse events
 #' @docType data
-#'
 #' @usage rADAE
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADAE
 "rADAE"
 
 #' Random lab analysis
-#'
-#' @description Random lab analysis
 #' @docType data
-#'
 #' @usage rADLB
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADLB
 "rADLB"
 
 #' Random response
-#'
-#' @description Random response
 #' @docType data
-#'
 #' @usage rADRS
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADRS
 "rADRS"
 
 #' Random patient listing
-#'
-#' @description Random patient listing
 #' @docType data
-#'
 #' @usage rADSL
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADSL
 "rADSL"
 
-#' Random Time to Event Analysis Dataset
-#'
-#' @description Random Time to Event Analysis Dataset
+#' Random time to event analysis dataset
 #' @docType data
-#'
 #' @usage rADTTE
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADTTE
 "rADTTE"

R/teal.modules.general.R

@@ -1,15 +1,14 @@
-#' teal.modules.general: General modules to add to a teal application
+#' `teal.modules.general`: General modules to add to a `teal` application
 #'
 #' The modules in this package are generic modules that should work with any data set
 #' (not necessarily for clinical trials data).
 #'
 #' @import ggplot2
 #' @import ggmosaic
 #' @import shiny
-#' @import shinyTree
 #' @import teal
 #' @import teal.transform
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 #'
 #'
 #' @name teal.modules.general
@@ -19,7 +18,7 @@
 # nolint start
 # Note ggmosaic (version <= 0.3.3) needs to be in DEPENDS as the following does not work if it is imported
 # df <- data.frame(x = c("A", "B", "C", "A"), y = c("Z", "Z", "W", "W"))
-# ggplot(df) +  ggmosaic::geom_mosaic(aes(x = ggmosaic::product(x), fill = y))
+# ggplot(df) + ggmosaic::geom_mosaic(aes(x = ggmosaic::product(x), fill = y))
 # nolint end
 
 # Needed to avoid R CMD note on no visible binding