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624 PACKAGE LEVEL pre-release activities #639

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Mar 1, 2024
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0072964
initial DESCRIPTION curation
m7pr Feb 19, 2024
e5813a9
change DESCRIPTION's Title and Description fields
m7pr Feb 19, 2024
72164f7
revisit README file
m7pr Feb 19, 2024
549b0fa
change Teal to `teal`
m7pr Feb 19, 2024
b3845f0
check /main/ to /latest-tag/ in workflows files
m7pr Feb 19, 2024
7537fcc
add latest-tag/ to urls
m7pr Feb 19, 2024
7d0ff63
Remove exception in .lintr: indentation_linter = NULL
m7pr Feb 19, 2024
6767f42
add LICENSE to .Rbuildignore
m7pr Feb 19, 2024
4d1d249
Merge branch 'main' into pre-release@main
m7pr Feb 19, 2024
ac43d53
extend WORDLIST
m7pr Feb 20, 2024
ee2d08b
Update vignettes/using-association-plot.Rmd
m7pr Feb 20, 2024
f8d3583
revert template changes
m7pr Feb 20, 2024
3bd9b71
Merge branch 'pre-release@main' of https://github.com/insightsenginee…
m7pr Feb 20, 2024
c57bc17
642 unused functions (#659)
chlebowa Feb 21, 2024
400d8cd
Adds common `@return` for modules and corrects linting (#670)
averissimo Feb 22, 2024
ec85748
Merge branch 'main' into pre-release@main
m7pr Feb 22, 2024
b67b957
pre-release: Typo with missing a full stop (#671)
averissimo Feb 22, 2024
57a1122
643 potential removal of dependencies (#663)
chlebowa Feb 22, 2024
2d89cfb
missed commit in #663 (#672)
chlebowa Feb 22, 2024
2ac9a4d
658 remove var labels@pre release@main (#673)
chlebowa Feb 23, 2024
3118bcb
docs: update the vignette author to "NEST CoreDev" (#679)
vedhav Feb 26, 2024
109065e
pre-release `tm_variable_browser` document update (#652)
kartikeyakirar Feb 26, 2024
b6f0d28
pre-release `tm_g_bivariate` document update (#660)
kartikeyakirar Feb 26, 2024
cb07cce
pre-release `tm_g_response` document update (#666)
averissimo Feb 26, 2024
51ef394
pre-release `tm_file_viewer` document update (#665)
averissimo Feb 26, 2024
0cb0b56
pre-release `tm_t_crosstable` document update (#664)
averissimo Feb 26, 2024
91d9e02
pre-release `tm_a_pca` document update (#646)
kartikeyakirar Feb 26, 2024
2e77e2a
pre-release `tm_outliers` document update (#653)
kartikeyakirar Feb 26, 2024
d5fbe8c
pre-release `tm_front_page` document update (#654)
kartikeyakirar Feb 26, 2024
33714ae
pre-release `tm_g_scatterplot` document update (#657)
kartikeyakirar Feb 26, 2024
2d70eab
pre-release ` tm_data_table` document update (#667)
kartikeyakirar Feb 26, 2024
b382d4c
pre-release other utils functions document update (#676)
kartikeyakirar Feb 26, 2024
4a34ee8
pre-release `tm_missing_data` document update (#668)
kartikeyakirar Feb 26, 2024
39ede58
pre-release `tm_g_scatterplotmatrix` document update (#661)
kartikeyakirar Feb 26, 2024
da6ab63
backticks for ggplot2
m7pr Feb 26, 2024
658743c
WORDLIST fixes
m7pr Feb 26, 2024
8d02d0c
pre-release: Update verdpecheck and pre-commit (#683)
averissimo Feb 26, 2024
7c6cde0
superlint fix
m7pr Feb 26, 2024
672b217
Merge branch 'pre-release@main' of https://github.com/insightsenginee…
m7pr Feb 26, 2024
b3ed9fa
pre-release `tm_g_association` document update (#656)
kartikeyakirar Feb 27, 2024
446ce56
pre-release `tm_g_distribution` document update (#669)
kartikeyakirar Feb 27, 2024
f097677
pre-release `tm_a_regression` document update (#655)
kartikeyakirar Feb 27, 2024
882a8d0
lintr issues
m7pr Feb 27, 2024
5fe302b
Standardise function titles similar to what we have in tmc (#691)
vedhav Feb 27, 2024
0cafa8f
Merge branch 'main' into pre-release@main
gogonzo Feb 27, 2024
3917094
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
dependabot-preview[bot] Feb 27, 2024
804d79a
pre-release vignettes review (#681)
kartikeyakirar Feb 28, 2024
ee8cd14
641 non exported functions (#680)
chlebowa Feb 28, 2024
fcd025a
missing comma
Feb 28, 2024
87f6eee
removed @noRd tags and added return from shared_params
kartikeyakirar Feb 28, 2024
bddee61
Update to roxygen2 `@template` for `ggplot2_args` arguments (#694)
averissimo Feb 28, 2024
7da5cae
Update R/tm_file_viewer.R
m7pr Feb 28, 2024
c47b104
Merge branch 'main' into pre-release@main
vedhav Feb 28, 2024
bc56c51
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
dependabot-preview[bot] Feb 28, 2024
65b1c06
Merge branch 'main' into pre-release@main
m7pr Feb 29, 2024
e5fc4c9
standardize the notation for optional parameters (#698)
kartikeyakirar Feb 29, 2024
bf9ef13
adding package check arg
kartikeyakirar Feb 29, 2024
962e059
removing non standard dir to Rbuildignore
kartikeyakirar Feb 29, 2024
3929aad
701 fixing the validation issue for x/y variable selection in `tm_g_b…
kartikeyakirar Mar 1, 2024
6aa97c0
removing tdata instance
kartikeyakirar Mar 1, 2024
cbae779
adding backtick on shiny keyword
kartikeyakirar Mar 1, 2024
8151b06
Adds missing assertions and reorganizes them (#696)
averissimo Mar 1, 2024
e209bf3
remove `latest-tag` from REPO url. this should onl stay in WEBSITE url
m7pr Mar 1, 2024
3f9889f
Merge branch 'pre-release@main' of https://github.com/insightsenginee…
m7pr Mar 1, 2024
92a25a5
Update .pre-commit-config.yaml
m7pr Mar 1, 2024
2aa7e85
Update .github/workflows/check.yaml
m7pr Mar 1, 2024
8f95a49
Update .github/workflows/release.yaml
m7pr Mar 1, 2024
f398140
Update DESCRIPTION
m7pr Mar 1, 2024
4dea7f3
Update vignettes/teal-modules-general.Rmd
m7pr Mar 1, 2024
92bdf31
Removes unnecessary `# nolint ` after `object_name_linter` was change…
averissimo Mar 1, 2024
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2 changes: 2 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ SECURITY.md
^Jenkinsfile$
^logs$
^Makefile$
^man/roxygen$
^man-roxygen$
^Meta$
^outputdir$
Expand All @@ -40,6 +41,7 @@ SECURITY.md
^staged_dependencies\.yaml$
^\.gitlab-ci\.yml$
^LICENSE\.md$
LICENSE
coverage.*
^sample_files$
^\.pre-commit-config\.yaml
Expand Down
6 changes: 3 additions & 3 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/bug.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/feature.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/question.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion .lintr
Original file line number Diff line number Diff line change
Expand Up @@ -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_?[0-9]*$", ADaM = "^r?AD[A-Z]{2,3}_?[0-9]*$"))
averissimo marked this conversation as resolved.
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)
8 changes: 3 additions & 5 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down
28 changes: 15 additions & 13 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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(
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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),
Expand All @@ -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,
Expand Down
3 changes: 1 addition & 2 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -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,"%>%")
27 changes: 1 addition & 26 deletions R/data.R
Original file line number Diff line number Diff line change
@@ -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"
7 changes: 3 additions & 4 deletions R/teal.modules.general.R
Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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
Expand Down
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