diff --git a/.Rbuildignore b/.Rbuildignore index fb16b94..132a9a5 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,6 +7,7 @@ ^ci/*$ ^NEWS\.md$ ^README\.md$ +^README\.qmd$ ^logfile\.md$ ^reconf\.sh$ ^cran-comments\.md$ @@ -18,4 +19,3 @@ ^dqagui\.Rproj$ ^man/figures$ ^Rplots\.pdf$ -^\.Rproj\.user$ diff --git a/.gitignore b/.gitignore index 6559426..ae71617 100644 --- a/.gitignore +++ b/.gitignore @@ -15,6 +15,7 @@ !NAMESPACE !/R/ !/README.md +!/README.qmd !/tests/ /.Rhistory !/*.Rproj @@ -35,4 +36,3 @@ !/docker/app.R !/docker/shiny-server.conf !/docker/show-log.sh -.Rproj.user diff --git a/DESCRIPTION b/DESCRIPTION index 5771510..9aeeac9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,7 @@ Package: DQAgui Title: Graphical User Interface for Data Quality Assessment Version: 0.2.3.9002 +Date: 2024-05-24 Authors@R: c( person("Lorenz A.", "Kapsner", , "lorenz.kapsner@gmail.com", role = c("cre", "aut"), comment = c(ORCID = "0000-0003-1866-860X")), @@ -9,12 +10,12 @@ Authors@R: c( person("MIRACUM - Medical Informatics in Research and Care in University Medicine", role = "fnd"), person("Universitätsklinikum Erlangen", role = "cph") ) -Description: A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'. Publication: Mang et al. (2021) . +Description: A graphical user interface (GUI) to the functions implemented + in the R package 'DQAstats'. Publication: Mang et al. (2021) + . License: GPL-3 URL: https://github.com/miracum/dqa-dqagui BugReports: https://github.com/miracum/dqa-dqagui/issues -Encoding: UTF-8 -Date: 2024-05-16 Imports: data.table, daterangepicker, @@ -37,4 +38,4 @@ Imports: Suggests: lintr, testthat (>= 3.0.0) -RoxygenNote: 7.3.1 +Encoding: UTF-8 diff --git a/NEWS.md b/NEWS.md index 4fe0eda..8d7cc6a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,16 @@ # DQAgui NEWS -## Unreleased (2023-10-30) +## Unreleased (2024-05-16) + +#### Bug fixes + +- replace write.csv with fwrite from data.table + ([927f72a](https://gitlab.miracum.org/miracum/dqa/dqagui/tree/927f72a6d2f43d4a6bd1ece6c96582423f9a78a8)) + +#### CI + +- fixing ci + ([8210403](https://gitlab.miracum.org/miracum/dqa/dqagui/tree/821040353538db5b2da58d393a9169ec2f6310a1)) #### Other changes @@ -10,7 +20,7 @@ ([1562003](https://gitlab.miracum.org/miracum/dqa/dqagui/tree/1562003e10995a56c53d09e7dc0d870cef41f4f7)) Full set of changes: -[`v0.2.3...6a6793a`](https://gitlab.miracum.org/miracum/dqa/dqagui/compare/v0.2.3...6a6793a) +[`v0.2.3...927f72a`](https://gitlab.miracum.org/miracum/dqa/dqagui/compare/v0.2.3...927f72a) ## v0.2.3 (2023-08-30) diff --git a/README.md b/README.md index 4ac4945..6ce250f 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,30 @@ + + # DQAgui -[![](https://img.shields.io/badge/doi-10.1186/s12911--022--01961--z-yellow.svg)](https://doi.org/10.1186/s12911-022-01961-z) -[![CRAN Status Badge](https://www.r-pkg.org/badges/version-ago/DQAgui)](https://cran.r-project.org/package=DQAgui) -[![CRAN Checks](https://badges.cranchecks.info/worst/DQAgui.svg)](https://cran.r-project.org/web/checks/check_results_DQAgui.html) + +[![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) +[![](https://www.r-pkg.org/badges/version/DQAgui)](https://cran.r-project.org/package=DQAgui) +[![CRAN +checks](https://badges.cranchecks.info/worst/DQAgui.svg)](https://cran.r-project.org/web/checks/check_results_DQAgui.html) [![](http://cranlogs.r-pkg.org/badges/grand-total/DQAgui?color=blue)](https://cran.r-project.org/package=DQAgui) [![](http://cranlogs.r-pkg.org/badges/last-month/DQAgui?color=blue)](https://cran.r-project.org/package=DQAgui) -[![Dependencies](https://tinyverse.netlify.com/badge/DQAgui)](https://cran.r-project.org/package=DQAgui) -[![R CMD Check via {tic}](https://github.com/miracum/dqa-dqagui/workflows/R%20CMD%20Check%20via%20{tic}/badge.svg?branch=master)](https://github.com/miracum/dqa-dqagui/actions) -[![linting](https://github.com/miracum/dqa-dqagui/workflows/lint/badge.svg?branch=master)](https://github.com/miracum/dqa-dqagui/actions) -[![test-coverage](https://github.com/miracum/dqa-dqagui/workflows/test-coverage/badge.svg?branch=master)](https://github.com/miracum/dqa-dqagui/actions) -[![codecov](https://codecov.io/gh/miracum/dqa-dqagui/branch/master/graph/badge.svg)](https://app.codecov.io/gh/miracum/dqa-dqagui) +[![Dependencies](https://tinyverse.netlify.app/badge/DQAgui)](https://cran.r-project.org/package=DQAgui) +[![R build +status](https://github.com/miracum/dqa-dqagui/workflows/R%20CMD%20Check%20via%20%7Btic%7D/badge.svg)](https://github.com/miracum/dqa-dqagui/actions) +[![R build +status](https://github.com/miracum/dqa-dqagui/workflows/lint/badge.svg)](https://github.com/miracum/dqa-dqagui/actions) +[![R build +status](https://github.com/miracum/dqa-dqagui/workflows/test-coverage/badge.svg)](https://github.com/miracum/dqa-dqagui/actions) +[![](https://codecov.io/gh/https://github.com/miracum/dqa-dqagui/branch/master/graph/badge.svg)](https://codecov.io/gh/https://github.com/miracum/dqa-dqagui) +[![](https://img.shields.io/badge/doi-10.1186/s12911--022--01961--z-yellow.svg)](https://doi.org/10.1186/s12911-022-01961-z) + -This is the repository of the R package 'DQAgui'. It provides a graphical user interface to the functionalities implemented in [`DQAstats`](https://github.com/miracum/dqa-dqastats). +This is the repository of the R package ‘DQAgui’. It provides a +graphical user interface to the functionalities implemented in +[`DQAstats`](https://github.com/miracum/dqa-dqastats). ## Installation @@ -26,15 +37,19 @@ remotes::install_github("miracum/dqa-dqagui") ## Configuration -The database connection can be configured using environment variables. These can be set using the base R command `Sys.setenv()`. +The database connection can be configured using environment variables. +These can be set using the base R command `Sys.setenv()`. -A detailed description, which environment variables need to be set for the specific databases can be found [here](https://github.com/miracum/misc-dizutils#db_connection). +A detailed description, which environment variables need to be set for +the specific databases can be found +[here](https://github.com/miracum/misc-dizutils#db_connection). ## Example -This is a basic example to demonstrate how to perform the data quality assessment with `DQAgui`: +This is a basic example to demonstrate how to perform the data quality +assessment with `DQAgui`: -```r +``` r library(DQAgui) # define base paths for shinyFiles::shinyDirChoose @@ -64,16 +79,20 @@ launch_app( ) ``` -To open the shiny application in your web-browser, go to `localhost:3838`. +To open the shiny application in your web-browser, go to +`localhost:3838`. ## Demo Usage / Deployment Examples -You can test the package without needing to install anything except [docker](https://docs.docker.com/get-docker/). -:bulb: For further details, see the [Wiki](https://github.com/miracum/dqa-dqastats/wiki/Deployment#dqagui-browser-based-gui-version-of-the-dqa-tool). +You can test the package without needing to install anything except +[docker](https://docs.docker.com/get-docker/). :bulb: For further +details, see the +[Wiki](https://github.com/miracum/dqa-dqastats/wiki/Deployment#dqagui-browser-based-gui-version-of-the-dqa-tool). ## More Infos - about MIRACUM: -- about the Medical Informatics Initiative: +- about the Medical Informatics Initiative: + - about Shiny: - RStudio and Shiny are trademarks of RStudio, Inc. diff --git a/README.qmd b/README.qmd new file mode 100644 index 0000000..bd71e7e --- /dev/null +++ b/README.qmd @@ -0,0 +1,101 @@ +--- +format: gfm +default-image-extension: "" +editor_options: + chunk_output_type: console +--- + +# DQAgui + + + +```{r} +#| echo: false +#| message: false +#| results: asis + +pkg <- desc::desc_get_field("Package") +cat_var <- paste( + badger::badge_lifecycle(), + badger::badge_cran_release(pkg = pkg), + gsub("summary", "worst", badger::badge_cran_checks(pkg = pkg)), + badger::badge_cran_download(pkg = pkg, type = "grand-total", color = "blue"), + badger::badge_cran_download(pkg = pkg, type = "last-month", color = "blue"), + gsub("netlify\\.com", "netlify.app", badger::badge_dependencies(pkg = pkg)), + badger::badge_github_actions(action = utils::URLencode("R CMD Check via {tic}")), + badger::badge_github_actions(action = "lint"), + badger::badge_github_actions(action = "test-coverage"), + badger::badge_codecov(ref = desc::desc_get_urls()), + badger::badge_doi("10.1186/s12911-022-01961-z", color = "yellow"), + sep = "\n" +) +cat_var |> cat() +``` + + +This is the repository of the R package 'DQAgui'. It provides a graphical user interface to the functionalities implemented in [`DQAstats`](https://github.com/miracum/dqa-dqastats). + +## Installation + +You can install `DQAgui` with: + +```{r} +#| eval: false +install.packages("remotes") +remotes::install_github("miracum/dqa-dqagui") +``` + +## Configuration + +The database connection can be configured using environment variables. These can be set using the base R command `Sys.setenv()`. + +A detailed description, which environment variables need to be set for the specific databases can be found [here](https://github.com/miracum/misc-dizutils#db_connection). + +## Example + +This is a basic example to demonstrate how to perform the data quality assessment with `DQAgui`: + +```{r} +#| eval: false +library(DQAgui) + +# define base paths for shinyFiles::shinyDirChoose +Sys.setenv( + "CSV_SOURCE_BASEPATH" = system.file("demo_data", package = "DQAstats") +) +Sys.setenv( + "CSV_TARGET_BASEPATH" = system.file("demo_data", package = "DQAstats") +) + +# define path to utilities-folder +utils_path <- system.file("demo_data/utilities", + package = "DQAstats") + +# filename of the metadata repository +mdr_filename <- "mdr_example_data.csv" + +# directory for storing logfiles +logfile_dir <- tempdir() + +launch_app( + port = 3838, + utils_path = utils_path, + mdr_filename = mdr_filename, + logfile_dir = logfile_dir, + parallel = FALSE +) +``` + +To open the shiny application in your web-browser, go to `localhost:3838`. + +## Demo Usage / Deployment Examples + +You can test the package without needing to install anything except [docker](https://docs.docker.com/get-docker/). +:bulb: For further details, see the [Wiki](https://github.com/miracum/dqa-dqastats/wiki/Deployment#dqagui-browser-based-gui-version-of-the-dqa-tool). + +## More Infos + +- about MIRACUM: +- about the Medical Informatics Initiative: +- about Shiny: +- RStudio and Shiny are trademarks of RStudio, Inc. diff --git a/data-raw/devstuffs.R b/data-raw/devstuffs.R index df9642b..35a7395 100644 --- a/data-raw/devstuffs.R +++ b/data-raw/devstuffs.R @@ -194,6 +194,7 @@ usethis::use_build_ignore(".lintr") usethis::use_build_ignore("ci/*") usethis::use_build_ignore("NEWS.md") usethis::use_build_ignore("README.md") +usethis::use_build_ignore("README.qmd") usethis::use_build_ignore("logfile.md") usethis::use_build_ignore("reconf.sh") usethis::use_build_ignore("cran-comments.md") @@ -228,6 +229,7 @@ usethis::use_git_ignore("!/man/") usethis::use_git_ignore("!NAMESPACE") usethis::use_git_ignore("!/R/") usethis::use_git_ignore("!/README.md") +usethis::use_git_ignore("!/README.qmd") usethis::use_git_ignore("!/tests/") usethis::use_git_ignore("/.Rhistory") usethis::use_git_ignore("!/*.Rproj") @@ -250,6 +252,10 @@ usethis::use_git_ignore("!/docker/app.R") usethis::use_git_ignore("!/docker/shiny-server.conf") usethis::use_git_ignore("!/docker/show-log.sh") +usethis::use_tidy_description() + +quarto::quarto_render(input = "README.qmd") + # create NEWS.md using the python-package "auto-changelog" (must be installed) # https://www.conventionalcommits.org/en/v1.0.0/ @@ -264,10 +270,6 @@ usethis::use_git_ignore("!/docker/show-log.sh") # command = 'auto-changelog -u -t "DQAgui NEWS" --tag-prefix "v" -o "NEWS.md"' # ) -badger::badge_cran_download("DQAgui", "grand-total", "blue") -badger::badge_cran_download("DQAgui", "last-month", "blue") -badger::badge_dependencies("DQAgui") -badger::badge_doi("10.1186/s12911-022-01961-z", color = "yellow") an <- autonewsmd::autonewsmd$new(repo_name = packagename) an$generate()