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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| format: gfm | ||
| default-image-extension: "" | ||
| editor_options: | ||
| chunk_output_type: console | ||
| --- | ||
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| # DQAgui <img src="man/figures/logo.png" align="right" width="120" /> | ||
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| <!-- badges: start --> | ||
| ```{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() | ||
| ``` | ||
| <!-- badges: end --> | ||
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| 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). | ||
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| ## Installation | ||
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| You can install `DQAgui` with: | ||
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| ```{r} | ||
| #| eval: false | ||
| install.packages("remotes") | ||
| remotes::install_github("miracum/dqa-dqagui") | ||
| ``` | ||
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| ## Configuration | ||
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| The database connection can be configured using environment variables. These can be set using the base R command `Sys.setenv()`. | ||
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| 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). | ||
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| ## Example | ||
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| This is a basic example to demonstrate how to perform the data quality assessment with `DQAgui`: | ||
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| ```{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 | ||
| ) | ||
| ``` | ||
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| To open the shiny application in your web-browser, go to `localhost:3838`. | ||
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| ## Demo Usage / Deployment Examples | ||
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| 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). | ||
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| ## More Infos | ||
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| - about MIRACUM: <https://www.miracum.org/> | ||
| - about the Medical Informatics Initiative: <https://www.medizininformatik-initiative.de/index.php/de> | ||
| - about Shiny: <https://www.rstudio.com/products/shiny/> | ||
| - RStudio and Shiny are trademarks of RStudio, Inc. |
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