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< title > Easy data analysis for clinicians • FreesearchR< / title >
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< meta name = "description" content = "Easily evaluate and analyse clinical health data in your browser, either based on a hosted version or run on your own device. Import data from multiple sources, summarise, modify and visualise data and create regression models. Export key metrics and regression analysis results in a publication ready document format." >
< meta property = "og:description" content = "Easily evaluate and analyse clinical health data in your browser, either based on a hosted version or run on your own device. Import data from multiple sources, summarise, modify and visualise data and create regression models. Export key metrics and regression analysis results in a publication ready document format." >
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< img src = "logo.png" class = "logo" alt = "" > < h1 id = "freesearchr-" > FreesearchR
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< p > The < a href = "https://app.freesearchr.org" class = "external-link" > < strong > < em > FreesearchR< / em > < / strong > < / a > is a simple, clinical health data exploration and analysis tool to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.< / p >
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< p > < a href = "https://app.freesearchr.org" class = "external-link" > < strong > < em > FreesearchR< / em > < / strong > < / a > is free and open-source, and is < a href = "https://app.freesearchr.org" class = "external-link" > accessible in your web browser through this link< / a > . The app can also run locally, please < a href = "#run-locally-on-your-own-machine-sec-run-locally" > see below< / a > .< / p >
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< p > All feedback is welcome and can be shared as a GitHub issue. Any suggestions on collaboration is much welcomed. Please reach out!< / p >
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< div class = "float" >
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< img src = "./reference/figures/demo.gif" alt = "FreesearchR demo" > < div class = "figcaption" > FreesearchR demo< / div >
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< / div >
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< div class = "section level2" >
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< h2 id = "motivation" > Motivation< a class = "anchor" aria-label = "anchor" href = "#motivation" > < / a >
< / h2 >
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< p > This app has the following simple goals:< / p >
< ol style = "list-style-type: decimal" >
< li > < p > help the health clinician getting an overview of data in quality improvement projects and clinical research< / p > < / li >
< li > < p > help learners get a good start analysing data and coding in < em > R< / em > < / p > < / li >
< li > < p > ease quick data overview and basic visualisations for any clinical researcher< / p > < / li >
< / ol >
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< p > Here’ < / p >
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< / div >
< div class = "section level2" >
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< h2 id = "run-locally-on-your-own-machine" > Run Locally on Your Own Machine< a class = "anchor" aria-label = "anchor" href = "#run-locally-on-your-own-machine" > < / a >
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< / h2 >
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< p > The < strong > FreesearchR< / strong > app can be run locally on your machine, ensuring no data is transmitted externally. Below are the available options for setup and configuration.< / p >
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< div class = "section level3" >
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< h3 id = "configuration--data-loading" > Configuration & Data Loading< a class = "anchor" aria-label = "anchor" href = "#configuration--data-loading" > < / a >
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< / h3 >
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< p > The app can be configured either by passing a named list to < code > run_app()< / code > or by setting environment variables in a < strong > Docker Compose< / strong > file. The following variables control data access and display behavior. If no values are provided, the app will use the defaults listed below.< / p >
< p > < strong > Configuration Variables< / strong > < / p >
< table class = "table" >
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< col width = "19%" >
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< col width = "19%" >
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< / colgroup >
< thead > < tr class = "header" >
< th > Variable< / th >
< th > Description< / th >
< th > Default< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td > < code > INCLUDE_GLOBALENV< / code > < / td >
< td > Load datasets already present in the global R environment into the app< / td >
< td > < code > FALSE< / code > < / td >
< / tr >
< tr class = "even" >
< td > < code > DATA_LIMIT_DEFAULT< / code > < / td >
< td > Default number of observations for previewing or working with a dataset< / td >
< td > < code > 10,000< / code > < / td >
< / tr >
< tr class = "odd" >
< td > < code > DATA_LIMIT_UPPER< / code > < / td >
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< td > Maximum number of observations a user can set for the upper limit. If set to 0, no uppper limit is applied.< / td >
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< td > < code > 100,000< / code > < / td >
< / tr >
< tr class = "even" >
< td > < code > DATA_LIMIT_LOWER< / code > < / td >
< td > Minimum number of observations a user can set for the lower limit< / td >
< td > < code > 1< / code > < / td >
< / tr >
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< tr class = "odd" >
< td > < code > CHECK_APP_VERSION< / code > < / td >
< td > Always print version check results. Checks app version against latest release on GitHub.< / td >
< td > < code > FALSE< / code > < / td >
< / tr >
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< / tbody >
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< div class = "section level3" >
< h3 id = "run-from-r-or-rstudio" > Run from R (or RStudio)< a class = "anchor" aria-label = "anchor" href = "#run-from-r-or-rstudio" > < / a >
< / h3 >
< p > If you’ < strong > FreesearchR< / strong > is a quick and easy tool for exploratory analysis.< / p >
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< ol style = "list-style-type: decimal" >
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< li > < p > < strong > Requirement:< / strong > Ensure you have < a href = "https://www.r-project.org/" class = "external-link" > R< / a > installed, and optionally an editor like < a href = "https://posit.co/download/rstudio-desktop/" class = "external-link" > RStudio< / a > .< / p > < / li >
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< li >
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< p > Open the < strong > R console< / strong > and run the following code to install the < a href = "https://github.com/agdamsbo/FreesearchR" class = "external-link" > FreesearchR< / a > package and launch the app:< / p >
< div class = "sourceCode" id = "cb1" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "op" > !< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://devtools.r-lib.org/" class = "external-link" > "devtools"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/install.packages.html" class = "external-link" > install.packages< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "devtools"< / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "fu" > devtools< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://devtools.r-lib.org/reference/install-deprecated.html" class = "external-link" > install_github< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "agdamsbo/FreesearchR"< / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://github.com/agdamsbo/FreesearchR" class = "external-link" > FreesearchR< / a > < / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "co" > # Load sample data (e.g., mtcars) to make it available in the app< / span > < / span >
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< span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/data.html" class = "external-link" > data< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mtcars< / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "fu" > < a href = "reference/launch_FreesearchR.html" > launch_FreesearchR< / a > < / span > < span class = "op" > (< / span > INCLUDE_GLOBALENV< span class = "op" > =< / span > < span class = "cn" > TRUE< / span > ,CHECK_APP_VERSION< span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
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< / li >
< / ol >
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< p > All the variables specified above can also be passed to the app on launch from R. Set DATA_LIMIT_UPPER=0 to remove upper data limit. This limit is set to protect the online app version from choking and crashing on large data sets.< / p >
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< / div >
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< div class = "section level3" >
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< h3 id = "running-with-docker-compose" > Running with Docker Compose< a class = "anchor" aria-label = "anchor" href = "#running-with-docker-compose" > < / a >
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< / h3 >
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< p > For advanced users, you can deploy < strong > FreesearchR< / strong > using Docker. A data folder can be mounted to < code > /app/data< / code > to automatically load supported file types (< code > .csv< / code > , < code > .tsv< / code > , < code > .txt< / code > , < code > .xls< / code > , < code > .xlsx< / code > , < code > .ods< / code > , < code > .dta< / code > , < code > .rds< / code > ) at startup.< / p >
< p > To mount a local data folder, add a < code > volumes< / code > entry to your < code > docker-compose.yml< / code > file:< / p >
< div class = "sourceCode" id = "cb2" > < pre class = "sourceCode yaml" > < code class = "sourceCode yaml" > < span id = "cb2-1" > < a href = "#cb2-1" tabindex = "-1" > < / a > < span class = "fu" > services< / span > < span class = "kw" > :< / span > < / span >
< span id = "cb2-2" > < a href = "#cb2-2" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "fu" > shiny< / span > < span class = "kw" > :< / span > < / span >
< span id = "cb2-3" > < a href = "#cb2-3" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "fu" > image< / span > < span class = "kw" > :< / span > < span class = "at" > ghcr.io/agdamsbo/freesearchr:latest< / span > < / span >
< span id = "cb2-4" > < a href = "#cb2-4" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "fu" > volumes< / span > < span class = "kw" > :< / span > < / span >
< span id = "cb2-5" > < a href = "#cb2-5" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "kw" > -< / span > < span class = "at" > ./data:/app/data:ro< / span > < / span >
< span id = "cb2-6" > < a href = "#cb2-6" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "fu" > environment< / span > < span class = "kw" > :< / span > < / span >
< span id = "cb2-7" > < a href = "#cb2-7" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "kw" > -< / span > < span class = "at" > INCLUDE_GLOBALENV=FALSE< / span > < / span >
< span id = "cb2-8" > < a href = "#cb2-8" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "kw" > -< / span > < span class = "at" > DATA_LIMIT_DEFAULT=10000< / span > < / span >
< span id = "cb2-9" > < a href = "#cb2-9" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "kw" > -< / span > < span class = "at" > DATA_LIMIT_UPPER=100000< / span > < / span >
< span id = "cb2-10" > < a href = "#cb2-10" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "kw" > -< / span > < span class = "at" > DATA_LIMIT_LOWER=1< / span > < / span >
< span id = "cb2-11" > < a href = "#cb2-11" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "fu" > ports< / span > < span class = "kw" > :< / span > < / span >
< span id = "cb2-12" > < a href = "#cb2-12" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "kw" > -< / span > < span class = "at" > < / span > < span class = "st" > '3838:3838'< / span > < / span >
< span id = "cb2-13" > < a href = "#cb2-13" tabindex = "-1" > < / a > < span class = "at" > < / span > < span class = "fu" > restart< / span > < span class = "kw" > :< / span > < span class = "at" > on-failure< / span > < / span > < / code > < / pre > < / div >
< ul >
< li > < p > The < code > :ro< / code > flag mounts the folder as < strong > read-only< / strong > , preventing the app from modifying your original data files.< / p > < / li >
< li > < p > If no volume is mounted, the app will start without any preloaded datasets.< / p > < / li >
< / ul >
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< / div >
< / div >
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< div class = "section level2" >
< h2 id = "code-of-conduct" > Code of Conduct< a class = "anchor" aria-label = "anchor" href = "#code-of-conduct" > < / a >
< / h2 >
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< p > Please note that the < strong > < em > FreesearchR< / em > < / strong > project is published with a < a href = "https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html" class = "external-link" > Contributor Code of Conduct< / a > . By contributing to this project, you agree to abide by its terms.< / p >
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< / div >
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< div class = "section level2" >
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< h2 id = "translators" > Translators< a class = "anchor" aria-label = "anchor" href = "#translators" > < / a >
< / h2 >
< p > Thank you very much to all translators having helped to translate and validate translation drafts.< / p >
< / div >
< div class = "section level2" >
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< h2 id = "acknowledgements" > Acknowledgements< a class = "anchor" aria-label = "anchor" href = "#acknowledgements" > < / a >
< / h2 >
< p > Like any other project, this project was never possible without the great work of others. These are some of the sources and packages I have used:< / p >
< ul >
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< li > < p > The < strong > < em > FreesearchR< / em > < / strong > app is built with < a href = "https://shiny.posit.co/" class = "external-link" > Shiny< / a > and based on < a href = "https://www.r-project.org/" class = "external-link" > < em > R< / em > < / a > .< / p > < / li >
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< li > < p > < a href = "https://www.danieldsjoberg.com/gtsummary/" class = "external-link" > gtsummary< / a > : superb and flexible way to create publication-ready analytical and summary tables.< / p > < / li >
< li > < p > < a href = "https://github.com/dreamRs" class = "external-link" > dreamRs< / a > : maintainers of a broad selection of great extensions and tools for < a href = "https://shiny.posit.co/" class = "external-link" > Shiny< / a > .< / p > < / li >
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< li > < p > < a href = "https://easystats.github.io/easystats/" class = "external-link" > easystats< / a > : the < a href = "https://easystats.github.io/performance/articles/check_model.html" class = "external-link" > < code > performance::check_model()< / code > < / a > function was central in sparking the idea to create a data analysis tool.< / p > < / li >
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< li > < p > < a href = "https://biogen-inc.github.io/IDEAFilter/" class = "external-link" > IDEAfilter< / a > : a visually appealing data filter function based on the < a href = "https://github.com/dgkf/shinyDataFilter" class = "external-link" > {shinyDataFilter}< / a > .< / p > < / li >
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< / ul >
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< p > This project was all written by a human and not by any AI-based tools.< / p >
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< p > The online < strong > < em > FreesearchR< / em > < / strong > app contains a tracking script, transmitting minimal data on usage. No uploaded data is transmitted anywhere. Have a look at the < a href = "https://analytics.gdamsbo.dk/share/2i4BNpMcDMB9lJvF/agdamsbo.shinyapps.io" class = "external-link" > tracking data here< / a > . No tracking data is sent running the app locally (see above).< / p >
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< / div >
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< / div >
< / main > < aside class = "col-md-3" > < div class = "links" >
< h2 data-toc-skip > Links< / h2 >
< ul class = "list-unstyled" >
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< li > < a href = "https://github.com/agdamsbo/FreesearchR/" class = "external-link" > Browse source code< / a > < / li >
< li > < a href = "https://github.com/agdamsbo/FreesearchR/issues" class = "external-link" > Report a bug< / a > < / li >
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< / ul >
< / div >
< div class = "license" >
< h2 data-toc-skip > License< / h2 >
< ul class = "list-unstyled" >
< li > < a href = "LICENSE.html" > Full license< / a > < / li >
< li > < small > AGPL (> = 3)< / small > < / li >
< / ul >
< / div >
< div class = "community" >
< h2 data-toc-skip > Community< / h2 >
< ul class = "list-unstyled" >
< li > < a href = "CODE_OF_CONDUCT.html" > Code of conduct< / a > < / li >
< / ul >
< / div >
< div class = "citation" >
< h2 data-toc-skip > Citation< / h2 >
< ul class = "list-unstyled" >
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< li > < a href = "authors.html#citation" > Citing FreesearchR< / a > < / li >
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< / ul >
< / div >
< div class = "developers" >
< h2 data-toc-skip > Developers< / h2 >
< ul class = "list-unstyled" >
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< li > Andreas Gammelgaard Damsbo < br > < small class = "roles" > Author, maintainer < / small > < a href = "https://orcid.org/0000-0002-7559-1154" target = "orcid.widget" aria-label = "ORCID" class = "external-link" > < span class = "fab fa-orcid orcid" aria-hidden = "true" > < / span > < / a > < / li >
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< li > < a href = "authors.html" > More about authors...< / a > < / li >
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< / ul >
< / div >
< div class = "dev-status" >
< h2 data-toc-skip > Dev status< / h2 >
< ul class = "list-unstyled" >
< li > < a href = "https://lifecycle.r-lib.org/articles/stages.html#experimental" class = "external-link" > < img src = "https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt = "Lifecycle: experimental" > < / a > < / li >
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< li > < a href = "https://doi.org/10.5281/zenodo.14527429" class = "external-link" > < img src = "https://zenodo.org/badge/DOI/10.5281/zenodo.14527429.svg" alt = "DOI" > < / a > < / li >
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< li > < a href = "https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml" class = "external-link" > < img src = "https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml/badge.svg" alt = "rhub" > < / a > < / li >
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< li > < a href = "https://agdamsbo.shinyapps.io/FreesearchR/" class = "external-link" > < img src = "https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue" alt = "FreesearchR" > < / a > < / li >
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< / ul >
< / div >
< / aside >
< / div >
< footer > < div class = "pkgdown-footer-left" >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a > 2.2.0.< / p >
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< / div >
< div class = "pkgdown-footer-right" >
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< p > Developed by Andreas Gammelgaard Damsbo. Provided without < strong > any warranty< / strong > .< / p >
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< / div >
< / footer >
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< / body >
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