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<table class="table"><colgroup><col width="100%"></colgroup><thead><tr class="header"><th>——————————– R environment ———————————</th> <table class="table"><colgroup><col width="100%"></colgroup><thead><tr class="header"><th>——————————– R environment ———————————</th>
</tr></thead><tbody><tr class="odd"><td>|setting |value | |:———–|:——————————————| |version |R version 4.5.2 (2025-10-31) | |os |macOS Tahoe 26.3 | |system |aarch64, darwin20 | |ui |RStudio | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |Europe/Copenhagen | |date |2026-03-11 | |rstudio |2026.01.1+403 Apple Blossom (desktop) | |pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) | |quarto |1.7.30 @ /usr/local/bin/quarto | |FreesearchR |26.3.2.260311 |</td> </tr></thead><tbody><tr class="odd"><td>|setting |value | |:———–|:——————————————| |version |R version 4.5.2 (2025-10-31) | |os |macOS Tahoe 26.3 | |system |aarch64, darwin20 | |ui |RStudio | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |Europe/Copenhagen | |date |2026-03-11 | |rstudio |2026.01.1+403 Apple Blossom (desktop) | |pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) | |quarto |1.7.30 @ /usr/local/bin/quarto | |FreesearchR |26.3.3.260311 |</td>
</tr></tbody></table><div class="section level2"> </tr></tbody></table><div class="section level2">
<h2 id="id_-packages-">———————————– packages ———————————–<a class="anchor" aria-label="anchor" href="#id_-packages-"></a></h2> <h2 id="id_-packages-">———————————– packages ———————————–<a class="anchor" aria-label="anchor" href="#id_-packages-"></a></h2>
<table class="table"><thead><tr class="header"><th align="left">package</th> <table class="table"><thead><tr class="header"><th align="left">package</th>
@ -291,7 +291,7 @@
<td align="left">2023-02-24</td> <td align="left">2023-02-24</td>
<td align="left">CRAN (R 4.5.0)</td> <td align="left">CRAN (R 4.5.0)</td>
</tr><tr class="odd"><td align="left">FreesearchR</td> </tr><tr class="odd"><td align="left">FreesearchR</td>
<td align="left">26.3.2</td> <td align="left">26.3.3</td>
<td align="left">NA</td> <td align="left">NA</td>
<td align="left">NA</td> <td align="left">NA</td>
</tr><tr class="even"><td align="left">fs</td> </tr><tr class="even"><td align="left">fs</td>

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| ——————————– R environment ——————————— | | ——————————– R environment ——————————— |
|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| |--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| \|setting \|value \| \|:———–\|:——————————————\| \|version \|R version 4.5.2 (2025-10-31) \| \|os \|macOS Tahoe 26.3 \| \|system \|aarch64, darwin20 \| \|ui \|RStudio \| \|language \|(EN) \| \|collate \|en_US.UTF-8 \| \|ctype \|en_US.UTF-8 \| \|tz \|Europe/Copenhagen \| \|date \|2026-03-11 \| \|rstudio \|2026.01.1+403 Apple Blossom (desktop) \| \|pandoc \|3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) \| \|quarto \|1.7.30 @ /usr/local/bin/quarto \| \|FreesearchR \|26.3.2.260311 \| | | \|setting \|value \| \|:———–\|:——————————————\| \|version \|R version 4.5.2 (2025-10-31) \| \|os \|macOS Tahoe 26.3 \| \|system \|aarch64, darwin20 \| \|ui \|RStudio \| \|language \|(EN) \| \|collate \|en_US.UTF-8 \| \|ctype \|en_US.UTF-8 \| \|tz \|Europe/Copenhagen \| \|date \|2026-03-11 \| \|rstudio \|2026.01.1+403 Apple Blossom (desktop) \| \|pandoc \|3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) \| \|quarto \|1.7.30 @ /usr/local/bin/quarto \| \|FreesearchR \|26.3.3.260311 \| |
## ———————————– packages ———————————– ## ———————————– packages ———————————–
@ -68,7 +68,7 @@
| foreach | 1.5.2 | 2022-02-02 | CRAN (R 4.5.0) | | foreach | 1.5.2 | 2022-02-02 | CRAN (R 4.5.0) |
| foreign | 0.8-90 | 2025-03-31 | CRAN (R 4.5.2) | | foreign | 0.8-90 | 2025-03-31 | CRAN (R 4.5.2) |
| Formula | 1.2-5 | 2023-02-24 | CRAN (R 4.5.0) | | Formula | 1.2-5 | 2023-02-24 | CRAN (R 4.5.0) |
| FreesearchR | 26.3.2 | NA | NA | | FreesearchR | 26.3.3 | NA | NA |
| fs | 1.6.6 | 2025-04-12 | CRAN (R 4.5.0) | | fs | 1.6.6 | 2025-04-12 | CRAN (R 4.5.0) |
| gdtools | 0.5.0 | 2026-02-09 | CRAN (R 4.5.2) | | gdtools | 0.5.0 | 2026-02-09 | CRAN (R 4.5.2) |
| generics | 0.1.4 | 2025-05-09 | CRAN (R 4.5.0) | | generics | 0.1.4 | 2025-05-09 | CRAN (R 4.5.0) |

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@ -149,7 +149,7 @@ packages and the latest build info.</p>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">FreesearchR</td> <td align="left">FreesearchR</td>
<td align="left">26.3.2.260311</td> <td align="left">26.3.3.260311</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -529,7 +529,7 @@ packages and the latest build info.</p>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">FreesearchR</td> <td align="left">FreesearchR</td>
<td align="left">26.3.2</td> <td align="left">26.3.3</td>
<td align="left">NA</td> <td align="left">NA</td>
<td align="left">NA</td> <td align="left">NA</td>
</tr> </tr>

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@ -32,7 +32,7 @@ FreesearchR:::session_data$platform |> knitr::kable()
| rstudio | 2026.01.1+403 Apple Blossom (desktop) | | rstudio | 2026.01.1+403 Apple Blossom (desktop) |
| pandoc | 3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) | | pandoc | 3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
| quarto | 1.7.30 @ /usr/local/bin/quarto | | quarto | 1.7.30 @ /usr/local/bin/quarto |
| FreesearchR | 26.3.2.260311 | | FreesearchR | 26.3.3.260311 |
## Libraries ## Libraries
@ -102,7 +102,7 @@ FreesearchR:::session_data$libs|> knitr::kable()
| foreach | 1.5.2 | 2022-02-02 | CRAN (R 4.5.0) | | foreach | 1.5.2 | 2022-02-02 | CRAN (R 4.5.0) |
| foreign | 0.8-90 | 2025-03-31 | CRAN (R 4.5.2) | | foreign | 0.8-90 | 2025-03-31 | CRAN (R 4.5.2) |
| Formula | 1.2-5 | 2023-02-24 | CRAN (R 4.5.0) | | Formula | 1.2-5 | 2023-02-24 | CRAN (R 4.5.0) |
| FreesearchR | 26.3.2 | NA | NA | | FreesearchR | 26.3.3 | NA | NA |
| fs | 1.6.6 | 2025-04-12 | CRAN (R 4.5.0) | | fs | 1.6.6 | 2025-04-12 | CRAN (R 4.5.0) |
| gdtools | 0.5.0 | 2026-02-09 | CRAN (R 4.5.2) | | gdtools | 0.5.0 | 2026-02-09 | CRAN (R 4.5.2) |
| generics | 0.1.4 | 2025-05-09 | CRAN (R 4.5.0) | | generics | 0.1.4 | 2025-05-09 | CRAN (R 4.5.0) |

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<li><p>help learners get a good start analysing data and coding in <em>R</em></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> <li><p>ease quick data overview and basic visualisations for any clinical researcher</p></li>
</ol> </ol>
<p>Here’s a polished and restructured version of your README section for clarity, conciseness, and user-friendliness:</p>
</div> </div>
<div class="section level2"> <div class="section level2">
<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> <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>
</h2> </h2>
<p>The <strong><em>FreesearchR</em></strong> app can also run on your own machine with no data transmitted anywhere. Blow are the available options.</p> <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>
<div class="section level3"> <div class="section level3">
<h3 id="run-from-r-or-rstduio">Run from R (or RStduio)<a class="anchor" aria-label="anchor" href="#run-from-r-or-rstduio"></a> <h3 id="configuration--data-loading">Configuration &amp; Data Loading<a class="anchor" aria-label="anchor" href="#configuration--data-loading"></a>
</h3> </h3>
<p>Working with data in R, FreesearchR is a quick and easy tool to get overview and perform the first explorative analyses to get you going.</p> <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>Any data available in the your R session will be available to the FreesearchR app. Just follow the below steps to get going:</p> <p><strong>Configuration Variables</strong></p>
<ol style="list-style-type: decimal"> <table class="table">
<li><p><strong>Requirement:</strong> You need to have <a href="https://www.r-project.org/" class="external-link"><em>R</em> installed</a> and possibly an editor like <a href="https://posit.co/download/rstudio-desktop/" class="external-link">RStudio</a>.</p></li> <colgroup>
<li> <col width="22%">
<p>Then open the <em>R</em> console and copy/paste the following code, that will install the <a href="https://devtools.r-lib.org/" class="external-link">devtools</a> package and then the <a href="https://github.com/agdamsbo/FreesearchR" class="external-link">FreesearchR</a> <em>R</em>-package with its dependencies:</p> <col width="68%">
<pre><code><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> <col width="9%">
<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"agdamsbo/FreesearchR"</span><span class="op">)</span></span> </colgroup>
<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> <thead><tr class="header">
<span><span class="co"># By loading mtcars to the environment, it will be available</span></span> <th>Variable</th>
<span><span class="co"># in the interface like any other data.frame</span></span> <th>Description</th>
<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> <th>Default</th>
<span><span class="fu"><a href="reference/launch_FreesearchR.html">launch_FreesearchR</a></span><span class="op">(</span><span class="op">)</span></span></code></pre> </tr></thead>
</li> <tbody>
</ol> <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>
<td>Maximum number of observations a user can set for the upper limit</td>
<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>
</tbody>
</table>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="running-with-docker-compose">Running with docker compose<a class="anchor" aria-label="anchor" href="#running-with-docker-compose"></a> <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> </h3>
<p>For advanced users, wanting to deploy the FreesearchR app to run anywhere, a docker image is available.</p> <p>If you’re working with data in R, <strong>FreesearchR</strong> is a quick and easy tool for exploratory analysis.</p>
<p>Below is the minimal <code>docker_compose.yml</code> file:</p> <ol style="list-style-type: decimal">
<pre><code><span><span class="va">services</span><span class="op">:</span></span> <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>
<span> <span class="va">freesearchr</span><span class="op">:</span></span> <li>
<span> <span class="va">image</span><span class="op">:</span> <span class="va">ghcr.io</span><span class="op">/</span><span class="va">agdamsbo</span><span class="op">/</span><span class="va">freesearchr</span><span class="op">:</span><span class="va">latest</span></span> <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>
<span> <span class="va">ports</span><span class="op">:</span></span> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<span> <span class="op">-</span> <span class="st">'3838:3838'</span></span> <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>
<span> <span class="va">restart</span><span class="op">:</span> <span class="va">on</span><span class="op">-</span><span class="va">failure</span></span></code></pre> <span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"agdamsbo/FreesearchR"</span><span class="op">)</span></span>
<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>
<span><span class="co"># Load sample data (e.g., mtcars) to make it available in the app</span></span>
<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>
<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><span class="op">)</span></span></code></pre></div>
</li>
</ol>
<p>All the variables specified above can also be passed to the app on launch from R.</p>
</div>
<div class="section level3">
<h3 id="running-with-docker-compose">Running with Docker Compose<a class="anchor" aria-label="anchor" href="#running-with-docker-compose"></a>
</h3>
<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>
</div> </div>
</div> </div>
<div class="section level2"> <div class="section level2">

86
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@ -29,49 +29,87 @@ This app has the following simple goals:
3. ease quick data overview and basic visualisations for any clinical 3. ease quick data overview and basic visualisations for any clinical
researcher researcher
## Run locally on your own machine Here’s a polished and restructured version of your README section for
clarity, conciseness, and user-friendliness:
The ***FreesearchR*** app can also run on your own machine with no data ## Run Locally on Your Own Machine
transmitted anywhere. Blow are the available options.
### Run from R (or RStduio) The **FreesearchR** app can be run locally on your machine, ensuring no
data is transmitted externally. Below are the available options for
setup and configuration.
Working with data in R, FreesearchR is a quick and easy tool to get ### Configuration & Data Loading
overview and perform the first explorative analyses to get you going.
Any data available in the your R session will be available to the The app can be configured either by passing a named list to `run_app()`
FreesearchR app. Just follow the below steps to get going: or by setting environment variables in a **Docker Compose** file. The
following variables control data access and display behavior. If no
values are provided, the app will use the defaults listed below.
1. **Requirement:** You need to have [*R* **Configuration Variables**
installed](https://www.r-project.org/) and possibly an editor like
| Variable | Description | Default |
|----------------------|-------------------------------------------------------------------------|-----------|
| `INCLUDE_GLOBALENV` | Load datasets already present in the global R environment into the app | `FALSE` |
| `DATA_LIMIT_DEFAULT` | Default number of observations for previewing or working with a dataset | `10,000` |
| `DATA_LIMIT_UPPER` | Maximum number of observations a user can set for the upper limit | `100,000` |
| `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
### Run from R (or RStudio)
If you’re working with data in R, **FreesearchR** is a quick and easy
tool for exploratory analysis.
1. **Requirement:** Ensure you have [R](https://www.r-project.org/)
installed, and optionally an editor like
[RStudio](https://posit.co/download/rstudio-desktop/). [RStudio](https://posit.co/download/rstudio-desktop/).
2. Then open the *R* console and copy/paste the following code, that 2. Open the **R console** and run the following code to install the
will install the [devtools](https://devtools.r-lib.org/) package and [FreesearchR](https://github.com/agdamsbo/FreesearchR) package and
then the [FreesearchR](https://github.com/agdamsbo/FreesearchR) launch the app:
*R*-package with its dependencies:
require("devtools") ``` r
if (!require("devtools")) install.packages("devtools")
devtools::install_github("agdamsbo/FreesearchR") devtools::install_github("agdamsbo/FreesearchR")
library(FreesearchR) library(FreesearchR)
# By loading mtcars to the environment, it will be available # Load sample data (e.g., mtcars) to make it available in the app
# in the interface like any other data.frame
data(mtcars) data(mtcars)
launch_FreesearchR() launch_FreesearchR(INCLUDE_GLOBALENV=TRUE)
```
### Running with docker compose All the variables specified above can also be passed to the app on
launch from R.
For advanced users, wanting to deploy the FreesearchR app to run ### Running with Docker Compose
anywhere, a docker image is available.
Below is the minimal `docker_compose.yml` file: For advanced users, you can deploy **FreesearchR** using Docker. A data
folder can be mounted to `/app/data` to automatically load supported
file types (`.csv`, `.tsv`, `.txt`, `.xls`, `.xlsx`, `.ods`, `.dta`,
`.rds`) at startup.
services: To mount a local data folder, add a `volumes` entry to your
freesearchr: `docker-compose.yml` file:
``` yaml
services:
shiny:
image: ghcr.io/agdamsbo/freesearchr:latest image: ghcr.io/agdamsbo/freesearchr:latest
volumes:
- ./data:/app/data:ro
environment:
- INCLUDE_GLOBALENV=FALSE
- DATA_LIMIT_DEFAULT=10000
- DATA_LIMIT_UPPER=100000
- DATA_LIMIT_LOWER=1
ports: ports:
- '3838:3838' - '3838:3838'
restart: on-failure restart: on-failure
```
- The `:ro` flag mounts the folder as **read-only**, preventing the app
from modifying your original data files.
- If no volume is mounted, the app will start without any preloaded
datasets.
## Code of Conduct ## Code of Conduct

86
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@ -29,49 +29,87 @@ This app has the following simple goals:
3. ease quick data overview and basic visualisations for any clinical 3. ease quick data overview and basic visualisations for any clinical
researcher researcher
## Run locally on your own machine Here’s a polished and restructured version of your README section for
clarity, conciseness, and user-friendliness:
The ***FreesearchR*** app can also run on your own machine with no data ## Run Locally on Your Own Machine
transmitted anywhere. Blow are the available options.
### Run from R (or RStduio) The **FreesearchR** app can be run locally on your machine, ensuring no
data is transmitted externally. Below are the available options for
setup and configuration.
Working with data in R, FreesearchR is a quick and easy tool to get ### Configuration & Data Loading
overview and perform the first explorative analyses to get you going.
Any data available in the your R session will be available to the The app can be configured either by passing a named list to `run_app()`
FreesearchR app. Just follow the below steps to get going: or by setting environment variables in a **Docker Compose** file. The
following variables control data access and display behavior. If no
values are provided, the app will use the defaults listed below.
1. **Requirement:** You need to have [*R* **Configuration Variables**
installed](https://www.r-project.org/) and possibly an editor like
| Variable | Description | Default |
|----------------------|-------------------------------------------------------------------------|-----------|
| `INCLUDE_GLOBALENV` | Load datasets already present in the global R environment into the app | `FALSE` |
| `DATA_LIMIT_DEFAULT` | Default number of observations for previewing or working with a dataset | `10,000` |
| `DATA_LIMIT_UPPER` | Maximum number of observations a user can set for the upper limit | `100,000` |
| `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
### Run from R (or RStudio)
If you’re working with data in R, **FreesearchR** is a quick and easy
tool for exploratory analysis.
1. **Requirement:** Ensure you have [R](https://www.r-project.org/)
installed, and optionally an editor like
[RStudio](https://posit.co/download/rstudio-desktop/). [RStudio](https://posit.co/download/rstudio-desktop/).
2. Then open the *R* console and copy/paste the following code, that 2. Open the **R console** and run the following code to install the
will install the [devtools](https://devtools.r-lib.org/) package and [FreesearchR](https://github.com/agdamsbo/FreesearchR) package and
then the [FreesearchR](https://github.com/agdamsbo/FreesearchR) launch the app:
*R*-package with its dependencies:
require("devtools") ``` r
if (!require("devtools")) install.packages("devtools")
devtools::install_github("agdamsbo/FreesearchR") devtools::install_github("agdamsbo/FreesearchR")
library(FreesearchR) library(FreesearchR)
# By loading mtcars to the environment, it will be available # Load sample data (e.g., mtcars) to make it available in the app
# in the interface like any other data.frame
data(mtcars) data(mtcars)
launch_FreesearchR() launch_FreesearchR(INCLUDE_GLOBALENV=TRUE)
```
### Running with docker compose All the variables specified above can also be passed to the app on
launch from R.
For advanced users, wanting to deploy the FreesearchR app to run ### Running with Docker Compose
anywhere, a docker image is available.
Below is the minimal `docker_compose.yml` file: For advanced users, you can deploy **FreesearchR** using Docker. A data
folder can be mounted to `/app/data` to automatically load supported
file types (`.csv`, `.tsv`, `.txt`, `.xls`, `.xlsx`, `.ods`, `.dta`,
`.rds`) at startup.
services: To mount a local data folder, add a `volumes` entry to your
freesearchr: `docker-compose.yml` file:
``` yaml
services:
shiny:
image: ghcr.io/agdamsbo/freesearchr:latest image: ghcr.io/agdamsbo/freesearchr:latest
volumes:
- ./data:/app/data:ro
environment:
- INCLUDE_GLOBALENV=FALSE
- DATA_LIMIT_DEFAULT=10000
- DATA_LIMIT_UPPER=100000
- DATA_LIMIT_LOWER=1
ports: ports:
- '3838:3838' - '3838:3838'
restart: on-failure restart: on-failure
```
- The `:ro` flag mounts the folder as **read-only**, preventing the app
from modifying your original data files.
- If no volume is mounted, the app will start without any preloaded
datasets.
## Code of Conduct ## Code of Conduct

3
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@ -43,7 +43,8 @@
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="26.3.3" id="freesearchr-2633">FreesearchR 26.3.3<a class="anchor" aria-label="anchor" href="#freesearchr-2633"></a></h2> <h2 class="pkg-version" data-toc-text="26.3.3" id="freesearchr-2633">FreesearchR 26.3.3<a class="anchor" aria-label="anchor" href="#freesearchr-2633"></a></h2>
<p><em>NEW</em> option to pass global settings when running as docker or launching from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Docs are missing…</p> <p><em>NEW</em> option to pass global settings when running as docker or launching from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Described in the README.</p>
<p><em>FIX</em> faster data description function.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="26.3.2" id="freesearchr-2632">FreesearchR 26.3.2<a class="anchor" aria-label="anchor" href="#freesearchr-2632"></a></h2> <h2 class="pkg-version" data-toc-text="26.3.2" id="freesearchr-2632">FreesearchR 26.3.2<a class="anchor" aria-label="anchor" href="#freesearchr-2632"></a></h2>

4
news/index.md
View file

@ -4,7 +4,9 @@
*NEW* option to pass global settings when running as docker or launching *NEW* option to pass global settings when running as docker or launching
from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT,
DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Docs are missing… DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Described in the README.
*FIX* faster data description function.
## FreesearchR 26.3.2 ## FreesearchR 26.3.2

2
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@ -7,7 +7,7 @@ articles:
missingness: missingness.html missingness: missingness.html
session: session.html session: session.html
visuals: visuals.html visuals: visuals.html
last_built: 2026-03-11T13:00Z last_built: 2026-03-12T10:26Z
urls: urls:
reference: https://agdamsbo.github.io/FreesearchR/reference reference: https://agdamsbo.github.io/FreesearchR/reference
article: https://agdamsbo.github.io/FreesearchR/articles article: https://agdamsbo.github.io/FreesearchR/articles

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@ -732,7 +732,7 @@ One of c("stack", "dodge", "fill")</p></dd>
<span class="r-out co"><span class="r-pr">#&gt;</span> list()</span> <span class="r-out co"><span class="r-pr">#&gt;</span> list()</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $plot_env</span> <span class="r-out co"><span class="r-pr">#&gt;</span> $plot_env</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x558a2b7351a8&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x56288e807a28&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $code</span> <span class="r-out co"><span class="r-pr">#&gt;</span> $code</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FreesearchR::plot_violin(pri = "mpg", sec = "cyl", ter = NULL)</span> <span class="r-out co"><span class="r-pr">#&gt;</span> FreesearchR::plot_violin(pri = "mpg", sec = "cyl", ter = NULL)</span>

2
reference/data-plots.md
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@ -688,7 +688,7 @@ create_plot(mtcars, "plot_violin", "mpg", "cyl") |> attributes()
#> list() #> list()
#> #>
#> $plot_env #> $plot_env
#> <environment: 0x558a2b7351a8> #> <environment: 0x56288e807a28>
#> #>
#> $code #> $code
#> FreesearchR::plot_violin(pri = "mpg", sec = "cyl", ter = NULL) #> FreesearchR::plot_violin(pri = "mpg", sec = "cyl", ter = NULL)

2
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@ -139,7 +139,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> z$qr &lt;- NULL</span> <span class="r-out co"><span class="r-pr">#&gt;</span> z$qr &lt;- NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z</span> <span class="r-out co"><span class="r-pr">#&gt;</span> z</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span> <span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x558a2eae42c0&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x56288c98c808&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:stats&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:stats&gt;</span>
</code></pre></div> </code></pre></div>
</div> </div>

2
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@ -95,6 +95,6 @@ getfun("stats::lm")
#> z$qr <- NULL #> z$qr <- NULL
#> z #> z
#> } #> }
#> <bytecode: 0x558a2eae42c0> #> <bytecode: 0x56288c98c808>
#> <environment: namespace:stats> #> <environment: namespace:stats>
``` ```

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