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@ -82,47 +82,43 @@
<div class="section level2">
<h2 id="getting-started-with-freesearchr">Getting started with <strong><em>FreesearchR</em></strong><a class="anchor" aria-label="anchor" href="#getting-started-with-freesearchr"></a>
</h2>
<p>Below is a simple walk-trough and basic instructions for the
functions on the FreesearchR app.</p>
<p>Below is a simple walk-trough and basic descriptions on the different
features of the <strong><em>FreesearchR</em></strong> app.</p>
<div class="section level3">
<h3 id="launching">Launching<a class="anchor" aria-label="anchor" href="#launching"></a>
</h3>
<p>The easiest way to get started is to launch <a href="https://agdamsbo.shinyapps.io/freesearcheR/" class="external-link">the hosted version of
the app on shinyapps.io (click this link)</a>.</p>
<p>Additionally you have the option to run the app locally with access
to any data in your current working environment.</p>
<p>To do this, open <em>R</em> (or RStudio or similar), and run the
following code to install the latest version of
<strong><em>FreesearchR</em></strong> and launch the app:</p>
<p>The easiest way to get started is to launch <a href="https://app.freesearchr.org/" class="external-link">the onlie version of the app (click
this link)</a>. Please be aware not to upload sensitive data in this
version as data security can not be guaranteed in this online
environment. The app can easily be run from <em>R</em> on your own
computer by running the code below (<a href="https://agdamsbo.github.io/FreesearchR/#run-locally-on-your-own-machine">read
more on running locally here</a>):</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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://pak.r-lib.org/" class="external-link">"pak"</a></span><span class="op">)</span></span>
<span><span class="fu">pak</span><span class="fu">::</span><span class="fu"><a href="https://pak.r-lib.org/reference/pak.html" class="external-link">pak</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="fu">FreesearchR</span><span class="fu">::</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></div>
<p>As a small note, a standalone Windows app version is on the drawing
board as well, but no time frame is available.</p>
board as well, but no time frame is currently available.</p>
</div>
<div class="section level3">
<h3 id="importing-data">Importing data<a class="anchor" aria-label="anchor" href="#importing-data"></a>
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
</h3>
<p>Once in the app and in the “<strong>Import</strong>”, you have three
<p>Once in the app, get started by loading your data. You have three
options available for importing data: file upload, REDCap server export
and local or sample data.</p>
<p>After choosing a data source, you can set a threshold to filter data
be completenes and further manually specify variables to include for
analyses.</p>
<p>After choosing a data source nad importing data, you can preview the
basic data structure and missing observations, set a threshold to filter
data by completeness and further manually specify variables to include
for analyses.</p>
<div class="section level4">
<h4 id="file-upload">File upload<a class="anchor" aria-label="anchor" href="#file-upload"></a>
</h4>
<p>Currently several data file formats are supported for easy import
(csv, txt, xls(x), ods, rds, dta). If importing workbooks (xls(x) or
ods), you are prompted to specify sheet(s) to import. If choosing
multiple sheets, these are automatically merged by common variable(s),
so please make sure that key variables are correctly named
identically.</p>
<p>A notification is posted with error or success. After succesfull
import data can be previewed directly by clicking “click to see data” in
the notification.</p>
<p>Several data file formats are supported for easy import (csv, txt,
xls(x), ods, rds, dta). If importing workbooks (xls(x) or ods), you are
prompted to specify sheet(s) to import. If choosing multiple sheets,
these are automatically merged by common variable(s), so please make
sure that key/ID variables are correctly named identically.</p>
</div>
<div class="section level4">
<h4 id="redcap-server-export">REDCap server export<a class="anchor" aria-label="anchor" href="#redcap-server-export"></a>
@ -134,7 +130,7 @@ rights to do so.</p>
<p>Please don’t store the API-key on your device unless encrypted or in
a keyring, as this may compromise data safety. Log in to your REDCap
server and retrieve the token when needed.</p>
<p>Type the correct webaddress of your REDCap server.</p>
<p>Type the correct web address of your REDCap server.</p>
<p>The module will validate the information and you can click
“Connect”.</p>
<p>This will unfold options to preview your data dictionary (the main
@ -144,19 +140,19 @@ filtering options.</p>
<div class="section level4">
<h4 id="local-or-sample-data">Local or sample data<a class="anchor" aria-label="anchor" href="#local-or-sample-data"></a>
</h4>
<p>When opening the online hosted app, this is mainly for testing
purposes. When running the app locally from <em>R</em> on your own
computer, you will find all data.frames in the current environment here.
This extends the possible uses of this app to allow for quick and easy
data insights and code generation for basic plotting to fine tune.</p>
<p>When opening the online hosted app, you can load some sample data to
try out the app. When running the app locally from <em>R</em> on your
own computer, you will find all data frames loaded in your environment
here. This extends the possible uses of this app to allow for quick and
easy data insights and code generation.</p>
</div>
</div>
<div class="section level3">
<h3 id="data">Data<a class="anchor" aria-label="anchor" href="#data"></a>
<h3 id="prepare">Prepare<a class="anchor" aria-label="anchor" href="#prepare"></a>
</h3>
<p>This is the panel to get a good overview of your data, check data is
classed and formatted correctly, perform simple modifications and filter
data.</p>
<p>This is the panel to prepare data for evaluation and analyses and get
a good overview of your data, check data is classed and formatted
correctly, perform simple modifications and filter data.</p>
<div class="section level4">
<h4 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
</h4>
@ -341,6 +337,9 @@ analyses you should probably just write the code yourself.</p>
</h4>
<p>Generate simple regression models and get the results in a nice
table. This will also be included in the exported report.</p>
<p>This will generate a combined table with both univariate regression
model results for each included variable and a multivariate model with
all variables included for explorative analyses.</p>
</div>
<div class="section level4">
<h4 id="plots">Plots<a class="anchor" aria-label="anchor" href="#plots"></a>
@ -349,7 +348,7 @@ table. This will also be included in the exported report.</p>
Choose which model(s) to include.</p>
</div>
<div class="section level4">
<h4 id="checks">Checks<a class="anchor" aria-label="anchor" href="#checks"></a>
<h4 id="model-checks">Model checks<a class="anchor" aria-label="anchor" href="#model-checks"></a>
</h4>
<p>Check model assumptions visually. Supported checks can be chosen.</p>
</div>
@ -364,7 +363,7 @@ Choose which model(s) to include.</p>
model results. Choose between MS Word or LibreOffice format.</p>
</div>
<div class="section level4">
<h4 id="data-1">Data<a class="anchor" aria-label="anchor" href="#data-1"></a>
<h4 id="data">Data<a class="anchor" aria-label="anchor" href="#data"></a>
</h4>
<p>Export the modified dataset in different formats.</p>
</div>