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<!DOCTYPE html>
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<title>The {squidSim} R Package Vignette Version 0.2.0 | The {squidSim} R Package Vignette Version 0.2.0</title>
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<meta name="author" content="Joel Pick" />
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<li class="chapter" data-level="" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i>The {squidSim} R package</a>
<ul>
<li class="chapter" data-level="" data-path="intro.html"><a href="intro.html#why-use-squidsim"><i class="fa fa-check"></i>Why use {squidSim}?</a></li>
<li class="chapter" data-level="" data-path="intro.html"><a href="intro.html#using-the-vignette"><i class="fa fa-check"></i>Using the vignette</a></li>
<li class="chapter" data-level="" data-path="intro.html"><a href="intro.html#installation"><i class="fa fa-check"></i>Installation</a></li>
<li class="chapter" data-level="" data-path="intro.html"><a href="intro.html#citing-squidsim"><i class="fa fa-check"></i>Citing {squidSim}</a></li>
<li class="chapter" data-level="" data-path="intro.html"><a href="intro.html#issues-and-bugs"><i class="fa fa-check"></i>Issues and bugs</a></li>
<li class="chapter" data-level="" data-path="simulate_population-function.html"><a href="simulate_population-function.html"><i class="fa fa-check"></i><code>simulate_population()</code> function</a></li>
<li class="chapter" data-level="" data-path="terminology-and-notation.html"><a href="terminology-and-notation.html"><i class="fa fa-check"></i>Terminology and notation</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">The {squidSim} R Package Vignette <br> Version 0.2.0</a>
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<section class="normal" id="section-">
<div id="header">
<h1 class="title">The {squidSim} R Package Vignette <br> Version 0.2.0</h1>
<p class="author"><em>Joel Pick</em></p>
<p class="date"><em>2025-09-06</em></p>
</div>
<div id="intro" class="section level1 unnumbered hasAnchor">
<h1>The {squidSim} R package<a href="intro.html#intro" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>The {squidSim} R package is designed to simplify data simulation from a highly flexible set of models, including:</p>
<ul>
<li>Correlated and interacting predictor variables</li>
<li>Non-Gaussian response variables (Poisson and binomial)</li>
<li>Crossed and nested hierarchical structures</li>
<li>Random intercepts and slopes</li>
<li>Univariate and multivariate data</li>
<li>Within level-specific residual variance (DHGLMs)</li>
<li>Additive genetic effects (animal models)</li>
<li>Phylogenetic effects with different models of evolution</li>
<li>Temporal and spatial autocorrelation</li>
<li>Missing data (MNAR, MAR and MCAR)</li>
<li>Temporal sampling</li>
</ul>
<p>The main idea is that anything you can model using a linear mixed effect model framework (assuming underlying multivariate normality) you can simulate using the {squidSim} package.</p>
<!-- ### SQuID ethos {-}
Create population and then sample from it
<br>
<div style="float: width: 40%; text-align: center;" >
Make Hierarchical Structure<br>
↓<br>
Simulate data<br>
↓<br>
Sample Data<br>
</div>
<br>
-->
<div id="why-use-squidsim" class="section level3 unnumbered hasAnchor">
<h3>Why use {squidSim}?<a href="intro.html#why-use-squidsim" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Starting with simulations can seem like a daunting task. The {squidSim} R package is designed to facilitate that transition, and to focus attention on the data structure and parameters needed for simulation, rather than programming knowledge.</p>
<p>{squidSim} also provides a useful tool for experienced programmers. One problematic aspect of collaborative coding (or reviewing someone else’s code) is that many people have very contrasting programming styles. A major motivation for the {squidSim} package is that it provides a consistent framework for simulations, which can be interpreted by many people rather than having to decipher someone’s personal code.</p>
</div>
<div id="using-the-vignette" class="section level3 unnumbered hasAnchor">
<h3>Using the vignette<a href="intro.html#using-the-vignette" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>If you are new to using the {squidSim} package, we recommend that you read Sections <a href="#linearmod"><strong>??</strong></a> and <a href="#hierarchical"><strong>??</strong></a> to familiarise yourself with the {squidSim} package before moving onto the more advanced topics. The later sections assume an certain level of understanding of how the functions work.</p>
<p>The vignette assumes that you have a working knowledge of R, in particular being comfortable using vectors, matrices and lists.</p>
<!--
## Functionality
This is a summary of the desired functionality laid out in the different SQuID working group documents.
| | |
| --- | --- |
| No limit in the number of predictors | ✅ |
| Interactions between predictors | ✅ |
| Temporal effects | |
| - Linear/non-linear/cyclical| ✅ |
| - Temporal autocorrelation| ❌ |
| Non-Gaussian data | ✅ |
| IxE / random slopes | ✅ |
| Within level-specific residual variance (DGLMM) | ✅ |
| - Equation on residual variance | ✅ |
| No limit in the number of responses | ✅ |
| Recursive relationships | ❌ |
| Environmental dependency of cov matrices | Needs Discussion |
| Additive genetic effects | ✅ |
| - Including indirect genetic effects | ✅ |
| G,E correlations | In Progress |
| Phylogenetic effects | In Progress |
| - Different models of evolution | ❌ |
<br>
-->
</div>
<div id="installation" class="section level3 unnumbered hasAnchor">
<h3>Installation<a href="intro.html#installation" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>The {squidSim} package is currently only available on github:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="intro.html#cb1-1" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"squidgroup/squidSim"</span>)</span>
<span id="cb1-2"><a href="intro.html#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(squidSim)</span></code></pre></div>
</div>
<div id="citing-squidsim" class="section level3 unnumbered hasAnchor">
<h3>Citing {squidSim}<a href="intro.html#citing-squidsim" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>R packages take a lot of investment to create and maintain. We would therefore appreciate it if you cited squidSim when you used it.</p>
<p>Please cite our pre-print:</p>
</div>
<div id="issues-and-bugs" class="section level3 unnumbered hasAnchor">
<h3>Issues and bugs<a href="intro.html#issues-and-bugs" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>It would be great if you could report any suggestions, issues or bugs; <a href="https://github.com/squidgroup/squidSim/issues">here</a> for issues relating to the package, and <a href="https://github.com/squidgroup/squidSim_vignette/issues">here</a> for issues relating to this vignette. It is worth checking to see if anyone else has a similar problem first, and adding comments to their issue, before starting a new one.</p>
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