This document presents the different steps to follow to produce a Joint Species Distribution Models (JSDM) and more precisely the one presented by Ovaskainen et al (2017) using the Hmsc package. This document is divided into several parts. First, the i...

Functions and iteration Introduction Functions in R allow us to automate things, instead of copy-pasting code. 3 major advantages : Functions can have names, so it makes code easier to read If your requirements change, you only have one place ...

Meta-analysis

<span class="n">library</span><span class="p">(</span><span class="n">dplyr</span><span class="p">)</span><span class="w"> </span><span class="c1"># data manipulation</span><span class="w">
</span><span class="n">library</span><span class="p">(</span><span class="n">ggplot2</span><span class="p">)</span><span class="w"> </span><span class="c1"># visualizations</span><span class="w">
</span><span class="n">library</span><span class="p">(</span><span class="n">metafor</span><span class="p">)</span><span class="w"> </span><span class="c1"># ready-made meta-analysis code</span><span class="w">
</span><span class="n">library</span><span class="p">(</span><span class="n">gt</span><span class="p">)</span><span class="w"> </span><span class="c1"># nice tables</span><span class="w">
</span>

Basic principle Scientific question Does playing Mozart to newborns improves their IQ? You look a bit around and find 3 studies :

<span class="n">etudes</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">data.frame</span><span class="p">(</span><span class="w">
  </span><span class="n">article</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="s2">"A"</span><span class="p">,</span><span class="s2">"B"</span><span class="p">,</span><span class="s2">"C"</span><span class="p">),</span><span class="w">
  </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="m">0.5</span><span class="p">,</span><span class="w"> </span><span class="m">0.01</span><span class="p">,</span><span class="w"> </span><span class="m">-0.1</span><span class="p">),</span><span class="w"> </span><span class="c1"># 0 no effect, <0 negative effect, >0 positive effect</span><span class="w">
  </span><span class="n">n</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="m">10</span><span class="p">,</span><span class="m">150</span><span class="p">,</span><span class="m">12</span><span class="p">),</span><span class="w">
  </span><span class="n">v</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="m">0.04</span><span class="p">,</span><span class="m">0.01</span><span class="p">,</span><span class="w"> </span><span class="m">0.03</span><span class="p">)</span><span class="w"> </span><span class="c1"># variance</span><span class="w">
</span><span class="p">)</span><span class="w">
</span><span class="n">etudes</span><span class="w"> </span><span class="o">%>%</span><span class="w"> </span><span class="n">gt</span><span class="w">
</span>

article y n v A 0.50 10 0.04 B 0.01 150 0.01 C -0.10 12 0.03 A simplistic way

<span class="n">etudes</span><span class="w"> </span><span class="o">%>%</span><span class="w">
  </span><span class="n">summarise</span><span class="p">(</span><span class="w">
    </span><span class="n">effet_resume</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">mean</span><span class="p">(</span><span class="n">y</span><span class="p">)</span><span class="w">
  </span><span class="p">)</span><span class="w">
</span>

  effet_resume
1    0.1366667

Weighted mean When we talk about mean, we usually refer to the arithmetic mean : {{...