Deploying to gh-pages from @ 2686dee 🚀

pgt52m/week-8/study_after_workshop.html

@@ -679,9 +679,9 @@ <h1 class="title">Independent Study to consolidate this week</h1>
 </div>
 <div class="cell">
 <details class="code-fold"><summary>Answer - don’t look until you have tried!</summary><div class="sourceCode" id="cb16"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="co"># Carry out the post-hoc test</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rvlenth/emmeans">emmeans</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://rvlenth.github.io/emmeans/">emmeans</a></span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu"><a href="https://rdrr.io/pkg/emmeans/man/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">spray</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">spray</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># the signifcant comparisons are:</span></span>
 <span><span class="co"># contrast         estimate   SE df t.ratio p.value</span></span>

pgt52m/week-8/workshop.html

@@ -735,11 +735,11 @@ <h1 class="title">Workshop</h1>
 <p>The ANOVA is significant but this only tells us that species matters, meaning at least two of the means differ. To find out which means differ, we need a post-hoc test. A post-hoc (“after this”) test is done after a significant ANOVA test. There are several possible post-hoc tests and we will be using Tukey’s HSD (honestly significant difference) test <span class="citation" data-cites="tukey1949">(<a href="#ref-tukey1949" role="doc-biblioref">Tukey 1949</a>)</span> implemented in the <strong><code>emmeans</code></strong> <span class="citation" data-cites="emmeans">(<a href="#ref-emmeans" role="doc-biblioref">Lenth 2023</a>)</span> package.</p>
 <p><img src="images/do_in_R.png" class="img-fluid"> Load the package</p>
 <div class="cell">
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rvlenth/emmeans">emmeans</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://rvlenth.github.io/emmeans/">emmeans</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p><img src="images/do_in_R.png" class="img-fluid"> Carry out the post-hoc test</p>
 <div class="cell">
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/emmeans/man/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code> contrast                        estimate   SE df t.ratio p.value
  Bladdernose Seal - Harbour Seal    -6.69 2.08 87  -3.224  0.0050
@@ -753,7 +753,7 @@ <h1 class="title">Workshop</h1>
 <p>A plot can be used to visualise the result of the post-hoc which can be especially useful when there are very many comparisons.</p>
 <p><img src="images/do_in_R.png" class="img-fluid"> Plot the results of the post-hoc test:</p>
 <div class="cell">
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/emmeans/man/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
 <div>
 <figure class="figure"><p><img src="workshop_files/figure-html/unnamed-chunk-9-1.png" class="img-fluid figure-img" width="672"></p>

r4babs2/week-4/study_after_workshop.html

@@ -547,9 +547,9 @@ <h1 class="title">Independent Study to consolidate this week</h1>
 </div>
 <div class="cell">
 <details class="code-fold"><summary>Answer - don’t look until you have tried!</summary><div class="sourceCode" id="cb16"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="co"># Carry out the post-hoc test</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rvlenth/emmeans">emmeans</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://rvlenth.github.io/emmeans/">emmeans</a></span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu"><a href="https://rdrr.io/pkg/emmeans/man/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">spray</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">spray</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># the signifcant comparisons are:</span></span>
 <span><span class="co"># contrast         estimate   SE df t.ratio p.value</span></span>

r4babs2/week-4/workshop.html

@@ -603,11 +603,11 @@ <h1 class="title">Workshop</h1>
 <p>The ANOVA is significant but this only tells us that species matters, meaning at least two of the means differ. To find out which means differ, we need a post-hoc test. A post-hoc (“after this”) test is done after a significant ANOVA test. There are several possible post-hoc tests and we will be using Tukey’s HSD (honestly significant difference) test <span class="citation" data-cites="tukey1949">(<a href="#ref-tukey1949" role="doc-biblioref">Tukey 1949</a>)</span> implemented in the <strong><code>emmeans</code></strong> <span class="citation" data-cites="emmeans">(<a href="#ref-emmeans" role="doc-biblioref">Lenth 2023</a>)</span> package.</p>
 <p><img src="images/do_in_R.png" class="img-fluid"> Load the package</p>
 <div class="cell">
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rvlenth/emmeans">emmeans</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://rvlenth.github.io/emmeans/">emmeans</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p><img src="images/do_in_R.png" class="img-fluid"> Carry out the post-hoc test</p>
 <div class="cell">
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/emmeans/man/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code> contrast                        estimate   SE df t.ratio p.value
  Bladdernose Seal - Harbour Seal    -6.69 2.08 87  -3.224  0.0050
@@ -621,7 +621,7 @@ <h1 class="title">Workshop</h1>
 <p>A plot can be used to visualise the result of the post-hoc which can be especially useful when there are very many comparisons.</p>
 <p><img src="images/do_in_R.png" class="img-fluid"> Plot the results of the post-hoc test:</p>
 <div class="cell">
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/emmeans/man/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">species</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
 <div>
 <figure class="figure"><p><img src="workshop_files/figure-html/unnamed-chunk-9-1.png" class="img-fluid figure-img" width="672"></p>

r4babs2/week-5/study_after_workshop.html

@@ -417,7 +417,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
 <p>If you have just opened RStudio you will want to load the <strong><code>tidyverse</code></strong> and <strong><code>emmeans</code></strong> packages.</p>
 <div class="cell">
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyverse.tidyverse.org">tidyverse</a></span><span class="op">)</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rvlenth/emmeans">emmeans</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://rvlenth.github.io/emmeans/">emmeans</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section><section id="exercises" class="level1"><h1>Exercises</h1>
 <ol type="1">
@@ -502,7 +502,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
 </details>
 </div>
 <div class="cell">
-<details class="code-fold"><summary>Answer - don’t look until you have tried!</summary><div class="sourceCode" id="cb8"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/emmeans/man/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">spp</span> <span class="op">*</span> <span class="va">region</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span>
+<details class="code-fold"><summary>Answer - don’t look until you have tried!</summary><div class="sourceCode" id="cb8"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rvlenth.github.io/emmeans/reference/emmeans.html">emmeans</a></span><span class="op">(</span><span class="va">mod</span>, <span class="op">~</span> <span class="va">spp</span> <span class="op">*</span> <span class="va">region</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/graphics/pairs.html">pairs</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># As we suspected all the difference are between  F.concocti north</span></span>
 <span><span class="co"># and the other three groups. </span></span>