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<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">IntroSlides with focus on statistics</h1>
<div class="quarto-title-authors">
</div>
</section>
<section id="basic-steps-in-workflow" class="slide level2">
<h2>Basic steps in workflow</h2>
<ol type="1">
<li><em>Define environment</em></li>
<li><em>Import</em></li>
<li><em>Transform</em></li>
<li><em>Explore (general/outlier/distribution) (go back to 3?)</em></li>
<li><em>Classify scale level / distribution (based on 3/4)</em></li>
<li><em>Describe</em></li>
<li><em>Test / Model (may include step 6)</em></li>
<li><em>Report</em></li>
</ol>
</section>
<section id="define-environment" class="slide level2">
<h2>Define environment</h2>
<ul>
<li><em>Activate packages to use: library() / pacman::p_load()</em></li>
<li><em>ggplot theme: theme_set() / theme_update()</em></li>
<li><em>flextable settings: set_flextable_defaults()</em></li>
<li><em>knitr::opts_chunk$set()</em></li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href=""></a><span class="cf">if</span>(<span class="sc">!</span><span class="fu">requireNamespace</span>(<span class="st">"pacman"</span>)){<span class="fu">install.packages</span>(<span class="st">"pacman"</span>)}</span>
<span id="cb1-2"><a href=""></a>pacman<span class="sc">::</span><span class="fu">p_load</span>(conflicted,tidyverse,wrappedtools, readxl,car, flextable,</span>
<span id="cb1-3"><a href=""></a> ggbeeswarm, ggsignif, ggridges, patchwork,ggrepel, easystats)</span>
<span id="cb1-4"><a href=""></a></span>
<span id="cb1-5"><a href=""></a><span class="fu">conflicts_prefer</span>(dplyr<span class="sc">::</span>filter,dplyr<span class="sc">::</span>select)</span>
<span id="cb1-6"><a href=""></a><span class="fu">theme_set</span>(<span class="fu">theme_light</span>(<span class="at">base_size =</span> <span class="dv">20</span>))</span>
<span id="cb1-7"><a href=""></a>gdtools<span class="sc">::</span><span class="fu">register_gfont</span>(<span class="st">'Roboto'</span>)<span class="co"># Mono')</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>[1] TRUE</code></pre>
</div>
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href=""></a><span class="fu">set_flextable_defaults</span>(</span>
<span id="cb3-2"><a href=""></a> <span class="at">theme_fun =</span> theme_zebra, <span class="at">font.size =</span> <span class="dv">18</span>, <span class="at">font.family =</span> <span class="st">'Roboto'</span>,</span>
<span id="cb3-3"><a href=""></a> <span class="at">table.layout =</span> <span class="st">'autofit'</span>,</span>
<span id="cb3-4"><a href=""></a> <span class="at">padding.bottom =</span> .<span class="dv">2</span>, <span class="at">padding.top =</span> .<span class="dv">2</span>, <span class="at">padding.left =</span> <span class="dv">2</span>, <span class="at">padding.right =</span> <span class="dv">2</span>)</span>
<span id="cb3-5"><a href=""></a></span>
<span id="cb3-6"><a href=""></a>knitr<span class="sc">::</span>opts_chunk<span class="sc">$</span><span class="fu">set</span>(<span class="at">message =</span> <span class="cn">FALSE</span>, <span class="at">warning =</span> <span class="cn">FALSE</span>, <span class="at">comment =</span> <span class="cn">NA</span>, <span class="at">echo =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="import" class="slide level2">
<h2>Import</h2>
<ul>
<li><em>read_xlsx() / read_csv() / read_csv2() / read_spss() / read_sas() / DBI::xx() / dbplyr::xx()</em></li>
<li>options related to separators, number formats, ranges etc.</li>
<li><em>rename() / rename_with()</em></li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href=""></a>rawdata <span class="ot"><-</span> <span class="fu">read_excel</span>(<span class="st">'Data/DOC-20230130-WA0000_.xlsx'</span>,</span>
<span id="cb4-2"><a href=""></a> <span class="at">sheet =</span> <span class="dv">1</span>,<span class="at">col_names =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="glimpse-at-data-find-the-problems" class="slide level2">
<h2>Glimpse at data: Find the problems?</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href=""></a><span class="fu">head</span>(rawdata,<span class="at">n =</span> <span class="dv">15</span>) <span class="sc">|></span> <span class="fu">flextable</span>()<span class="sc">|></span> </span>
<span id="cb5-2"><a href=""></a> <span class="fu">theme_zebra</span>(<span class="at">even_body =</span> <span class="st">'aquamarine'</span>,<span class="at">odd_body =</span> <span class="st">'antiquewhite'</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 class="tabwid"><style>.cl-78492e46{table-layout:auto;}.cl-78423afa{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-78423b0e{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-784506f4{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-784506fe{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-78451dd8{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-78451de2{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-78451de3{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-78451dec{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-78451ded{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-78451df6{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-78492e46"><thead><tr style="overflow-wrap:break-word;"><th class="cl-78451dd8"><p class="cl-784506f4"><span class="cl-78423afa">CODE OF CUP</span></p></th><th class="cl-78451dd8"><p class="cl-784506f4"><span class="cl-78423afa">CODE OF SAMPLE</span></p></th><th class="cl-78451de2"><p class="cl-784506fe"><span class="cl-78423afa">WEIGHT OF EMPTY ALUMINUM(wt)</span></p></th><th class="cl-78451de2"><p class="cl-784506fe"><span class="cl-78423afa">WEIGTH OF ALMINIUM CUP + SAMPLE (Wt + s)</span></p></th><th class="cl-78451de2"><p class="cl-784506fe"><span class="cl-78423afa">WEIGTH OF ALUMINIUM CAP + SAMPLE AFTER DRYING (Wt-AL +s+d)</span></p></th><th class="cl-78451de2"><p class="cl-784506fe"><span class="cl-78423afa">weight of sample before drying (Wts)</span></p></th><th class="cl-78451de2"><p class="cl-784506fe"><span class="cl-78423afa">weight of sample after drying (Wts+d)</span></p></th><th class="cl-78451de2"><p class="cl-784506fe"><span class="cl-78423afa">MOISTURE CONTENT (%)</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">69</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.1974</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">9.3865</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.7000</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">5.1891</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.6865</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">90.31431</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e"></span></p></td><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.1964</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">9.2734</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.4670</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">5.0770</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.8064</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">94.67008</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">A</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.2108</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">9.2653</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.6670</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">5.0545</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.5983</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">90.97438</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">114</span></p></td><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.2134</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">9.3146</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.6345</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">5.1012</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.6801</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">91.74508</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">M1</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.1856</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">9.3147</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.6171</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">5.1291</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.6976</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">91.58722</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">a/17</span></p></td><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.2090</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">9.3204</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.5661</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">5.1114</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.7543</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">93.01366</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">8</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.1894</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">9.2661</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.5778</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">5.0767</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.6883</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">92.34936</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">33</span></p></td><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.1968</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">9.2880</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.6057</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">5.0912</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.6823</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">91.96849</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">M</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.1535</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">9.2872</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.6350</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">5.1337</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.6522</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">90.62080</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">E/18/1</span></p></td><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.2534</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">9.2476</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.7403</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.9942</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.5073</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">90.25069</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">24/A2</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">D</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.2066</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">8.3463</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.5849</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.1397</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">3.7614</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">90.86166</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">13</span></p></td><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">A</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.1554</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">9.2384</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.7402</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">5.0830</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.4982</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">88.49498</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">Xp</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">A</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.1893</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">9.2495</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.7381</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">5.0602</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.5114</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">89.15458</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">2p/029</span></p></td><td class="cl-78451ded"><p class="cl-784506f4"><span class="cl-78423b0e">A</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.0654</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">9.2173</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.6940</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">5.1519</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">4.5233</span></p></td><td class="cl-78451df6"><p class="cl-784506fe"><span class="cl-78423b0e">87.79868</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">15</span></p></td><td class="cl-78451de3"><p class="cl-784506f4"><span class="cl-78423b0e">A</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.0641</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">9.2032</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.8124</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">5.1391</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">4.3908</span></p></td><td class="cl-78451dec"><p class="cl-784506fe"><span class="cl-78423b0e">85.43908</span></p></td></tr></tbody></table></div>
</div>
</div>
</section>
<section id="rename" class="slide level2">
<h2>Rename</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href=""></a><span class="fu">colnames</span>(rawdata)</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>[1] "CODE OF CUP"
[2] "CODE OF SAMPLE"
[3] "WEIGHT OF EMPTY ALUMINUM(wt)"
[4] "WEIGTH OF ALMINIUM CUP + SAMPLE (Wt + s)"
[5] "WEIGTH OF ALUMINIUM CAP + SAMPLE AFTER DRYING (Wt-AL +s+d)"
[6] "weight of sample before drying (Wts)"
[7] "weight of sample after drying (Wts+d)"
[8] "MOISTURE CONTENT (%)" </code></pre>
</div>
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href=""></a>rawdata <span class="ot"><-</span> rawdata <span class="sc">|></span> </span>
<span id="cb8-2"><a href=""></a> <span class="fu">rename</span>(<span class="at">Region=</span><span class="st">`</span><span class="at">CODE OF SAMPLE</span><span class="st">`</span>) <span class="sc">|></span> </span>
<span id="cb8-3"><a href=""></a> <span class="fu">rename_with</span>(<span class="at">.fn =</span> <span class="sc">~</span><span class="fu">str_replace_all</span>(</span>
<span id="cb8-4"><a href=""></a> .,</span>
<span id="cb8-5"><a href=""></a> <span class="fu">c</span>(<span class="st">"GTH"</span><span class="ot">=</span><span class="st">"GHT"</span>, <span class="st">'AL.+UM'</span><span class="ot">=</span> <span class="st">'Cup'</span>, </span>
<span id="cb8-6"><a href=""></a> <span class="st">'C[UA]P'</span> <span class="ot">=</span> <span class="st">'Cup'</span>,<span class="st">'</span><span class="sc">\\</span><span class="st">(</span><span class="sc">\\</span><span class="st">w+.*</span><span class="sc">\\</span><span class="st">)'</span><span class="ot">=</span><span class="st">''</span>,</span>
<span id="cb8-7"><a href=""></a> <span class="st">'Cup Cup'</span><span class="ot">=</span><span class="st">'Cup'</span>,<span class="st">' '</span><span class="ot">=</span><span class="st">' '</span>)) <span class="sc">|></span> </span>
<span id="cb8-8"><a href=""></a> <span class="fu">str_to_title</span>() <span class="sc">|></span> <span class="fu">str_trim</span>())</span>
<span id="cb8-9"><a href=""></a><span class="fu">cn</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>[1] "Code Of Cup" "Region"
[3] "Weight Of Empty Cup" "Weight Of Cup + Sample"
[5] "Weight Of Cup + Sample After Drying" "Weight Of Sample Before Drying"
[7] "Weight Of Sample After Drying" "Moisture Content (%)" </code></pre>
</div>
</div>
</section>
<section id="transform" class="slide level2">
<h2>Transform</h2>
<ul>
<li><em>Change or create columns with mutate() / mutate(across())</em></li>
<li><em>e.g. for log-transformation, creation of factors, text recoding</em></li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb10"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href=""></a>rawdata <span class="ot"><-</span> rawdata <span class="sc">|></span> </span>
<span id="cb10-2"><a href=""></a> <span class="fu">mutate</span>(</span>
<span id="cb10-3"><a href=""></a> <span class="st">`</span><span class="at">Code Of Cup</span><span class="st">`</span><span class="ot">=</span><span class="fu">case_when</span>(</span>
<span id="cb10-4"><a href=""></a> <span class="fu">is.na</span>(<span class="st">`</span><span class="at">Code Of Cup</span><span class="st">`</span>)<span class="sc">~</span><span class="fu">paste</span>(<span class="st">"sample"</span>,<span class="fu">row_number</span>()),</span>
<span id="cb10-5"><a href=""></a> <span class="at">.default =</span> <span class="st">`</span><span class="at">Code Of Cup</span><span class="st">`</span>),</span>
<span id="cb10-6"><a href=""></a> <span class="st">`</span><span class="at">Weight Of Sample After Drying</span><span class="st">`</span><span class="ot">=</span><span class="st">`</span><span class="at">Weight Of Cup + Sample After Drying</span><span class="st">`</span><span class="sc">-</span></span>
<span id="cb10-7"><a href=""></a> <span class="st">`</span><span class="at">Weight Of Empty Cup</span><span class="st">`</span>,</span>
<span id="cb10-8"><a href=""></a> <span class="st">`</span><span class="at">Dry Content (%)</span><span class="st">`</span><span class="ot">=</span><span class="st">`</span><span class="at">Weight Of Sample After Drying</span><span class="st">`</span><span class="sc">*</span><span class="dv">100</span><span class="sc">/</span></span>
<span id="cb10-9"><a href=""></a> <span class="st">`</span><span class="at">Weight Of Sample Before Drying</span><span class="st">`</span>,</span>
<span id="cb10-10"><a href=""></a> <span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span><span class="ot">=</span><span class="dv">100</span><span class="sc">-</span><span class="st">`</span><span class="at">Dry Content (%)</span><span class="st">`</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="cell-output-display">
<div class="tabwid"><style>.cl-787b3652{table-layout:auto;}.cl-7874fefe{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7874ff08{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-78779c2c{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-78779c36{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7877aff0{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7877affa{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7877affb{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7877b004{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7877b00e{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7877b00f{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-787b3652"><thead><tr style="overflow-wrap:break-word;"><th class="cl-7877aff0"><p class="cl-78779c2c"><span class="cl-7874fefe">Code Of Cup</span></p></th><th class="cl-7877aff0"><p class="cl-78779c2c"><span class="cl-7874fefe">Region</span></p></th><th class="cl-7877affa"><p class="cl-78779c36"><span class="cl-7874fefe">Weight Of Empty Cup</span></p></th><th class="cl-7877affa"><p class="cl-78779c36"><span class="cl-7874fefe">Weight Of Cup + Sample</span></p></th><th class="cl-7877affa"><p class="cl-78779c36"><span class="cl-7874fefe">Weight Of Cup + Sample After Drying</span></p></th><th class="cl-7877affa"><p class="cl-78779c36"><span class="cl-7874fefe">Weight Of Sample Before Drying</span></p></th><th class="cl-7877affa"><p class="cl-78779c36"><span class="cl-7874fefe">Weight Of Sample After Drying</span></p></th><th class="cl-7877affa"><p class="cl-78779c36"><span class="cl-7874fefe">Moisture Content (%)</span></p></th><th class="cl-7877affa"><p class="cl-78779c36"><span class="cl-7874fefe">Dry Content (%)</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-7877affb"><p class="cl-78779c2c"><span class="cl-7874ff08">69</span></p></td><td class="cl-7877affb"><p class="cl-78779c2c"><span class="cl-7874ff08">D</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">4.1974</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">9.3865</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">4.7000</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">5.1891</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">0.5026</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">90.31431</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">9.685687</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7877b00e"><p class="cl-78779c2c"><span class="cl-7874ff08">sample 2</span></p></td><td class="cl-7877b00e"><p class="cl-78779c2c"><span class="cl-7874ff08">D</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">4.1964</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">9.2734</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">4.4670</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">5.0770</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">0.2706</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">94.67008</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">5.329919</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7877affb"><p class="cl-78779c2c"><span class="cl-7874ff08">A</span></p></td><td class="cl-7877affb"><p class="cl-78779c2c"><span class="cl-7874ff08">D</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">4.2108</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">9.2653</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">4.6670</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">5.0545</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">0.4562</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">90.97438</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">9.025621</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7877b00e"><p class="cl-78779c2c"><span class="cl-7874ff08">114</span></p></td><td class="cl-7877b00e"><p class="cl-78779c2c"><span class="cl-7874ff08">D</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">4.2134</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">9.3146</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">4.6345</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">5.1012</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">0.4211</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">91.74508</span></p></td><td class="cl-7877b00f"><p class="cl-78779c36"><span class="cl-7874ff08">8.254920</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7877affb"><p class="cl-78779c2c"><span class="cl-7874ff08">M1</span></p></td><td class="cl-7877affb"><p class="cl-78779c2c"><span class="cl-7874ff08">D</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">4.1856</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">9.3147</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">4.6171</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">5.1291</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">0.4315</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">91.58722</span></p></td><td class="cl-7877b004"><p class="cl-78779c36"><span class="cl-7874ff08">8.412782</span></p></td></tr></tbody></table></div>
</div>
</div>
</section>
<section id="explore-group-variables" class="slide level2">
<h2>Explore / group variables</h2>
<h3 id="explore-generaloutlierdistribution"><em>Explore (general/outlier/distribution)</em></h3>
<ul>
<li><em>ggplot()+geom_boxplot() / geom_beeswarm() / geom_density()</em></li>
<li><em>ks.test() / ksnormal() / shapiro.test()</em></li>
</ul>
<h3 id="classify-scale-level-distribution"><em>Classify scale level / distribution</em></h3>
<ul>
<li><em>gaussvars / ordvars / factvars, possibly more…</em></li>
<li><em>Store variables accordingly, e.g. ColSeeker()</em></li>
</ul>
</section>
<section id="explore-outlier" class="slide level2">
<h2><em>Explore: Outlier</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href=""></a>p1 <span class="ot"><-</span> <span class="fu">ggplot</span>(<span class="at">data =</span> rawdata, <span class="fu">aes</span>(<span class="at">x =</span> <span class="st">`</span><span class="at">Region</span><span class="st">`</span>, <span class="at">y =</span> <span class="st">`</span><span class="at">Weight Of Empty Cup</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb11-2"><a href=""></a> <span class="fu">geom_boxplot</span>(<span class="at">outlier.alpha =</span> <span class="dv">0</span>) <span class="sc">+</span> <span class="co">#hide outliers, beeswarm will plot them</span></span>
<span id="cb11-3"><a href=""></a> <span class="fu">geom_beeswarm</span>(<span class="at">alpha=</span>.<span class="dv">5</span>, <span class="at">color=</span><span class="st">"darkorange"</span>)</span>
<span id="cb11-4"><a href=""></a>p2 <span class="ot"><-</span> <span class="fu">ggplot</span>(<span class="at">data =</span> rawdata, <span class="fu">aes</span>(<span class="at">x =</span> <span class="st">`</span><span class="at">Region</span><span class="st">`</span>, <span class="at">y =</span> <span class="st">`</span><span class="at">Weight Of Sample Before Drying</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb11-5"><a href=""></a> <span class="fu">geom_boxplot</span>(<span class="at">outlier.alpha =</span> <span class="dv">0</span>) <span class="sc">+</span> </span>
<span id="cb11-6"><a href=""></a> <span class="fu">geom_beeswarm</span>(<span class="at">alpha=</span>.<span class="dv">5</span>, <span class="at">color=</span><span class="st">"darkorange"</span>) </span>
<span id="cb11-7"><a href=""></a>p2 <span class="ot"><-</span> <span class="fu">label_outliers</span>(p2, <span class="at">labelvar =</span> <span class="st">"Code Of Cup"</span>)<span class="co">#+</span></span>
<span id="cb11-8"><a href=""></a>p1<span class="sc">|</span>p2</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-7-1.png" class="r-stretch"></section>
<section id="handle-outliers" class="slide level2">
<h2>Handle outliers?</h2>
<p>Removal is the worst strategy possible, correct errors, think about distributions, winsorize…</p>
<img data-src="Figures/outlier.jpg" class="r-stretch"></section>
<section id="explore-unexpecteds" class="slide level2">
<h2><em>Explore: Unexpecteds</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb12"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb12-1"><a href=""></a><span class="fu">ggplot</span>(<span class="at">data =</span> rawdata,</span>
<span id="cb12-2"><a href=""></a> <span class="fu">aes</span>(<span class="at">x =</span> <span class="st">`</span><span class="at">Region</span><span class="st">`</span>,</span>
<span id="cb12-3"><a href=""></a> <span class="at">y =</span> <span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb12-4"><a href=""></a> <span class="fu">geom_boxplot</span>(<span class="at">outlier.alpha =</span> <span class="dv">0</span>) <span class="sc">+</span> </span>
<span id="cb12-5"><a href=""></a> <span class="fu">geom_beeswarm</span>(<span class="at">alpha=</span>.<span class="dv">5</span>, <span class="at">size =</span> <span class="fl">2.5</span>, <span class="at">color=</span><span class="st">"darkorange"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-8-1.png" class="r-stretch"></section>
<section id="transform-subregions" class="slide level2">
<h2>Transform Subregions?</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href=""></a>rawdata <span class="ot"><-</span> <span class="fu">mutate</span>(rawdata, <span class="at">Subregion =</span> <span class="fu">case_when</span>(</span>
<span id="cb13-2"><a href=""></a> <span class="st">`</span><span class="at">Region</span><span class="st">`</span><span class="sc">==</span><span class="st">'D'</span> <span class="sc">~</span> <span class="st">'D'</span>,</span>
<span id="cb13-3"><a href=""></a> <span class="st">`</span><span class="at">Region</span><span class="st">`</span><span class="sc">==</span><span class="st">'A'</span> <span class="sc">&</span> <span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span> <span class="sc">></span> <span class="dv">90</span> <span class="sc">~</span> <span class="st">'A high'</span>,</span>
<span id="cb13-4"><a href=""></a> <span class="st">`</span><span class="at">Region</span><span class="st">`</span><span class="sc">==</span><span class="st">'A'</span> <span class="sc">&</span> <span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span> <span class="sc"><=</span> <span class="dv">90</span> <span class="sc">~</span> <span class="st">'A low'</span>) <span class="sc">|></span></span>
<span id="cb13-5"><a href=""></a> <span class="fu">factor</span>())</span>
<span id="cb13-6"><a href=""></a><span class="co"># Test for Region A is redundant here, but more verbose.</span></span>
<span id="cb13-7"><a href=""></a></span>
<span id="cb13-8"><a href=""></a><span class="fu">ggplot</span>(<span class="at">data =</span> rawdata,<span class="fu">aes</span>(<span class="at">x =</span> <span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>,<span class="at">y=</span>Subregion))<span class="sc">+</span></span>
<span id="cb13-9"><a href=""></a> <span class="fu">geom_density_ridges</span>(<span class="at">alpha=</span>.<span class="dv">5</span>, <span class="at">scale=</span><span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-9-1.png" class="r-stretch"></section>
<section id="explore-normal-distribution-1" class="slide level2">
<h2><em>Explore: Normal distribution 1</em></h2>
<ul>
<li><p>Gaussian Normal distribution is required for many statistical procedures</p></li>
<li><p>Common tests are graphical exploration, Shapiro-Wilk-test and Kolmogorov-Smirnov-test</p></li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb14"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href=""></a>p_normal <span class="ot"><-</span> </span>
<span id="cb14-2"><a href=""></a> <span class="fu">shapiro.test</span>(<span class="at">x =</span> rawdata<span class="sc">$</span><span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>)</span>
<span id="cb14-3"><a href=""></a>p_normal</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>
Shapiro-Wilk normality test
data: rawdata$`Moisture Content (%)`
W = 0.89133, p-value = 0.003752</code></pre>
</div>
</div>
</section>
<section id="section" class="slide level2">
<h2></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href=""></a><span class="fu">ggplot</span>(<span class="at">data =</span> rawdata,<span class="fu">aes</span>(<span class="at">x =</span> <span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>,<span class="at">fill=</span><span class="st">`</span><span class="at">Subregion</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb16-2"><a href=""></a> <span class="fu">geom_density</span>(<span class="at">linewidth=</span><span class="dv">3</span>, <span class="at">alpha=</span>.<span class="dv">5</span>)<span class="sc">+</span></span>
<span id="cb16-3"><a href=""></a> <span class="fu">labs</span>(<span class="at">title =</span> <span class="fu">paste</span>(<span class="st">'p (Shapiro) global'</span>,</span>
<span id="cb16-4"><a href=""></a> <span class="fu">formatP</span>(<span class="at">pIn =</span> p_normal<span class="sc">$</span>p.value, <span class="at">pretext =</span> T)),</span>
<span id="cb16-5"><a href=""></a> <span class="at">subtitle =</span> rawdata <span class="sc">|></span> <span class="fu">group_by</span>(Subregion) <span class="sc">|></span> </span>
<span id="cb16-6"><a href=""></a> <span class="fu">summarize</span>(<span class="at">pNormal=</span><span class="fu">shapiro.test</span>(<span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>)<span class="sc">$</span>p.value <span class="sc">|></span> <span class="fu">formatP</span>()) <span class="sc">|></span> </span>
<span id="cb16-7"><a href=""></a> <span class="fu">unite</span>(<span class="st">'p(Normal)'</span>,<span class="at">sep =</span> <span class="st">': p='</span>) <span class="sc">|></span> <span class="fu">pull</span>(<span class="dv">1</span>) <span class="sc">|></span> <span class="fu">paste</span>(<span class="at">collapse =</span> <span class="st">'; '</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-11-1.png" class="r-stretch"></section>
<section id="explore-normal-distribution-2" class="slide level2">
<h2><em>Explore: Normal distribution 2</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href=""></a>rawdata <span class="sc">|></span> </span>
<span id="cb17-2"><a href=""></a> <span class="fu">group_by</span>(<span class="st">`</span><span class="at">Subregion</span><span class="st">`</span>) <span class="sc">|></span> </span>
<span id="cb17-3"><a href=""></a> <span class="fu">summarize</span>(<span class="fu">across</span>(<span class="at">.cols =</span> <span class="fu">where</span>(is.numeric), </span>
<span id="cb17-4"><a href=""></a> <span class="at">.fns =</span> <span class="sc">~</span><span class="fu">ksnormal</span>(.x) <span class="sc">|></span> <span class="co">#computing p-value</span></span>
<span id="cb17-5"><a href=""></a> <span class="fu">formatP</span>(<span class="at">mark =</span> T))) <span class="sc">|></span> <span class="co">#formatting p-value</span></span>
<span id="cb17-6"><a href=""></a> <span class="fu">pivot_longer</span>(<span class="at">cols =</span> <span class="sc">-</span><span class="dv">1</span>, <span class="at">names_to =</span> <span class="st">'Variable'</span>, </span>
<span id="cb17-7"><a href=""></a> <span class="at">values_to =</span> <span class="st">'pKS'</span>) <span class="sc">|></span> <span class="co">#intermediate, all p-values in 1 column</span></span>
<span id="cb17-8"><a href=""></a> <span class="fu">pivot_wider</span>(<span class="at">names_from =</span> <span class="st">`</span><span class="at">Subregion</span><span class="st">`</span>, </span>
<span id="cb17-9"><a href=""></a> <span class="at">values_from =</span> pKS) <span class="co">#spreading across subregions</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># A tibble: 7 × 4
Variable `A high` `A low` D
<chr> <chr> <chr> <chr>
1 Weight Of Empty Cup 0.842 n.s. 0.033 * 0.173 n.s.
2 Weight Of Cup + Sample 0.270 n.s. 0.767 n.s. 0.001 ***
3 Weight Of Cup + Sample After Drying 0.481 n.s. 0.177 n.s. 0.718 n.s.
4 Weight Of Sample Before Drying 0.002 ** 0.952 n.s. 0.001 ***
5 Weight Of Sample After Drying 0.755 n.s. 0.074 + 0.983 n.s.
6 Moisture Content (%) 0.747 n.s. 0.199 n.s. 0.651 n.s.
7 Dry Content (%) 0.747 n.s. 0.199 n.s. 0.651 n.s.</code></pre>
</div>
</div>
</section>
<section id="explore-group-variables-by-typedistribution" class="slide level2">
<h2><em>Explore: Group variables by type/distribution</em></h2>
<p>Scale level determines what statistics are appropriate</p>
<p>Typical scale levels are</p>
<ul>
<li><p>nominal/categorical/factorial/qualitative: just different groups<br>
(species, eye color, genotype, treatment)</p></li>
<li><p>ordered categories: few groups with inherent order<br>
(quality bad<medium<good, pain between 0 and 10)</p></li>
<li><p>ordinal measures: many different values, natural order, no distribution assumption (satisfaction on a scale from 0 to 100)</p></li>
<li><p>measures following a Normal distribution</p></li>
<li><p>possibly measures from other known distributions<br>
(beta, log-normal, poisson…), often treated as ordinal</p></li>
</ul>
</section>
<section id="make-type-decision-obviousreproducible" class="slide level2">
<h2><em>Make type decision obvious/reproducible</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb19"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href=""></a>gaussvars <span class="ot"><-</span> <span class="fu">ColSeeker</span>(<span class="at">data=</span>rawdata,<span class="at">namepattern =</span> <span class="fu">c</span>(<span class="st">'Weight'</span>,<span class="st">'Content'</span>))</span>
<span id="cb19-2"><a href=""></a>gaussvars</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>$index
[1] 3 4 5 6 7 8 9
$names
[1] "Weight Of Empty Cup" "Weight Of Cup + Sample"
[3] "Weight Of Cup + Sample After Drying" "Weight Of Sample Before Drying"
[5] "Weight Of Sample After Drying" "Moisture Content (%)"
[7] "Dry Content (%)"
$bticked
[1] "`Weight Of Empty Cup`"
[2] "`Weight Of Cup + Sample`"
[3] "`Weight Of Cup + Sample After Drying`"
[4] "`Weight Of Sample Before Drying`"
[5] "`Weight Of Sample After Drying`"
[6] "`Moisture Content (%)`"
[7] "`Dry Content (%)`"
$count
[1] 7</code></pre>
</div>
<div class="sourceCode cell-code" id="cb21"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb21-1"><a href=""></a>ordvars <span class="ot"><-</span> <span class="fu">ColSeeker</span>(<span class="at">namepattern=</span><span class="st">'Weight.+Sample'</span>, <span class="at">exclude =</span> <span class="st">'After'</span>)</span>
<span id="cb21-2"><a href=""></a>ordvars<span class="sc">$</span>names</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>[1] "Weight Of Cup + Sample" "Weight Of Sample Before Drying"</code></pre>
</div>
<div class="sourceCode cell-code" id="cb23"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href=""></a>factvars <span class="ot"><-</span> <span class="fu">ColSeeker</span>(<span class="at">namepattern=</span><span class="st">'region'</span>,<span class="at">casesensitive =</span> <span class="cn">FALSE</span>)</span>
<span id="cb23-2"><a href=""></a>factvars<span class="sc">$</span>bticked</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>[1] "`Region`" "`Subregion`"</code></pre>
</div>
</div>
</section>
<section id="model" class="slide level2">
<h2>Model</h2>
<h3 id="describe"><em>Describe</em></h3>
<ul>
<li><em>mean() / sd() / meansd()</em></li>
<li><em>median() / quantile() / median_quart()</em></li>
<li><em>table() / prop.table() / cat_desc_stats()</em></li>
</ul>
<h3 id="test"><em>Test</em></h3>
<ul>
<li><em>t.test() / lm()+[Aa]nova() / compare2numvars()</em></li>
<li><em>wilcox.test()</em></li>
<li><em>fisher.test() / glm(family=binomial)</em></li>
</ul>
</section>
<section id="model-describe" class="slide level2">
<h2><em>Model: Describe</em></h2>
<table>
<colgroup>
<col style="width: 50%">
<col style="width: 50%">
</colgroup>
<tbody>
<tr class="odd">
<td><strong>Sample size n:</strong> per variable, if there are NAs</td>
<td></td>
</tr>
<tr class="even">
<td><strong>Mean</strong>: central tendency, the expected <em>typical</em> value</td>
<td><span class="math display">\[\frac{\sum{x}}{n}\]</span></td>
</tr>
<tr class="odd">
<td><strong>Variance</strong>: measure for variability/heterogeneity of data</td>
<td><span class="math display">\[\frac{\sum{(x-mean)^2}}{n-1}\]</span></td>
</tr>
<tr class="even">
<td><strong>Standard deviation SD</strong>: the <em>typical</em> weighted deviation from the mean</td>
<td><span class="math display">\[\sqrt{Var}\]</span></td>
</tr>
</tbody>
</table>
</section>
<section id="section-1" class="slide level2">
<h2></h2>
<table>
<colgroup>
<col style="width: 50%">
<col style="width: 50%">
</colgroup>
<tbody>
<tr class="odd">
<td><strong>Standard error of the mean SEM</strong>: how reliable is the mean <em>estimate</em>, what would be the expected SD of means from repeated experiments?</td>
<td><span class="math display">\[\frac{SD}{\sqrt{n}}\]</span></td>
</tr>
<tr class="even">
<td><strong>Median</strong>: Split between lower/upper 50% of data</td>
<td></td>
</tr>
<tr class="odd">
<td><strong>Quartiles</strong>: Split at 25%/50%/75% of data (more general: <strong>Quantiles</strong>, e.g.<strong>Percentiles</strong>), used in boxplot</td>
<td>various computational approaches</td>
</tr>
</tbody>
</table>
</section>
<section id="section-2" class="slide level2">
<h2></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href=""></a>desc_gauss <span class="ot"><-</span> rawdata <span class="sc">|></span> </span>
<span id="cb25-2"><a href=""></a> <span class="fu">summarize</span>(<span class="fu">across</span>(<span class="at">.cols =</span> gaussvars<span class="sc">$</span>names,</span>
<span id="cb25-3"><a href=""></a> <span class="at">.fns =</span> meansd))</span>
<span id="cb25-4"><a href=""></a>desc_gauss</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 1 × 7
`Weight Of Empty Cup` `Weight Of Cup + Sample` Weight Of Cup + Sample After …¹
<chr> <chr> <chr>
1 4.1 ± 0.1 9.2 ± 0.2 4.6 ± 0.1
# ℹ abbreviated name: ¹`Weight Of Cup + Sample After Drying`
# ℹ 4 more variables: `Weight Of Sample Before Drying` <chr>,
# `Weight Of Sample After Drying` <chr>, `Moisture Content (%)` <chr>,
# `Dry Content (%)` <chr></code></pre>
</div>
<div class="sourceCode cell-code" id="cb27"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb27-1"><a href=""></a>desc_ord <span class="ot"><-</span> rawdata <span class="sc">|></span> </span>
<span id="cb27-2"><a href=""></a> <span class="fu">summarize</span>(<span class="fu">across</span>(ordvars<span class="sc">$</span>names,<span class="at">.fns=</span><span class="sc">~</span><span class="fu">median_quart</span>(.x,<span class="at">roundDig =</span> <span class="dv">3</span>))) <span class="sc">|></span> </span>
<span id="cb27-3"><a href=""></a> <span class="fu">pivot_longer</span>(<span class="fu">everything</span>(),</span>
<span id="cb27-4"><a href=""></a> <span class="at">names_to =</span> <span class="st">'Measure'</span>, <span class="at">values_to =</span> <span class="st">'Median[1Q/3Q]'</span>)</span>
<span id="cb27-5"><a href=""></a>desc_ord</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># A tibble: 2 × 2
Measure `Median[1Q/3Q]`
<chr> <chr>
1 Weight Of Cup + Sample 9.25 (9.22/9.29)
2 Weight Of Sample Before Drying 5.14 (5.09/5.18)</code></pre>
</div>
</div>
</section>
<section id="descriptive-stats-should-match-distribution-and-data" class="slide level2">
<h2>Descriptive Stats should match distribution and data</h2>
<img data-src="Figures/MeanMedian.jpg" class="quarto-figure quarto-figure-center r-stretch"></section>
<section id="model-test" class="slide level2">
<h2><em>Model: Test</em></h2>
<p>Tests require hypotheses</p>
<img data-src="Figures/guestimate.gif" class="quarto-figure quarto-figure-center r-stretch"></section>
<section id="null-hypothesis" class="slide level2">
<h2>Null hypothesis ?</h2>
<ul>
<li><p>Working hypothesis: This is what you expect!<br>
E.g. treatment is lowering blood pressure more than placebo, transgenic animals become obese, bio reactor A is more efficient than B, concentration of substance is correlated with speed of reaction …</p></li>
<li><p>Null hypothesis: This is what you test!<br>
No difference / relation, BP under therapy = BP under placebo</p></li>
</ul>
</section>
<section id="possibilities" class="slide level2">
<h2>4 possibilities:</h2>
<ul>
<li><p>Null hypothesis correct, test false positive (case A): alpha-error</p></li>
<li><p>Null hypothesis correct, test correct negative (case B)</p></li>
<li><p>Null hypothesis false, test false negative (case C): beta-error</p></li>
<li><p>Null hypothesis false, test correct positive (case D)</p></li>
</ul>
<p><strong>Significance</strong>: NOT probability of case A, but probability of your data given the NULL hypothesis, calculated from your data, conventionally <0.05</p>
<p><strong>Power</strong>: Probability of case D, <em>estimated</em> based on assumptions about effects and sample size, <em>calculation</em> would require knowledge of true difference, conventionally set at 0.80</p>
</section>
<section id="test-functions" class="slide level2">
<h2>Test functions</h2>
<h3 id="t-test-wilcoxon-test-aka-mann-whitney-u-test">t-test / Wilcoxon-test (aka Mann-Whitney U-test)</h3>
<img data-src="Figures/MeanDiff.png" class="quarto-figure quarto-figure-center r-stretch" width="800"></section>
<section id="t-test" class="slide level2">
<h2>t-test</h2>
<ul>
<li><p>Assumptions: Continuous data with Normal distribution</p></li>
<li><p>1 or 2 (independent or dependent) samples with/without equal variances</p></li>
<li><p>how big is the mean difference relative to uncertainty?<br>
t = (mean<sub>1</sub> - mean<sub>2</sub>)/SEM</p></li>
<li><p>t follows a t-distribution, allows estimation of probability of t under the NULL hypothesis</p></li>
</ul>
<h3 id="wilcoxon-test">Wilcoxon-test</h3>
<ul>
<li><p>nonparametric, no distribution is assumed</p></li>
<li><p>based on rank-transformed data</p></li>
<li><p>insensitive to extreme values</p></li>
</ul>
</section>
<section id="test-examples-single-variables" class="slide level2">
<h2>Test examples: <em>single variables</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb29"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb29-1"><a href=""></a><span class="co">#t-Test with test for equal variances</span></span>
<span id="cb29-2"><a href=""></a>t_out <span class="ot"><-</span> <span class="fu">t.test</span>(<span class="at">formula=</span><span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span><span class="sc">~</span><span class="st">`</span><span class="at">Region</span><span class="st">`</span>, <span class="at">data=</span>rawdata,</span>
<span id="cb29-3"><a href=""></a> <span class="at">var.equal=</span><span class="fu">var.test</span>(</span>
<span id="cb29-4"><a href=""></a> <span class="at">formula=</span><span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span><span class="sc">~</span><span class="st">`</span><span class="at">Region</span><span class="st">`</span>, </span>
<span id="cb29-5"><a href=""></a> <span class="at">data=</span>rawdata)<span class="sc">$</span>p.value<span class="sc">></span>.<span class="dv">05</span>)</span>
<span id="cb29-6"><a href=""></a>t_out</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>
Welch Two Sample t-test
data: Moisture Content (%) by Region
t = -1.7274, df = 29.239, p-value = 0.09465
alternative hypothesis: true difference in means between group A and group D is not equal to 0
95 percent confidence interval:
-2.9624835 0.2490486
sample estimates:
mean in group A mean in group D
90.31199 91.66870 </code></pre>
</div>
<div class="sourceCode cell-code" id="cb31"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb31-1"><a href=""></a><span class="co">#Wilcoxon-Test</span></span>
<span id="cb31-2"><a href=""></a><span class="fu">wilcox.test</span>(<span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span><span class="sc">~</span><span class="st">`</span><span class="at">Region</span><span class="st">`</span>, </span>
<span id="cb31-3"><a href=""></a> <span class="at">data =</span> rawdata)</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>
Wilcoxon rank sum exact test
data: Moisture Content (%) by Region
W = 107, p-value = 0.7547
alternative hypothesis: true location shift is not equal to 0</code></pre>
</div>
</div>
</section>
<section id="from-t-to-p" class="slide level2">
<h2>From t to p</h2>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-16-1.png" class="r-stretch"></section>
<section id="model-test-2-multiple-variables" class="slide level2">
<h2><em>Model: Test 2 / multiple variables</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb33"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb33-1"><a href=""></a>test_gauss <span class="ot"><-</span> <span class="fu">compare2numvars</span>(<span class="at">data =</span> rawdata,</span>
<span id="cb33-2"><a href=""></a> <span class="at">dep_vars =</span> gaussvars<span class="sc">$</span>names,</span>
<span id="cb33-3"><a href=""></a> <span class="at">indep_var =</span> <span class="st">'Region'</span>,</span>
<span id="cb33-4"><a href=""></a> <span class="at">gaussian =</span> <span class="cn">TRUE</span>,</span>
<span id="cb33-5"><a href=""></a> <span class="at">round_p =</span> <span class="dv">5</span>)</span>
<span id="cb33-6"><a href=""></a>test_gauss <span class="sc">|></span> <span class="fu">flextable</span>()<span class="sc">|></span> </span>
<span id="cb33-7"><a href=""></a> <span class="fu">theme_zebra</span>(<span class="at">even_body =</span> <span class="st">'aquamarine'</span>,<span class="at">odd_body =</span> <span class="st">'antiquewhite'</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 class="tabwid"><style>.cl-7ab9d0ea{table-layout:auto;}.cl-7ab392e8{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7ab392f2{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7ab62e54{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7ab64632{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7ab6463c{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7ab64646{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-7ab9d0ea"><thead><tr style="overflow-wrap:break-word;"><th class="cl-7ab64632"><p class="cl-7ab62e54"><span class="cl-7ab392e8">Variable</span></p></th><th class="cl-7ab64632"><p class="cl-7ab62e54"><span class="cl-7ab392e8">desc_all</span></p></th><th class="cl-7ab64632"><p class="cl-7ab62e54"><span class="cl-7ab392e8">Region A</span></p></th><th class="cl-7ab64632"><p class="cl-7ab62e54"><span class="cl-7ab392e8">Region D</span></p></th><th class="cl-7ab64632"><p class="cl-7ab62e54"><span class="cl-7ab392e8">p</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">Weight Of Empty Cup</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">4.1 ± 0.1</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">4.1 ± 0.0</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">4.2 ± 0.0</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.00001</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">Weight Of Cup + Sample</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">9.2 ± 0.2</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">9.2 ± 0.0</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">9.2 ± 0.3</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.74227</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">Weight Of Cup + Sample After Drying</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">4.6 ± 0.1</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">4.6 ± 0.2</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">4.6 ± 0.1</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.42213</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">Weight Of Sample Before Drying</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">5.1 ± 0.2</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">5.2 ± 0.1</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">5.0 ± 0.3</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.12830</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">Weight Of Sample After Drying</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.47 ± 0.14</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.50 ± 0.16</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.42 ± 0.07</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.04937</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">Moisture Content (%)</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">91 ± 3</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">90 ± 3</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">92 ± 1</span></p></td><td class="cl-7ab64646"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.09465</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">Dry Content (%)</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">9.2 ± 2.7</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">9.7 ± 3.1</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">8.3 ± 1.3</span></p></td><td class="cl-7ab6463c"><p class="cl-7ab62e54"><span class="cl-7ab392f2">0.09465</span></p></td></tr></tbody></table></div>
</div>
</div>
</section>
<section id="section-3" class="slide level2">
<h2></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb34"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb34-1"><a href=""></a>test_ord <span class="ot"><-</span> <span class="fu">compare2numvars</span>(<span class="at">data =</span> rawdata,</span>
<span id="cb34-2"><a href=""></a> <span class="at">dep_vars =</span> ordvars<span class="sc">$</span>names,</span>
<span id="cb34-3"><a href=""></a> <span class="at">indep_var =</span> <span class="st">'Region'</span>,</span>
<span id="cb34-4"><a href=""></a> <span class="at">gaussian =</span> <span class="cn">FALSE</span>,<span class="at">round_desc =</span> <span class="dv">3</span>)</span>
<span id="cb34-5"><a href=""></a>test_ord <span class="sc">|></span> <span class="fu">flextable</span>() <span class="sc">|></span> </span>
<span id="cb34-6"><a href=""></a> <span class="fu">theme_zebra</span>(<span class="at">even_body =</span> <span class="st">'aquamarine'</span>,<span class="at">odd_body =</span> <span class="st">'antiquewhite'</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 class="tabwid"><style>.cl-7af1b136{table-layout:auto;}.cl-7ad32bc6{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7ad32bda{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7ad5dd44{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7ad5f3f6{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7ad5f400{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7ad5f401{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-7af1b136"><thead><tr style="overflow-wrap:break-word;"><th class="cl-7ad5f3f6"><p class="cl-7ad5dd44"><span class="cl-7ad32bc6">Variable</span></p></th><th class="cl-7ad5f3f6"><p class="cl-7ad5dd44"><span class="cl-7ad32bc6">desc_all</span></p></th><th class="cl-7ad5f3f6"><p class="cl-7ad5dd44"><span class="cl-7ad32bc6">Region A</span></p></th><th class="cl-7ad5f3f6"><p class="cl-7ad5dd44"><span class="cl-7ad32bc6">Region D</span></p></th><th class="cl-7ad5f3f6"><p class="cl-7ad5dd44"><span class="cl-7ad32bc6">p</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-7ad5f400"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">Weight Of Cup + Sample</span></p></td><td class="cl-7ad5f400"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">9.25 (9.22/9.29)</span></p></td><td class="cl-7ad5f400"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">9.24 (9.22/9.25)</span></p></td><td class="cl-7ad5f400"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">9.29 (9.27/9.31)</span></p></td><td class="cl-7ad5f400"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">0.003</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ad5f401"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">Weight Of Sample Before Drying</span></p></td><td class="cl-7ad5f401"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">5.14 (5.09/5.18)</span></p></td><td class="cl-7ad5f401"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">5.14 (5.13/5.20)</span></p></td><td class="cl-7ad5f401"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">5.09 (5.06/5.13)</span></p></td><td class="cl-7ad5f401"><p class="cl-7ad5dd44"><span class="cl-7ad32bda">0.001</span></p></td></tr></tbody></table></div>
</div>
</div>
</section>
<section id="show-results" class="slide level2">
<h2>Show results</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb35"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb35-1"><a href=""></a><span class="fu">ggplot</span>(rawdata, <span class="fu">aes</span>(<span class="at">x =</span> <span class="st">`</span><span class="at">Region</span><span class="st">`</span>,<span class="at">y =</span> <span class="st">`</span><span class="at">Weight Of Sample Before Drying</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb35-2"><a href=""></a> <span class="fu">geom_boxplot</span>(<span class="at">outlier.alpha =</span> <span class="dv">0</span>)<span class="sc">+</span></span>
<span id="cb35-3"><a href=""></a> <span class="fu">geom_beeswarm</span>(<span class="at">alpha=</span>.<span class="dv">7</span>, <span class="at">size=</span><span class="fl">2.5</span>,<span class="at">cex =</span> <span class="fl">1.5</span>, <span class="at">color=</span><span class="st">"darkorange"</span>)<span class="sc">+</span></span>
<span id="cb35-4"><a href=""></a> <span class="fu">annotate</span>(<span class="at">geom =</span> <span class="st">'label'</span>,<span class="at">x=</span><span class="dv">2</span>,<span class="at">y=</span><span class="fl">4.2</span>,</span>
<span id="cb35-5"><a href=""></a> <span class="at">label=</span><span class="st">'extreme value -> high SD -> high SEM ->low t-statistic->high p-value'</span>,</span>
<span id="cb35-6"><a href=""></a> <span class="at">hjust=</span><span class="fl">0.8</span>,<span class="at">vjust=</span><span class="dv">0</span>)<span class="sc">+</span></span>
<span id="cb35-7"><a href=""></a> <span class="fu">geom_signif</span>(<span class="at">comparisons =</span> <span class="fu">list</span>(<span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">2</span>)),</span>
<span id="cb35-8"><a href=""></a> <span class="at">annotations =</span> <span class="fu">paste</span>(<span class="st">'p'</span>,<span class="fu">formatP</span>(t_out<span class="sc">$</span>p.value)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-20-1.png" class="r-stretch"></section>
<section id="re-thinking-test-decision" class="slide level2">
<h2>Re-thinking test decision?</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb36"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb36-1"><a href=""></a><span class="fu">ggplot</span>(rawdata, <span class="fu">aes</span>(<span class="at">x =</span> <span class="st">`</span><span class="at">Region</span><span class="st">`</span>,<span class="at">y =</span> <span class="st">`</span><span class="at">Weight Of Sample Before Drying</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb36-2"><a href=""></a> <span class="fu">geom_boxplot</span>(<span class="at">outlier.alpha =</span> <span class="dv">0</span>)<span class="sc">+</span></span>
<span id="cb36-3"><a href=""></a> <span class="fu">geom_beeswarm</span>(<span class="at">alpha=</span>.<span class="dv">7</span>, <span class="at">size =</span> <span class="fl">2.5</span>,<span class="at">cex =</span> <span class="fl">1.5</span>, <span class="at">color=</span><span class="st">"darkorange"</span>)<span class="sc">+</span></span>
<span id="cb36-4"><a href=""></a> <span class="fu">geom_signif</span>(<span class="at">comparisons =</span> <span class="fu">list</span>(<span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">2</span>)),<span class="at">test =</span> wilcox.test)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-21-1.png" class="r-stretch"></section>
<section id="model-linear-models-1-univariable" class="slide level2">
<h2><em>Model: linear models 1 / univariable</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb37"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb37-1"><a href=""></a>plottmp <span class="ot"><-</span> <span class="fu">ggplot</span>(rawdata,<span class="fu">aes</span>(Subregion,<span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb37-2"><a href=""></a> <span class="fu">geom_violin</span>(<span class="at">draw_quantiles =</span> <span class="fu">c</span>(.<span class="dv">25</span>,.<span class="dv">5</span>,.<span class="dv">75</span>))<span class="sc">+</span></span>
<span id="cb37-3"><a href=""></a> <span class="fu">geom_beeswarm</span>(<span class="at">color=</span><span class="st">"darkorange"</span>)<span class="sc">+</span></span>
<span id="cb37-4"><a href=""></a> </span>
<span id="cb37-5"><a href=""></a> <span class="fu">ggtitle</span>(<span class="st">'Are all Subregions equal?'</span>)</span>
<span id="cb37-6"><a href=""></a><span class="fu">print</span>(plottmp)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-22-1.png" class="r-stretch"></section>
<section id="anova-build-model" class="slide level2">
<h2>ANOVA: build model</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb38"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb38-1"><a href=""></a>rawdata <span class="sc">|></span> <span class="fu">group_by</span>(Subregion) <span class="sc">|></span> </span>
<span id="cb38-2"><a href=""></a> <span class="fu">summarize</span>(<span class="at">MeanMoisture=</span><span class="fu">mean</span>(<span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>) <span class="sc">|></span> <span class="fu">roundR</span>(<span class="dv">4</span>)) <span class="sc">|></span> </span>
<span id="cb38-3"><a href=""></a> <span class="fu">pivot_wider</span>(<span class="at">names_from =</span> Subregion,<span class="at">values_from =</span> MeanMoisture) <span class="sc">|></span> </span>
<span id="cb38-4"><a href=""></a> <span class="fu">rename_with</span>(<span class="sc">~</span><span class="fu">paste</span>(<span class="st">'Mean moisture %</span><span class="sc">\n</span><span class="st">'</span>,.x)) <span class="sc">|></span> <span class="fu">flextable</span>()<span class="sc">|></span></span>
<span id="cb38-5"><a href=""></a> <span class="fu">theme_zebra</span>(<span class="at">even_body =</span> <span class="st">'aquamarine'</span>,<span class="at">odd_body =</span> <span class="st">'antiquewhite'</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 class="tabwid"><style>.cl-7bd17564{table-layout:auto;}.cl-7bcb88b6{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7bcb88c0{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7bcdedea{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7bce0564{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7bce056e{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-7bd17564"><thead><tr style="overflow-wrap:break-word;"><th class="cl-7bce0564"><p class="cl-7bcdedea"><span class="cl-7bcb88b6">Mean moisture %</span><br><span class="cl-7bcb88b6"> A high</span></p></th><th class="cl-7bce0564"><p class="cl-7bcdedea"><span class="cl-7bcb88b6">Mean moisture %</span><br><span class="cl-7bcb88b6"> A low</span></p></th><th class="cl-7bce0564"><p class="cl-7bcdedea"><span class="cl-7bcb88b6">Mean moisture %</span><br><span class="cl-7bcb88b6"> D</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-7bce056e"><p class="cl-7bcdedea"><span class="cl-7bcb88c0">93.11</span></p></td><td class="cl-7bce056e"><p class="cl-7bcdedea"><span class="cl-7bcb88c0">87.23</span></p></td><td class="cl-7bce056e"><p class="cl-7bcdedea"><span class="cl-7bcb88c0">91.67</span></p></td></tr></tbody></table></div>
</div>
<div class="sourceCode cell-code" id="cb39"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb39-1"><a href=""></a>lm1<span class="ot"><-</span> <span class="fu">lm</span>(<span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span><span class="sc">~</span>Subregion, <span class="at">data=</span>rawdata)</span>
<span id="cb39-2"><a href=""></a>lm1</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>
Call:
lm(formula = `Moisture Content (%)` ~ Subregion, data = rawdata)
Coefficients:
(Intercept) SubregionA low SubregionD
93.112 -5.879 -1.443 </code></pre>
</div>
</div>
</section>
<section id="anova-get-p-values" class="slide level2">
<h2>ANOVA: get p-values</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb41"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb41-1"><a href=""></a><span class="fu">anova</span>(lm1) <span class="sc">|></span> broom<span class="sc">::</span><span class="fu">tidy</span>() <span class="sc">|></span> <span class="fu">flextable</span>()<span class="sc">|></span> </span>
<span id="cb41-2"><a href=""></a> <span class="fu">theme_zebra</span>(<span class="at">even_body =</span> <span class="st">'aquamarine'</span>,<span class="at">odd_body =</span> <span class="st">'antiquewhite'</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 class="tabwid"><style>.cl-7bed75f2{table-layout:auto;}.cl-7be7071c{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7be70726{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7be9a4ea{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7be9a4f4{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7be9b9f8{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7be9b9f9{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7be9ba02{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7be9ba03{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7be9ba04{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7be9ba0c{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-7bed75f2"><thead><tr style="overflow-wrap:break-word;"><th class="cl-7be9b9f8"><p class="cl-7be9a4ea"><span class="cl-7be7071c">term</span></p></th><th class="cl-7be9b9f9"><p class="cl-7be9a4f4"><span class="cl-7be7071c">df</span></p></th><th class="cl-7be9b9f9"><p class="cl-7be9a4f4"><span class="cl-7be7071c">sumsq</span></p></th><th class="cl-7be9b9f9"><p class="cl-7be9a4f4"><span class="cl-7be7071c">meansq</span></p></th><th class="cl-7be9b9f9"><p class="cl-7be9a4f4"><span class="cl-7be7071c">statistic</span></p></th><th class="cl-7be9b9f9"><p class="cl-7be9a4f4"><span class="cl-7be7071c">p.value</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-7be9ba02"><p class="cl-7be9a4ea"><span class="cl-7be70726">Subregion</span></p></td><td class="cl-7be9ba03"><p class="cl-7be9a4f4"><span class="cl-7be70726">2</span></p></td><td class="cl-7be9ba03"><p class="cl-7be9a4f4"><span class="cl-7be70726">194.34239</span></p></td><td class="cl-7be9ba03"><p class="cl-7be9a4f4"><span class="cl-7be70726">97.1711969</span></p></td><td class="cl-7be9ba03"><p class="cl-7be9a4f4"><span class="cl-7be70726">97.76477</span></p></td><td class="cl-7be9ba03"><p class="cl-7be9a4f4"><span class="cl-7be70726">0.0000000000001292127</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7be9ba04"><p class="cl-7be9a4ea"><span class="cl-7be70726">Residuals</span></p></td><td class="cl-7be9ba0c"><p class="cl-7be9a4f4"><span class="cl-7be70726">29</span></p></td><td class="cl-7be9ba0c"><p class="cl-7be9a4f4"><span class="cl-7be70726">28.82393</span></p></td><td class="cl-7be9ba0c"><p class="cl-7be9a4f4"><span class="cl-7be70726">0.9939285</span></p></td><td class="cl-7be9ba0c"><p class="cl-7be9a4f4"><span class="cl-7be70726"></span></p></td><td class="cl-7be9ba0c"><p class="cl-7be9a4f4"><span class="cl-7be70726"></span></p></td></tr></tbody></table></div>
</div>
<div class="sourceCode cell-code" id="cb42"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb42-1"><a href=""></a><span class="co">#post-hoc</span></span>
<span id="cb42-2"><a href=""></a>(posthoc_out <span class="ot"><-</span> <span class="fu">pairwise.t.test</span>(<span class="at">x =</span> rawdata<span class="sc">$</span><span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>, </span>
<span id="cb42-3"><a href=""></a> <span class="at">g =</span> rawdata<span class="sc">$</span>Subregion, </span>
<span id="cb42-4"><a href=""></a> <span class="at">p.adjust.method =</span> <span class="st">'fdr'</span>)<span class="sc">$</span>p.value <span class="sc">|></span> </span>
<span id="cb42-5"><a href=""></a> <span class="fu">formatP</span>(<span class="at">ndigits =</span> <span class="dv">5</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> A high A low
A low "0.00001" ""
D "0.00201" "0.00001"</code></pre>
</div>
</div>
<!-- ## *Model: linear models 2 / multivariable* -->
</section>
<section id="visualize-anova" class="slide level2">
<h2><em>Visualize ANOVA</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb44"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb44-1"><a href=""></a><span class="fu">ggplot</span>(rawdata,<span class="fu">aes</span>(Subregion,<span class="st">`</span><span class="at">Moisture Content (%)</span><span class="st">`</span>))<span class="sc">+</span></span>
<span id="cb44-2"><a href=""></a> <span class="fu">geom_violin</span>(<span class="at">draw_quantiles =</span> <span class="fu">c</span>(.<span class="dv">25</span>,.<span class="dv">5</span>,.<span class="dv">75</span>))<span class="sc">+</span></span>
<span id="cb44-3"><a href=""></a> <span class="fu">geom_beeswarm</span>(<span class="at">color=</span><span class="st">"darkorange"</span>)<span class="sc">+</span></span>
<span id="cb44-4"><a href=""></a> <span class="fu">geom_signif</span>(<span class="at">comparisons =</span> <span class="fu">list</span>(<span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">2</span>),<span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">3</span>),<span class="fu">c</span>(<span class="dv">2</span>,<span class="dv">3</span>)),</span>
<span id="cb44-5"><a href=""></a> <span class="at">annotations =</span> <span class="fu">c</span>(posthoc_out[,<span class="dv">1</span>], posthoc_out[<span class="dv">2</span>,<span class="dv">2</span>]),</span>
<span id="cb44-6"><a href=""></a> <span class="at">step_increase =</span> .<span class="dv">25</span>)<span class="sc">+</span></span>
<span id="cb44-7"><a href=""></a> <span class="fu">scale_y_continuous</span>(<span class="at">expand =</span> <span class="fu">expansion</span>(<span class="at">mult =</span> .<span class="dv">1</span>))<span class="sc">+</span></span>
<span id="cb44-8"><a href=""></a> <span class="fu">ggtitle</span>(<span class="st">'All Subregions are unequal'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-26-1.png" class="r-stretch"></section>
<section id="analyze-more-than-1-outcome" class="slide level2">
<h2><em>Analyze more than 1 outcome</em></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb45"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb45-1"><a href=""></a>test_out <span class="ot"><-</span> <span class="fu">compare_n_numvars</span>(<span class="at">.data=</span>rawdata,</span>
<span id="cb45-2"><a href=""></a> <span class="at">dep_vars=</span>gaussvars<span class="sc">$</span>names,</span>
<span id="cb45-3"><a href=""></a> <span class="at">indep_var=</span><span class="st">'Subregion'</span>,</span>
<span id="cb45-4"><a href=""></a> <span class="at">gaussian=</span><span class="cn">TRUE</span>)</span>
<span id="cb45-5"><a href=""></a>test_out<span class="sc">$</span>results <span class="sc">|></span> </span>
<span id="cb45-6"><a href=""></a> <span class="fu">select</span>(Variable,<span class="fu">contains</span>(<span class="st">"fn"</span>),multivar_p) <span class="sc">|></span> </span>
<span id="cb45-7"><a href=""></a> <span class="fu">rename_with</span>(<span class="sc">~</span><span class="fu">str_remove</span>(.x,<span class="st">" fn"</span>)) <span class="sc">|></span> </span>
<span id="cb45-8"><a href=""></a> <span class="fu">flextable</span>()<span class="sc">|></span> </span>
<span id="cb45-9"><a href=""></a> <span class="fu">theme_zebra</span>(<span class="at">even_body =</span> <span class="st">'aquamarine'</span>,<span class="at">odd_body =</span> <span class="st">'antiquewhite'</span>) <span class="sc">|></span> </span>
<span id="cb45-10"><a href=""></a> <span class="fu">add_footer_lines</span>(</span>
<span id="cb45-11"><a href=""></a> <span class="at">values=</span><span class="st">'b indicates difference from group 2, c indicates difference from group 3'</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 class="tabwid"><style>.cl-7ca5e718{table-layout:auto;}.cl-7c9f87ce{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7c9f87d8{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7ca26d40{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7ca28136{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7ca28140{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7ca28141{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7ca2814a{background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(255, 255, 255, 0.00);border-top: 0 solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-7ca5e718"><thead><tr style="overflow-wrap:break-word;"><th class="cl-7ca28136"><p class="cl-7ca26d40"><span class="cl-7c9f87ce">Variable</span></p></th><th class="cl-7ca28136"><p class="cl-7ca26d40"><span class="cl-7c9f87ce">Subregion A high</span></p></th><th class="cl-7ca28136"><p class="cl-7ca26d40"><span class="cl-7c9f87ce">Subregion A low</span></p></th><th class="cl-7ca28136"><p class="cl-7ca26d40"><span class="cl-7c9f87ce">Subregion D</span></p></th><th class="cl-7ca28136"><p class="cl-7ca26d40"><span class="cl-7c9f87ce">multivar_p</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">Weight Of Empty Cup</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">4.1 ± 0.0 c</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">4.1 ± 0.1 c</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">4.2 ± 0.0</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.001</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">Weight Of Cup + Sample</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">9.2 ± 0.0</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">9.2 ± 0.0</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">9.2 ± 0.3</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.894</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">Weight Of Cup + Sample After Drying</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">4.4 ± 0.0 bc</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">4.8 ± 0.1 c</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">4.6 ± 0.1</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.001</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">Weight Of Sample Before Drying</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">5.2 ± 0.0</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">5.1 ± 0.1</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">5.0 ± 0.3</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.095</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">Weight Of Sample After Drying</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.36 ± 0.02 bc</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.66 ± 0.06 c</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.42 ± 0.07</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.001</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">Moisture Content (%)</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">93 ± 0 bc</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">87 ± 1 c</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">92 ± 1</span></p></td><td class="cl-7ca28141"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.001</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">Dry Content (%)</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">7 ± 0 bc</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">13 ± 1 c</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">8 ± 1</span></p></td><td class="cl-7ca28140"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">0.001</span></p></td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="5" class="cl-7ca2814a"><p class="cl-7ca26d40"><span class="cl-7c9f87d8">b indicates difference from group 2, c indicates difference from group 3</span></p></td></tr></tfoot></table></div>
</div>
</div>
</section>
<section id="regression-scatterplot" class="slide level2">
<h2>Regression: Scatterplot</h2>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-28-1.png" class="r-stretch"></section>
<section id="regression-underlying-mechanics" class="slide level2">
<h2>Regression: Underlying <em>mechanics</em></h2>
<img data-src="Figures/RegressionSprings.png" class="quarto-figure quarto-figure-center r-stretch"></section>
<section id="regression-statistics" class="slide level2">
<h2>Regression: Statistics</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb46"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb46-1"><a href=""></a>lm_out0 <span class="ot"><-</span> <span class="fu">lm</span>(<span class="st">`</span><span class="at">Weight Of Sample Before Drying</span><span class="st">`</span> <span class="sc">~</span> <span class="st">`</span><span class="at">Weight Of Empty Cup</span><span class="st">`</span>, </span>
<span id="cb46-2"><a href=""></a> <span class="at">data=</span>rawdata)</span>
<span id="cb46-3"><a href=""></a>lm_out0</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>
Call:
lm(formula = `Weight Of Sample Before Drying` ~ `Weight Of Empty Cup`,
data = rawdata)
Coefficients:
(Intercept) `Weight Of Empty Cup`
10.169 -1.228 </code></pre>
</div>
<div class="sourceCode cell-code" id="cb48"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb48-1"><a href=""></a><span class="co"># filtering outlier</span></span>
<span id="cb48-2"><a href=""></a>lm_out <span class="ot"><-</span> <span class="fu">lm</span>(<span class="st">`</span><span class="at">Weight Of Sample Before Drying</span><span class="st">`</span> <span class="sc">~</span> <span class="st">`</span><span class="at">Weight Of Empty Cup</span><span class="st">`</span>, </span>
<span id="cb48-3"><a href=""></a> <span class="at">data=</span>rawdata <span class="sc">|></span> <span class="fu">filter</span>(<span class="st">`</span><span class="at">Weight Of Sample Before Drying</span><span class="st">`</span><span class="sc">></span><span class="fl">4.5</span>))</span>
<span id="cb48-4"><a href=""></a>lm_out</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>
Call:
lm(formula = `Weight Of Sample Before Drying` ~ `Weight Of Empty Cup`,
data = filter(rawdata, `Weight Of Sample Before Drying` >
4.5))
Coefficients:
(Intercept) `Weight Of Empty Cup`
7.9612 -0.6854 </code></pre>
</div>
</div>
</section>
<section id="regression-visualize" class="slide level2">
<h2><em>Regression: Visualize</em></h2>
<img data-src="IntroSlides_files/figure-revealjs/unnamed-chunk-30-1.png" class="r-stretch"></section>
<section id="regression-significance" class="slide level2">
<h2>Regression: Significance</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb50"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb50-1"><a href=""></a><span class="fu">anova</span>(lm_out) <span class="sc">|></span> broom<span class="sc">::</span><span class="fu">tidy</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># A tibble: 2 × 6
term df sumsq meansq statistic p.value
<chr> <int> <dbl> <dbl> <dbl> <dbl>
1 `Weight Of Empty Cup` 1 0.0638 0.0638 42.1 0.000000425
2 Residuals 29 0.0440 0.00152 NA NA </code></pre>
</div>
<div class="sourceCode cell-code" id="cb52"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb52-1"><a href=""></a><span class="fu">model_parameters</span>(lm_out)</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>Parameter | Coefficient | SE | 95% CI | t(29) | p
--------------------------------------------------------------------------
(Intercept) | 7.96 | 0.44 | [ 7.07, 8.85] | 18.28 | < .001
Weight Of Empty Cup | -0.69 | 0.11 | [-0.90, -0.47] | -6.49 | < .001</code></pre>
</div>
</div>
</section>
<section id="report" class="slide level2">
<h2><em>Report</em></h2>
<ul>
<li><p><em>RMarkdown and quarto are powerful tools to create reports and presentations</em></p></li>
<li><p>Export figures: ggsave() / png() / pdf()</p></li>
<li><p>Export tables: write_xlsx()</p></li>
<li><p><em>Package flextable provides nice features for table formatting</em></p></li>
</ul>
</section>
<section id="flextable-example" class="slide level2">
<h2>Flextable example</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb54"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb54-1"><a href=""></a>test_ord <span class="sc">|></span> <span class="fu">select</span>(<span class="sc">-</span>desc_all) <span class="sc">|></span> <span class="fu">rename_with</span>(<span class="sc">~</span><span class="fu">str_remove</span>(.,<span class="st">'Code Of '</span>)) <span class="sc">|></span> </span>
<span id="cb54-2"><a href=""></a> <span class="fu">flextable</span>() <span class="sc">|></span> </span>
<span id="cb54-3"><a href=""></a> <span class="fu">theme_zebra</span>(<span class="at">even_body =</span> <span class="st">'aquamarine'</span>,<span class="at">odd_body =</span> <span class="st">'antiquewhite'</span>)<span class="sc">|></span> </span>
<span id="cb54-4"><a href=""></a> <span class="fu">italic</span>(<span class="sc">~</span>p<span class="sc"><=</span><span class="fl">0.05</span>,<span class="at">j =</span> <span class="dv">1</span>) <span class="sc">|></span> <span class="fu">bg</span>(<span class="sc">~</span>p<span class="sc"><=</span><span class="fl">0.05</span>,<span class="at">j =</span> <span class="dv">4</span>,<span class="at">bg =</span> <span class="st">'yellow'</span>) <span class="sc">|></span> </span>
<span id="cb54-5"><a href=""></a> <span class="fu">set_caption</span>(<span class="st">'Treatment effects, measures following a normal distribution'</span>) <span class="sc">|></span> </span>
<span id="cb54-6"><a href=""></a> <span class="fu">add_footer_lines</span>(<span class="st">'Significance level is set at 0.05'</span>) <span class="sc">|></span> </span>
<span id="cb54-7"><a href=""></a> <span class="fu">fontsize</span>(<span class="at">size =</span> <span class="dv">12</span>,<span class="at">part =</span> <span class="st">'footer'</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 class="tabwid"><style>.cl-7e02452a{table-layout:auto;}.cl-7dfbbc1e{font-family:'Roboto';font-size:18pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7dfbbc28{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:italic;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7dfbbc32{font-family:'Roboto';font-size:18pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7dfbbc33{font-family:'Roboto';font-size:12pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-7dfef19a{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:0.2pt;padding-top:0.2pt;padding-left:2pt;padding-right:2pt;line-height: 1;background-color:transparent;}.cl-7dff0658{background-color:rgba(207, 207, 207, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7dff0662{background-color:rgba(250, 235, 215, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7dff0663{background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7dff0664{background-color:rgba(127, 255, 212, 1.00);vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-7dff066c{background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(255, 255, 255, 0.00);border-top: 0 solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing="true" class="cl-7e02452a"><thead><tr style="overflow-wrap:break-word;"><th class="cl-7dff0658"><p class="cl-7dfef19a"><span class="cl-7dfbbc1e">Variable</span></p></th><th class="cl-7dff0658"><p class="cl-7dfef19a"><span class="cl-7dfbbc1e">Region A</span></p></th><th class="cl-7dff0658"><p class="cl-7dfef19a"><span class="cl-7dfbbc1e">Region D</span></p></th><th class="cl-7dff0658"><p class="cl-7dfef19a"><span class="cl-7dfbbc1e">p</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-7dff0662"><p class="cl-7dfef19a"><span class="cl-7dfbbc28">Weight Of Cup + Sample</span></p></td><td class="cl-7dff0662"><p class="cl-7dfef19a"><span class="cl-7dfbbc32">9.24 (9.22/9.25)</span></p></td><td class="cl-7dff0662"><p class="cl-7dfef19a"><span class="cl-7dfbbc32">9.29 (9.27/9.31)</span></p></td><td class="cl-7dff0663"><p class="cl-7dfef19a"><span class="cl-7dfbbc32">0.003</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-7dff0664"><p class="cl-7dfef19a"><span class="cl-7dfbbc28">Weight Of Sample Before Drying</span></p></td><td class="cl-7dff0664"><p class="cl-7dfef19a"><span class="cl-7dfbbc32">5.14 (5.13/5.20)</span></p></td><td class="cl-7dff0664"><p class="cl-7dfef19a"><span class="cl-7dfbbc32">5.09 (5.06/5.13)</span></p></td><td class="cl-7dff0663"><p class="cl-7dfef19a"><span class="cl-7dfbbc32">0.001</span></p></td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="4" class="cl-7dff066c"><p class="cl-7dfef19a"><span class="cl-7dfbbc33">Significance level is set at 0.05</span></p></td></tr></tfoot></table></div>
</div>
</div>
</section>
<section id="useful-tools-along-the-way" class="slide level2">
<h2>Useful tools along the way</h2>
<ul>
<li><p>Pick columns / rows: select() / pull() / filter() / slice()</p></li>
<li><p>Change format of tibble wide <–> long (e.g. for repeated measures):<br>
pivot_longer()/pivot_wider()</p></li>
<li><p>Regular expressions: str_replace() / str_detect() / str_…</p></li>
<li><p>Merge text elements: paste() / str_glue()</p></li>
<li><p>Apply functions: purrr::map_xxx</p></li>
</ul>
</section>
</div>
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