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ReactionTimeAnalysis.html
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<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#load-packages" id="toc-load-packages" class="nav-link active" data-scroll-target="#load-packages">Load packages</a></li>
<li><a href="#split-violin" id="toc-split-violin" class="nav-link" data-scroll-target="#split-violin">Split violin</a></li>
<li><a href="#interaction-plots" id="toc-interaction-plots" class="nav-link" data-scroll-target="#interaction-plots">Interaction plots</a>
<ul class="collapse">
<li><a href="#subset-by-agent" id="toc-subset-by-agent" class="nav-link" data-scroll-target="#subset-by-agent">Subset by Agent</a></li>
</ul></li>
<li><a href="#x2x2-anova" id="toc-x2x2-anova" class="nav-link" data-scroll-target="#x2x2-anova">3x2x2 ANOVA</a></li>
<li><a href="#anova-for-biological-action" id="toc-anova-for-biological-action" class="nav-link" data-scroll-target="#anova-for-biological-action">ANOVA for biological action</a>
<ul class="collapse">
<li><a href="#anova-for-nonbio-motion" id="toc-anova-for-nonbio-motion" class="nav-link" data-scroll-target="#anova-for-nonbio-motion">ANOVA for nonbio motion</a></li>
</ul></li>
<li><a href="#check-assumptions-for-anova" id="toc-check-assumptions-for-anova" class="nav-link" data-scroll-target="#check-assumptions-for-anova">Check Assumptions for ANOVA</a>
<ul class="collapse">
<li><a href="#perform-tost-between-robots" id="toc-perform-tost-between-robots" class="nav-link" data-scroll-target="#perform-tost-between-robots">Perform TOST between robots</a></li>
<li><a href="#anova-for-nonbio" id="toc-anova-for-nonbio" class="nav-link" data-scroll-target="#anova-for-nonbio">ANOVA for nonbio</a></li>
<li><a href="#more-equivalence-tests" id="toc-more-equivalence-tests" class="nav-link" data-scroll-target="#more-equivalence-tests">More equivalence tests</a></li>
</ul></li>
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<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Reaction Time Data Analysis</h1>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">April 25, 2023</p>
</div>
</div>
</div>
</header>
<section id="load-packages" class="level3">
<h3 class="anchored" data-anchor-id="load-packages">Load packages</h3>
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(knitr, <span class="at">include.only =</span> <span class="st">'kable'</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(pwr)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(rcompanion) <span class="co"># such interesting documentation </span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(lsr) </span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(car)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(broom)</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(afex) </span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(emmeans)</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(cowplot, <span class="at">include.only =</span> <span class="fu">c</span>(<span class="st">'plot_grid'</span>, <span class="st">'ggdraw'</span>))</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplotify, <span class="at">include.only=</span> <span class="st">'as.grob'</span>)</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(TOSTER)</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(performance)</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(wesanderson)</span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(effectsize, <span class="at">include.only =</span> <span class="st">'cohens_d'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<section id="load-data" class="level4">
<h4 class="anchored" data-anchor-id="load-data">Load data</h4>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>reactionTime <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"reactionTime_preprocess.csv"</span>, </span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="at">show_col_types =</span> <span class="cn">FALSE</span>) <span class="sc">|></span> </span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">agent =</span> <span class="fu">case_when</span>(</span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Human"</span>) <span class="sc">~</span> <span class="st">"Human"</span>, </span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Milo"</span>) <span class="sc">~</span> <span class="st">"Humanoid"</span>, </span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Theo"</span>) <span class="sc">~</span> <span class="st">"Robotic Arm"</span>, </span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span> </span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">motion_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Bio"</span>) <span class="sc">~</span> <span class="st">"Biological"</span>,</span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Nonbio"</span>) <span class="sc">~</span> <span class="st">"Nonbiological"</span>, </span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span></span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">outcome_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Correct"</span>) <span class="sc">~</span> <span class="st">"Correct"</span>, </span>
<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Spill"</span>) <span class="sc">~</span> <span class="st">"Error"</span>)) </span>
<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-16"><a href="#cb2-16" aria-hidden="true" tabindex="-1"></a>summary_statistics <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"reactionTime_summary_statistics.csv"</span>, </span>
<span id="cb2-17"><a href="#cb2-17" aria-hidden="true" tabindex="-1"></a> <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span>
<span id="cb2-18"><a href="#cb2-18" aria-hidden="true" tabindex="-1"></a>plotting <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"plottingReactionTime.csv"</span>, </span>
<span id="cb2-19"><a href="#cb2-19" aria-hidden="true" tabindex="-1"></a> <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span>
<span id="cb2-20"><a href="#cb2-20" aria-hidden="true" tabindex="-1"></a><span class="co"># summary_statistics_error <- summary_statistics |> filter(outcome_type == "Error")</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</section>
</section>
<section id="split-violin" class="level2">
<h2 class="anchored" data-anchor-id="split-violin">Split violin</h2>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># https://stackoverflow.com/questions/35717353/split-violin-plot-with-ggplot2</span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="co"># trying the solution with the nudge</span></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a>GeomSplitViolin <span class="ot"><-</span> ggplot2<span class="sc">::</span><span class="fu">ggproto</span>(</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a> <span class="st">"GeomSplitViolin"</span>,</span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a> ggplot2<span class="sc">::</span>GeomViolin,</span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a> <span class="at">draw_group =</span> <span class="cf">function</span>(self,</span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a> data,</span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a> ...,</span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a> <span class="co"># add the nudge here</span></span>
<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a> <span class="at">nudge =</span> <span class="dv">0</span>,</span>
<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a> <span class="at">draw_quantiles =</span> <span class="cn">NULL</span>) {</span>
<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a> data <span class="ot"><-</span> <span class="fu">transform</span>(data,</span>
<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a> <span class="at">xminv =</span> x <span class="sc">-</span> violinwidth <span class="sc">*</span> (x <span class="sc">-</span> xmin),</span>
<span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a> <span class="at">xmaxv =</span> x <span class="sc">+</span> violinwidth <span class="sc">*</span> (xmax <span class="sc">-</span> x))</span>
<span id="cb3-16"><a href="#cb3-16" aria-hidden="true" tabindex="-1"></a> grp <span class="ot"><-</span> data[<span class="dv">1</span>, <span class="st">"group"</span>]</span>
<span id="cb3-17"><a href="#cb3-17" aria-hidden="true" tabindex="-1"></a> newdata <span class="ot"><-</span> plyr<span class="sc">::</span><span class="fu">arrange</span>(<span class="fu">transform</span>(data,</span>
<span id="cb3-18"><a href="#cb3-18" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="cf">if</span> (grp <span class="sc">%%</span> <span class="dv">2</span> <span class="sc">==</span> <span class="dv">1</span>) xminv <span class="cf">else</span> xmaxv),</span>
<span id="cb3-19"><a href="#cb3-19" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (grp <span class="sc">%%</span> <span class="dv">2</span> <span class="sc">==</span> <span class="dv">1</span>) y <span class="cf">else</span> <span class="sc">-</span>y)</span>
<span id="cb3-20"><a href="#cb3-20" aria-hidden="true" tabindex="-1"></a> newdata <span class="ot"><-</span> <span class="fu">rbind</span>(newdata[<span class="dv">1</span>, ],</span>
<span id="cb3-21"><a href="#cb3-21" aria-hidden="true" tabindex="-1"></a> newdata,</span>
<span id="cb3-22"><a href="#cb3-22" aria-hidden="true" tabindex="-1"></a> newdata[<span class="fu">nrow</span>(newdata), ],</span>
<span id="cb3-23"><a href="#cb3-23" aria-hidden="true" tabindex="-1"></a> newdata[<span class="dv">1</span>, ])</span>
<span id="cb3-24"><a href="#cb3-24" aria-hidden="true" tabindex="-1"></a> newdata[<span class="fu">c</span>(<span class="dv">1</span>, <span class="fu">nrow</span>(newdata)<span class="sc">-</span><span class="dv">1</span>, <span class="fu">nrow</span>(newdata)), <span class="st">"x"</span>] <span class="ot"><-</span> <span class="fu">round</span>(newdata[<span class="dv">1</span>, <span class="st">"x"</span>])</span>
<span id="cb3-25"><a href="#cb3-25" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-26"><a href="#cb3-26" aria-hidden="true" tabindex="-1"></a> <span class="co"># now nudge them apart</span></span>
<span id="cb3-27"><a href="#cb3-27" aria-hidden="true" tabindex="-1"></a> newdata<span class="sc">$</span>x <span class="ot"><-</span> <span class="fu">ifelse</span>(newdata<span class="sc">$</span>group <span class="sc">%%</span> <span class="dv">2</span> <span class="sc">==</span> <span class="dv">1</span>,</span>
<span id="cb3-28"><a href="#cb3-28" aria-hidden="true" tabindex="-1"></a> newdata<span class="sc">$</span>x <span class="sc">-</span> nudge,</span>
<span id="cb3-29"><a href="#cb3-29" aria-hidden="true" tabindex="-1"></a> newdata<span class="sc">$</span>x <span class="sc">+</span> nudge)</span>
<span id="cb3-30"><a href="#cb3-30" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-31"><a href="#cb3-31" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (<span class="fu">length</span>(draw_quantiles) <span class="sc">></span> <span class="dv">0</span> <span class="sc">&</span> <span class="sc">!</span>scales<span class="sc">::</span><span class="fu">zero_range</span>(<span class="fu">range</span>(data<span class="sc">$</span>y))) {</span>
<span id="cb3-32"><a href="#cb3-32" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-33"><a href="#cb3-33" aria-hidden="true" tabindex="-1"></a> <span class="fu">stopifnot</span>(<span class="fu">all</span>(draw_quantiles <span class="sc">>=</span> <span class="dv">0</span>), <span class="fu">all</span>(draw_quantiles <span class="sc"><=</span> <span class="dv">1</span>))</span>
<span id="cb3-34"><a href="#cb3-34" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-35"><a href="#cb3-35" aria-hidden="true" tabindex="-1"></a> quantiles <span class="ot"><-</span> ggplot2<span class="sc">:::</span><span class="fu">create_quantile_segment_frame</span>(data,</span>
<span id="cb3-36"><a href="#cb3-36" aria-hidden="true" tabindex="-1"></a> draw_quantiles)</span>
<span id="cb3-37"><a href="#cb3-37" aria-hidden="true" tabindex="-1"></a> aesthetics <span class="ot"><-</span> data[<span class="fu">rep</span>(<span class="dv">1</span>, <span class="fu">nrow</span>(quantiles)),</span>
<span id="cb3-38"><a href="#cb3-38" aria-hidden="true" tabindex="-1"></a> <span class="fu">setdiff</span>(<span class="fu">names</span>(data), <span class="fu">c</span>(<span class="st">"x"</span>, <span class="st">"y"</span>)),</span>
<span id="cb3-39"><a href="#cb3-39" aria-hidden="true" tabindex="-1"></a> drop <span class="ot">=</span> <span class="cn">FALSE</span>]</span>
<span id="cb3-40"><a href="#cb3-40" aria-hidden="true" tabindex="-1"></a> aesthetics<span class="sc">$</span>alpha <span class="ot"><-</span> <span class="fu">rep</span>(<span class="dv">1</span>, <span class="fu">nrow</span>(quantiles))</span>
<span id="cb3-41"><a href="#cb3-41" aria-hidden="true" tabindex="-1"></a> both <span class="ot"><-</span> <span class="fu">cbind</span>(quantiles, aesthetics)</span>
<span id="cb3-42"><a href="#cb3-42" aria-hidden="true" tabindex="-1"></a> quantile_grob <span class="ot"><-</span> ggplot2<span class="sc">::</span>GeomPath<span class="sc">$</span><span class="fu">draw_panel</span>(both, ...)</span>
<span id="cb3-43"><a href="#cb3-43" aria-hidden="true" tabindex="-1"></a> ggplot2<span class="sc">:::</span><span class="fu">ggname</span>(<span class="st">"geom_split_violin"</span>,</span>
<span id="cb3-44"><a href="#cb3-44" aria-hidden="true" tabindex="-1"></a> grid<span class="sc">::</span><span class="fu">grobTree</span>(ggplot2<span class="sc">::</span>GeomPolygon<span class="sc">$</span><span class="fu">draw_panel</span>(newdata, ...),</span>
<span id="cb3-45"><a href="#cb3-45" aria-hidden="true" tabindex="-1"></a> quantile_grob))</span>
<span id="cb3-46"><a href="#cb3-46" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb3-47"><a href="#cb3-47" aria-hidden="true" tabindex="-1"></a> <span class="cf">else</span> {</span>
<span id="cb3-48"><a href="#cb3-48" aria-hidden="true" tabindex="-1"></a> ggplot2<span class="sc">:::</span><span class="fu">ggname</span>(<span class="st">"geom_split_violin"</span>,</span>
<span id="cb3-49"><a href="#cb3-49" aria-hidden="true" tabindex="-1"></a> ggplot2<span class="sc">::</span>GeomPolygon<span class="sc">$</span><span class="fu">draw_panel</span>(newdata, ...))</span>
<span id="cb3-50"><a href="#cb3-50" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb3-51"><a href="#cb3-51" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb3-52"><a href="#cb3-52" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb3-53"><a href="#cb3-53" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-54"><a href="#cb3-54" aria-hidden="true" tabindex="-1"></a>geom_split_violin <span class="ot"><-</span> <span class="cf">function</span>(<span class="at">mapping =</span> <span class="cn">NULL</span>,</span>
<span id="cb3-55"><a href="#cb3-55" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> <span class="cn">NULL</span>,</span>
<span id="cb3-56"><a href="#cb3-56" aria-hidden="true" tabindex="-1"></a> <span class="at">stat =</span> <span class="st">"ydensity"</span>,</span>
<span id="cb3-57"><a href="#cb3-57" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="st">"identity"</span>,</span>
<span id="cb3-58"><a href="#cb3-58" aria-hidden="true" tabindex="-1"></a> <span class="co"># nudge param here</span></span>
<span id="cb3-59"><a href="#cb3-59" aria-hidden="true" tabindex="-1"></a> <span class="at">nudge =</span> <span class="fl">0.01</span>,</span>
<span id="cb3-60"><a href="#cb3-60" aria-hidden="true" tabindex="-1"></a> ...,</span>
<span id="cb3-61"><a href="#cb3-61" aria-hidden="true" tabindex="-1"></a> <span class="at">draw_quantiles =</span> <span class="cn">NULL</span>,</span>
<span id="cb3-62"><a href="#cb3-62" aria-hidden="true" tabindex="-1"></a> <span class="at">trim =</span> <span class="cn">FALSE</span>,</span>
<span id="cb3-63"><a href="#cb3-63" aria-hidden="true" tabindex="-1"></a> <span class="at">scale =</span> <span class="st">"area"</span>,</span>
<span id="cb3-64"><a href="#cb3-64" aria-hidden="true" tabindex="-1"></a> <span class="at">na.rm =</span> <span class="cn">TRUE</span>,</span>
<span id="cb3-65"><a href="#cb3-65" aria-hidden="true" tabindex="-1"></a> <span class="at">show.legend =</span> <span class="cn">NA</span>,</span>
<span id="cb3-66"><a href="#cb3-66" aria-hidden="true" tabindex="-1"></a> <span class="at">inherit.aes =</span> <span class="cn">TRUE</span>) {</span>
<span id="cb3-67"><a href="#cb3-67" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-68"><a href="#cb3-68" aria-hidden="true" tabindex="-1"></a> ggplot2<span class="sc">::</span><span class="fu">layer</span>(<span class="at">data =</span> data,</span>
<span id="cb3-69"><a href="#cb3-69" aria-hidden="true" tabindex="-1"></a> <span class="at">mapping =</span> mapping,</span>
<span id="cb3-70"><a href="#cb3-70" aria-hidden="true" tabindex="-1"></a> <span class="at">stat =</span> stat,</span>
<span id="cb3-71"><a href="#cb3-71" aria-hidden="true" tabindex="-1"></a> <span class="at">geom =</span> GeomSplitViolin,</span>
<span id="cb3-72"><a href="#cb3-72" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> position,</span>
<span id="cb3-73"><a href="#cb3-73" aria-hidden="true" tabindex="-1"></a> <span class="at">show.legend =</span> show.legend,</span>
<span id="cb3-74"><a href="#cb3-74" aria-hidden="true" tabindex="-1"></a> <span class="at">inherit.aes =</span> inherit.aes,</span>
<span id="cb3-75"><a href="#cb3-75" aria-hidden="true" tabindex="-1"></a> <span class="at">check.aes =</span> <span class="cn">TRUE</span>,</span>
<span id="cb3-76"><a href="#cb3-76" aria-hidden="true" tabindex="-1"></a> <span class="at">params =</span> <span class="fu">list</span>(<span class="at">trim =</span> trim,</span>
<span id="cb3-77"><a href="#cb3-77" aria-hidden="true" tabindex="-1"></a> <span class="at">scale =</span> scale,</span>
<span id="cb3-78"><a href="#cb3-78" aria-hidden="true" tabindex="-1"></a> <span class="co"># don't forget the nudge</span></span>
<span id="cb3-79"><a href="#cb3-79" aria-hidden="true" tabindex="-1"></a> <span class="at">nudge =</span> nudge,</span>
<span id="cb3-80"><a href="#cb3-80" aria-hidden="true" tabindex="-1"></a> <span class="at">draw_quantiles =</span> draw_quantiles,</span>
<span id="cb3-81"><a href="#cb3-81" aria-hidden="true" tabindex="-1"></a> <span class="at">na.rm =</span> na.rm,</span>
<span id="cb3-82"><a href="#cb3-82" aria-hidden="true" tabindex="-1"></a> ...))</span>
<span id="cb3-83"><a href="#cb3-83" aria-hidden="true" tabindex="-1"></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>Plot_bio <span class="ot"><-</span> plotting <span class="sc">|></span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">agent =</span> <span class="fu">case_when</span>(</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Human"</span>) <span class="sc">~</span> <span class="st">"Human"</span>, </span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Milo"</span>) <span class="sc">~</span> <span class="st">"Humanoid"</span>, </span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Theo"</span>) <span class="sc">~</span> <span class="st">"Robotic Arm"</span>, </span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span> </span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">motion_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Bio"</span>) <span class="sc">~</span> <span class="st">"Biological"</span>,</span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Nonbio"</span>) <span class="sc">~</span> <span class="st">"Nonbiological"</span>, </span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span></span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">outcome_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Correct"</span>) <span class="sc">~</span> <span class="st">"Correct"</span>, </span>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Spill"</span>) <span class="sc">~</span> <span class="st">"Error"</span>)) <span class="sc">|></span> <span class="fu">filter</span>(motion_type <span class="sc">==</span> <span class="st">"Biological"</span>) </span>
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a>Plot_bio<span class="sc">$</span>title <span class="ot"><-</span> <span class="st">"Biological Motion"</span></span>
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a>Plot_bio <span class="sc">|></span> </span>
<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> <span class="fu">fct_rev</span>(agent), <span class="at">y =</span> mean_of_3_rounds, <span class="at">fill =</span> outcome_type, <span class="at">alpha =</span> .<span class="dv">9</span>)) <span class="sc">+</span> <span class="fu">geom_split_violin</span>() <span class="sc">+</span> </span>
<span id="cb4-19"><a href="#cb4-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="at">width =</span> .<span class="dv">15</span>, <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">3</span>), <span class="at">na.rm =</span> <span class="cn">TRUE</span>) <span class="sc">+</span></span>
<span id="cb4-20"><a href="#cb4-20" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun =</span> <span class="st">"mean"</span>, <span class="at">geom =</span> <span class="st">"point"</span>, <span class="at">size =</span> <span class="dv">2</span>,</span>
<span id="cb4-21"><a href="#cb4-21" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.3</span>), <span class="at">na.rm =</span> <span class="cn">TRUE</span>) <span class="sc">+</span></span>
<span id="cb4-22"><a href="#cb4-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"mean_se"</span>, <span class="at">geom =</span> <span class="st">"errorbar"</span>, <span class="at">width =</span> .<span class="dv">1</span>,</span>
<span id="cb4-23"><a href="#cb4-23" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.3</span>), <span class="at">na.rm =</span> <span class="cn">TRUE</span>) <span class="sc">+</span></span>
<span id="cb4-24"><a href="#cb4-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"median_se"</span>, <span class="at">geom =</span> <span class="st">"crossbar"</span>, <span class="at">width =</span> .<span class="dv">1</span>,</span>
<span id="cb4-25"><a href="#cb4-25" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.3</span>), <span class="at">na.rm =</span> <span class="cn">TRUE</span>) <span class="sc">+</span></span>
<span id="cb4-26"><a href="#cb4-26" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">limits =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">500</span>, <span class="dv">1000</span>), <span class="at">name =</span> <span class="st">"Response time</span><span class="sc">\n</span><span class="st">in advance of outcome (ms)"</span>, </span>
<span id="cb4-27"><a href="#cb4-27" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(<span class="fl">0.05</span>, <span class="fl">0.05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>)) <span class="sc">+</span> </span>
<span id="cb4-28"><a href="#cb4-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Agent"</span>) <span class="sc">+</span></span>
<span id="cb4-29"><a href="#cb4-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"lightblue"</span>, <span class="st">"#A0522D"</span>))<span class="sc">+</span></span>
<span id="cb4-30"><a href="#cb4-30" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_linedraw</span>() <span class="sc">+</span> <span class="fu">guides</span>(<span class="at">alpha =</span> <span class="st">"none"</span>) <span class="sc">+</span> </span>
<span id="cb4-31"><a href="#cb4-31" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="fu">guide_legend</span>(<span class="at">title=</span><span class="st">"Outcome"</span>)) <span class="sc">+</span></span>
<span id="cb4-32"><a href="#cb4-32" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb4-33"><a href="#cb4-33" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb4-34"><a href="#cb4-34" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text.x =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>, <span class="at">face=</span><span class="st">"bold"</span>), </span>
<span id="cb4-35"><a href="#cb4-35" aria-hidden="true" tabindex="-1"></a><span class="co"># plot.title = element_text(hjust = 0.6, face = "bold", size = 16), </span></span>
<span id="cb4-36"><a href="#cb4-36" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>, <span class="at">vjust =</span> <span class="sc">+</span><span class="dv">2</span>), </span>
<span id="cb4-37"><a href="#cb4-37" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="dv">2</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb4-38"><a href="#cb4-38" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text=</span><span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">12</span>)) <span class="sc">+</span> <span class="fu">facet_wrap</span>(<span class="sc">~</span>title)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/unnamed-chunk-2-1.png" class="img-fluid" width="672"></p>
</div>
</div>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>Plot_nonbio <span class="ot"><-</span> plotting <span class="sc">|></span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">agent =</span> <span class="fu">case_when</span>(</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Human"</span>) <span class="sc">~</span> <span class="st">"Human"</span>, </span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Milo"</span>) <span class="sc">~</span> <span class="st">"Humanoid"</span>, </span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Theo"</span>) <span class="sc">~</span> <span class="st">"Robotic Arm"</span>, </span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span> </span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">motion_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Bio"</span>) <span class="sc">~</span> <span class="st">"Biological"</span>,</span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Nonbio"</span>) <span class="sc">~</span> <span class="st">"Nonbiological"</span>, </span>
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span></span>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">outcome_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Correct"</span>) <span class="sc">~</span> <span class="st">"Correct"</span>, </span>
<span id="cb5-13"><a href="#cb5-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Spill"</span>) <span class="sc">~</span> <span class="st">"Error"</span>)) <span class="sc">|></span> <span class="fu">filter</span>(motion_type <span class="sc">==</span> <span class="st">"Nonbiological"</span>) </span>
<span id="cb5-14"><a href="#cb5-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-15"><a href="#cb5-15" aria-hidden="true" tabindex="-1"></a>Plot_nonbio<span class="sc">$</span>title <span class="ot"><-</span> <span class="st">"Nonbiological Motion"</span></span>
<span id="cb5-16"><a href="#cb5-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-17"><a href="#cb5-17" aria-hidden="true" tabindex="-1"></a>Plot_nonbio <span class="sc">|></span> </span>
<span id="cb5-18"><a href="#cb5-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> <span class="fu">fct_rev</span>(agent), <span class="at">y =</span> mean_of_3_rounds, <span class="at">fill =</span> outcome_type, <span class="at">alpha =</span> .<span class="dv">9</span>)) <span class="sc">+</span> </span>
<span id="cb5-19"><a href="#cb5-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_split_violin</span>() <span class="sc">+</span></span>
<span id="cb5-20"><a href="#cb5-20" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="at">width =</span> .<span class="dv">15</span>, </span>
<span id="cb5-21"><a href="#cb5-21" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">3</span>), <span class="at">fatten =</span> <span class="cn">NULL</span>, <span class="at">na.rm =</span> <span class="cn">TRUE</span>) <span class="sc">+</span></span>
<span id="cb5-22"><a href="#cb5-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun =</span> <span class="st">"mean"</span>, <span class="at">geom =</span> <span class="st">"point"</span>, <span class="at">na.rm =</span> <span class="cn">TRUE</span>, <span class="at">size =</span> <span class="dv">2</span>,</span>
<span id="cb5-23"><a href="#cb5-23" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.3</span>)) <span class="sc">+</span></span>
<span id="cb5-24"><a href="#cb5-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"mean_se"</span>, <span class="at">geom =</span> <span class="st">"errorbar"</span>, <span class="at">na.rm =</span> <span class="cn">TRUE</span>, <span class="at">width =</span> .<span class="dv">1</span>,</span>
<span id="cb5-25"><a href="#cb5-25" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.3</span>)) <span class="sc">+</span></span>
<span id="cb5-26"><a href="#cb5-26" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"mean_se"</span>, <span class="at">geom =</span> <span class="st">"errorbar"</span>, <span class="at">width =</span> .<span class="dv">1</span>,</span>
<span id="cb5-27"><a href="#cb5-27" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.3</span>), <span class="at">na.rm =</span> <span class="cn">TRUE</span>) <span class="sc">+</span></span>
<span id="cb5-28"><a href="#cb5-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"lightblue"</span>, <span class="st">"#A0522D"</span>)) <span class="sc">+</span></span>
<span id="cb5-29"><a href="#cb5-29" aria-hidden="true" tabindex="-1"></a><span class="co"># scale_fill_manual(values = wes_palette("Royal1", n=2))+</span></span>
<span id="cb5-30"><a href="#cb5-30" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_linedraw</span>()<span class="sc">+</span> </span>
<span id="cb5-31"><a href="#cb5-31" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb5-32"><a href="#cb5-32" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb5-33"><a href="#cb5-33" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb5-34"><a href="#cb5-34" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="dv">4</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb5-35"><a href="#cb5-35" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">12</span>), </span>
<span id="cb5-36"><a href="#cb5-36" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>, <span class="at">face =</span> <span class="st">"bold"</span>)) <span class="sc">+</span></span>
<span id="cb5-37"><a href="#cb5-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">limits =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">500</span>, <span class="dv">1000</span>), <span class="at">name =</span> <span class="st">"Response time</span><span class="sc">\n</span><span class="st">in advance of outcome (ms)"</span>, </span>
<span id="cb5-38"><a href="#cb5-38" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(<span class="fl">0.05</span>, <span class="fl">0.05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>)) <span class="sc">+</span> </span>
<span id="cb5-39"><a href="#cb5-39" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Agent"</span>) <span class="sc">+</span></span>
<span id="cb5-40"><a href="#cb5-40" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">alpha =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb5-41"><a href="#cb5-41" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="fu">guide_legend</span>(<span class="at">title=</span><span class="st">"Outcome"</span>)) <span class="sc">+</span> <span class="fu">facet_wrap</span>(<span class="sc">~</span>title)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/unnamed-chunk-3-1.png" class="img-fluid" width="672"></p>
</div>
</div>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="st">"%||%"</span> <span class="ot"><-</span> <span class="cf">function</span>(a, b) {</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (<span class="sc">!</span><span class="fu">is.null</span>(a)) a <span class="cf">else</span> b</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a>geom_half_violin <span class="ot"><-</span> <span class="cf">function</span>(<span class="at">mapping =</span> <span class="cn">NULL</span>, <span class="at">data =</span> <span class="cn">NULL</span>, <span class="at">stat =</span> <span class="st">"ydensity"</span>,</span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="st">"dodge"</span>, <span class="at">trim =</span> <span class="cn">TRUE</span>, <span class="at">scale =</span> <span class="st">"area"</span>,</span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a> <span class="at">show.legend =</span> <span class="cn">NA</span>, <span class="at">inherit.aes =</span> <span class="cn">TRUE</span>, ...) {</span>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">layer</span>(</span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> data,</span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a> <span class="at">mapping =</span> mapping,</span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a> <span class="at">stat =</span> stat,</span>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a> <span class="at">geom =</span> GeomHalfViolin,</span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> position,</span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a> <span class="at">show.legend =</span> show.legend,</span>
<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a> <span class="at">inherit.aes =</span> inherit.aes,</span>
<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a> <span class="at">params =</span> <span class="fu">list</span>(</span>
<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a> <span class="at">trim =</span> trim,</span>
<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a> <span class="at">scale =</span> scale,</span>
<span id="cb6-19"><a href="#cb6-19" aria-hidden="true" tabindex="-1"></a> ...</span>
<span id="cb6-20"><a href="#cb6-20" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb6-21"><a href="#cb6-21" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb6-22"><a href="#cb6-22" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb6-23"><a href="#cb6-23" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-24"><a href="#cb6-24" aria-hidden="true" tabindex="-1"></a>GeomHalfViolin <span class="ot"><-</span></span>
<span id="cb6-25"><a href="#cb6-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggproto</span>(<span class="st">"Violinist"</span>, Geom,</span>
<span id="cb6-26"><a href="#cb6-26" aria-hidden="true" tabindex="-1"></a> <span class="at">setup_data =</span> <span class="cf">function</span>(data, params) {</span>
<span id="cb6-27"><a href="#cb6-27" aria-hidden="true" tabindex="-1"></a> data<span class="sc">$</span>width <span class="ot"><-</span> data<span class="sc">$</span>width <span class="sc">%||%</span></span>
<span id="cb6-28"><a href="#cb6-28" aria-hidden="true" tabindex="-1"></a> params<span class="sc">$</span>width <span class="sc">%||%</span> (<span class="fu">resolution</span>(data<span class="sc">$</span>x, <span class="cn">FALSE</span>) <span class="sc">*</span> <span class="fl">0.9</span>)</span>
<span id="cb6-29"><a href="#cb6-29" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-30"><a href="#cb6-30" aria-hidden="true" tabindex="-1"></a> <span class="co"># ymin, ymax, xmin, and xmax define the bounding rectangle for each group</span></span>
<span id="cb6-31"><a href="#cb6-31" aria-hidden="true" tabindex="-1"></a> data <span class="sc">%>%</span></span>
<span id="cb6-32"><a href="#cb6-32" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(group) <span class="sc">%>%</span></span>
<span id="cb6-33"><a href="#cb6-33" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">ymin =</span> <span class="fu">min</span>(y),</span>
<span id="cb6-34"><a href="#cb6-34" aria-hidden="true" tabindex="-1"></a> <span class="at">ymax =</span> <span class="fu">max</span>(y),</span>
<span id="cb6-35"><a href="#cb6-35" aria-hidden="true" tabindex="-1"></a> <span class="at">xmin =</span> x,</span>
<span id="cb6-36"><a href="#cb6-36" aria-hidden="true" tabindex="-1"></a> <span class="at">xmax =</span> x <span class="sc">+</span> width <span class="sc">/</span> <span class="dv">2</span>)</span>
<span id="cb6-37"><a href="#cb6-37" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-38"><a href="#cb6-38" aria-hidden="true" tabindex="-1"></a> },</span>
<span id="cb6-39"><a href="#cb6-39" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-40"><a href="#cb6-40" aria-hidden="true" tabindex="-1"></a> <span class="at">draw_group =</span> <span class="cf">function</span>(data, panel_scales, coord) {</span>
<span id="cb6-41"><a href="#cb6-41" aria-hidden="true" tabindex="-1"></a> <span class="co"># Find the points for the line to go all the way around</span></span>
<span id="cb6-42"><a href="#cb6-42" aria-hidden="true" tabindex="-1"></a> data <span class="ot"><-</span> <span class="fu">transform</span>(data, <span class="at">xminv =</span> x,</span>
<span id="cb6-43"><a href="#cb6-43" aria-hidden="true" tabindex="-1"></a> <span class="at">xmaxv =</span> x <span class="sc">+</span> violinwidth <span class="sc">*</span> (xmax <span class="sc">-</span> x))</span>
<span id="cb6-44"><a href="#cb6-44" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-45"><a href="#cb6-45" aria-hidden="true" tabindex="-1"></a> <span class="co"># Make sure it's sorted properly to draw the outline</span></span>
<span id="cb6-46"><a href="#cb6-46" aria-hidden="true" tabindex="-1"></a> newdata <span class="ot"><-</span> <span class="fu">rbind</span>(plyr<span class="sc">::</span><span class="fu">arrange</span>(<span class="fu">transform</span>(data, <span class="at">x =</span> xminv), y),</span>
<span id="cb6-47"><a href="#cb6-47" aria-hidden="true" tabindex="-1"></a> plyr<span class="sc">::</span><span class="fu">arrange</span>(<span class="fu">transform</span>(data, <span class="at">x =</span> xmaxv), <span class="sc">-</span>y))</span>
<span id="cb6-48"><a href="#cb6-48" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-49"><a href="#cb6-49" aria-hidden="true" tabindex="-1"></a> <span class="co"># Close the polygon: set first and last point the same</span></span>
<span id="cb6-50"><a href="#cb6-50" aria-hidden="true" tabindex="-1"></a> <span class="co"># Needed for coord_polar and such</span></span>
<span id="cb6-51"><a href="#cb6-51" aria-hidden="true" tabindex="-1"></a> newdata <span class="ot"><-</span> <span class="fu">rbind</span>(newdata, newdata[<span class="dv">1</span>,])</span>
<span id="cb6-52"><a href="#cb6-52" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-53"><a href="#cb6-53" aria-hidden="true" tabindex="-1"></a> ggplot2<span class="sc">:::</span><span class="fu">ggname</span>(<span class="st">"geom_flat_violin"</span>, GeomPolygon<span class="sc">$</span><span class="fu">draw_panel</span>(newdata, panel_scales, coord))</span>
<span id="cb6-54"><a href="#cb6-54" aria-hidden="true" tabindex="-1"></a> },</span>
<span id="cb6-55"><a href="#cb6-55" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-56"><a href="#cb6-56" aria-hidden="true" tabindex="-1"></a> <span class="at">draw_key =</span> draw_key_polygon,</span>
<span id="cb6-57"><a href="#cb6-57" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-58"><a href="#cb6-58" aria-hidden="true" tabindex="-1"></a> <span class="at">default_aes =</span> <span class="fu">aes</span>(<span class="at">weight =</span> <span class="dv">1</span>, <span class="at">colour =</span> <span class="st">"grey20"</span>, <span class="at">fill =</span> <span class="st">"white"</span>, <span class="at">size =</span> <span class="fl">0.5</span>,</span>
<span id="cb6-59"><a href="#cb6-59" aria-hidden="true" tabindex="-1"></a> <span class="at">alpha =</span> <span class="cn">NA</span>, <span class="at">linetype =</span> <span class="st">"solid"</span>),</span>
<span id="cb6-60"><a href="#cb6-60" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-61"><a href="#cb6-61" aria-hidden="true" tabindex="-1"></a> <span class="at">required_aes =</span> <span class="fu">c</span>(<span class="st">"x"</span>, <span class="st">"y"</span>)</span>
<span id="cb6-62"><a href="#cb6-62" aria-hidden="true" tabindex="-1"></a> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>Plot_bio <span class="sc">|></span> </span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> stimulus, <span class="at">y =</span> <span class="sc">-</span>(mean_of_3_rounds), <span class="at">fill =</span> outcome_type)) <span class="sc">+</span> </span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_half_violin</span>(<span class="at">trim=</span><span class="cn">FALSE</span>, <span class="at">na.rm =</span> <span class="cn">TRUE</span>, <span class="at">width =</span> <span class="dv">1</span>, </span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span><span class="fu">position_nudge</span>(<span class="at">x =</span> <span class="sc">-</span>.<span class="dv">15</span>, <span class="at">y =</span> <span class="dv">0</span>)) <span class="sc">+</span> </span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="at">fill =</span> <span class="st">"white"</span>, <span class="at">width =</span> .<span class="dv">17</span>, <span class="at">alpha =</span> <span class="fl">0.5</span>, <span class="at">fatten =</span> <span class="cn">NULL</span>, </span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(.<span class="dv">15</span>)</span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun =</span> <span class="st">"mean"</span>, <span class="at">geom =</span> <span class="st">"point"</span>) <span class="sc">+</span></span>
<span id="cb7-9"><a href="#cb7-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"lightblue"</span>, <span class="st">"#A0522D"</span>)) <span class="sc">+</span></span>
<span id="cb7-10"><a href="#cb7-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"mean_se"</span>, <span class="at">geom =</span> <span class="st">"errorbar"</span>, <span class="at">width =</span> .<span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb7-11"><a href="#cb7-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span> </span>
<span id="cb7-12"><a href="#cb7-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">alpha =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb7-13"><a href="#cb7-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="fu">guide_legend</span>(<span class="at">title=</span><span class="st">"Outcome"</span>)) <span class="sc">+</span> </span>
<span id="cb7-14"><a href="#cb7-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">size =</span> <span class="dv">1</span>, <span class="at">color =</span> <span class="st">"#303030"</span>) <span class="sc">+</span> </span>
<span id="cb7-15"><a href="#cb7-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_linedraw</span>() <span class="sc">+</span> </span>
<span id="cb7-16"><a href="#cb7-16" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Conditions"</span>, </span>
<span id="cb7-17"><a href="#cb7-17" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Human"</span>, <span class="st">"Humanoid"</span>, <span class="st">"Robotic Arm"</span>), </span>
<span id="cb7-18"><a href="#cb7-18" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(<span class="fl">0.15</span>, .<span class="dv">05</span>, .<span class="dv">35</span>, .<span class="dv">05</span>)) <span class="sc">+</span></span>
<span id="cb7-19"><a href="#cb7-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">"Response time before seeing outcome (ms)"</span>, </span>
<span id="cb7-20"><a href="#cb7-20" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(<span class="fl">0.05</span>, <span class="fl">0.05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>), <span class="at">n.breaks =</span> <span class="dv">7</span>, </span>
<span id="cb7-21"><a href="#cb7-21" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"1000</span><span class="sc">\n</span><span class="st">before</span><span class="sc">\n</span><span class="st">pouring"</span>, <span class="st">"750"</span>, <span class="st">"500"</span>, <span class="st">"250"</span>, <span class="st">"0</span><span class="sc">\n</span><span class="st">outcome</span><span class="sc">\n</span><span class="st">shown"</span>, <span class="st">"-250"</span>, <span class="st">"-500"</span>),</span>
<span id="cb7-22"><a href="#cb7-22" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">1000</span>, <span class="dv">500</span>)) <span class="sc">+</span></span>
<span id="cb7-23"><a href="#cb7-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb7-24"><a href="#cb7-24" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb7-25"><a href="#cb7-25" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb7-26"><a href="#cb7-26" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="dv">4</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb7-27"><a href="#cb7-27" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">12</span>), </span>
<span id="cb7-28"><a href="#cb7-28" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>, <span class="at">face =</span> <span class="st">"bold"</span>), </span>
<span id="cb7-29"><a href="#cb7-29" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.spacing =</span> <span class="fu">unit</span>(<span class="dv">2</span>, <span class="st">"lines"</span>), <span class="at">legend.position =</span> <span class="st">"none"</span></span>
<span id="cb7-30"><a href="#cb7-30" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span> <span class="fu">facet_wrap</span>(<span class="sc">~</span> outcome_type, <span class="at">scales =</span> <span class="st">"free"</span>, <span class="at">nrow =</span> <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/RT%20violin%20bio-1.png" class="img-fluid" width="864"></p>
</div>
</div>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>Plot_nonbio <span class="sc">|></span> </span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> stimulus, <span class="at">y =</span> <span class="sc">-</span>(mean_of_3_rounds), <span class="at">fill =</span> outcome_type)) <span class="sc">+</span> </span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_half_violin</span>(<span class="at">trim=</span><span class="cn">FALSE</span>, <span class="at">na.rm =</span> <span class="cn">TRUE</span>, <span class="at">width =</span> <span class="dv">1</span>, </span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_nudge</span>(<span class="at">x =</span> <span class="sc">-</span>.<span class="dv">11</span>, <span class="at">y =</span> <span class="dv">0</span>)) <span class="sc">+</span> </span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="at">fill =</span> <span class="st">"white"</span>, <span class="at">width =</span> .<span class="dv">17</span>,<span class="at">fatten =</span> <span class="dv">2</span>, <span class="at">na.rm =</span> T, <span class="at">alpha =</span> <span class="fl">0.6</span>) <span class="sc">+</span></span>
<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun =</span> <span class="st">"mean"</span>, <span class="at">geom =</span> <span class="st">"point"</span>, <span class="at">na.rm =</span> T) <span class="sc">+</span></span>
<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"lightblue"</span>, <span class="st">"#A0522D"</span>)) <span class="sc">+</span></span>
<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"mean_se"</span>, <span class="at">geom =</span> <span class="st">"errorbar"</span>, <span class="at">width =</span> .<span class="dv">1</span>, <span class="at">na.rm =</span> T) <span class="sc">+</span></span>
<span id="cb8-9"><a href="#cb8-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span> </span>
<span id="cb8-10"><a href="#cb8-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">alpha =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb8-11"><a href="#cb8-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="fu">guide_legend</span>(<span class="at">title=</span><span class="st">"Outcome"</span>)) <span class="sc">+</span> </span>
<span id="cb8-12"><a href="#cb8-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">size =</span> <span class="dv">1</span>, <span class="at">color =</span> <span class="st">"#303030"</span>) <span class="sc">+</span> </span>
<span id="cb8-13"><a href="#cb8-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_linedraw</span>() <span class="sc">+</span> </span>
<span id="cb8-14"><a href="#cb8-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Conditions"</span>, </span>
<span id="cb8-15"><a href="#cb8-15" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Human"</span>, <span class="st">"Humanoid"</span>, <span class="st">"Robotic Arm"</span>), </span>
<span id="cb8-16"><a href="#cb8-16" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(.<span class="dv">15</span>, .<span class="dv">05</span>, .<span class="dv">35</span>, .<span class="dv">05</span>)) <span class="sc">+</span></span>
<span id="cb8-17"><a href="#cb8-17" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">"Response time before seeing outcome (ms)"</span>, </span>
<span id="cb8-18"><a href="#cb8-18" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(.<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>), <span class="at">n.breaks =</span> <span class="dv">7</span>, </span>
<span id="cb8-19"><a href="#cb8-19" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"1000</span><span class="sc">\n</span><span class="st">before</span><span class="sc">\n</span><span class="st">pouring"</span>, <span class="st">"750"</span>, <span class="st">"500"</span>, <span class="st">"250"</span>, <span class="st">"0</span><span class="sc">\n</span><span class="st">outcome</span><span class="sc">\n</span><span class="st">shown"</span>, <span class="st">"-250"</span>, <span class="st">"-500"</span>),</span>
<span id="cb8-20"><a href="#cb8-20" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">1000</span>, <span class="dv">500</span>)) <span class="sc">+</span></span>
<span id="cb8-21"><a href="#cb8-21" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb8-22"><a href="#cb8-22" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,.<span class="dv">5</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb8-23"><a href="#cb8-23" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb8-24"><a href="#cb8-24" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="dv">4</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb8-25"><a href="#cb8-25" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">12</span>), </span>
<span id="cb8-26"><a href="#cb8-26" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>, <span class="at">face =</span> <span class="st">"bold"</span>), </span>
<span id="cb8-27"><a href="#cb8-27" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.spacing =</span> <span class="fu">unit</span>(<span class="dv">2</span>, <span class="st">"lines"</span>), <span class="at">legend.position =</span> <span class="st">"none"</span></span>
<span id="cb8-28"><a href="#cb8-28" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span><span class="fu">facet_wrap</span>(<span class="sc">~</span>outcome_type, <span class="at">scales =</span> <span class="st">"free"</span>, <span class="at">nrow=</span><span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/RT%20violin%20nonbio-1.png" class="img-fluid" width="864"></p>
</div>
</div>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>Plot_bio <span class="sc">|></span> </span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> agent, <span class="at">y =</span> <span class="sc">-</span>(mean_of_3_rounds), <span class="at">fill =</span> outcome_type, <span class="at">alpha =</span> .<span class="dv">8</span>)) <span class="sc">+</span> </span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_half_violin</span>(<span class="at">position =</span> <span class="fu">position_nudge</span>(<span class="at">x =</span> .<span class="dv">25</span>, <span class="at">y =</span> <span class="dv">0</span>), </span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a> <span class="at">trim=</span><span class="cn">FALSE</span>, <span class="at">na.rm =</span> <span class="cn">TRUE</span>, <span class="at">width =</span> .<span class="dv">8</span>) <span class="sc">+</span> </span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="at">width =</span> .<span class="dv">3</span>, <span class="at">alpha =</span> <span class="fl">0.5</span>, <span class="at">fatten =</span> <span class="cn">NULL</span>, <span class="at">na.rm =</span> T) <span class="sc">+</span></span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun =</span> <span class="st">"mean"</span>, <span class="at">geom =</span> <span class="st">"point"</span>,</span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.25</span>), <span class="at">na.rm =</span> T) <span class="sc">+</span></span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"lightblue"</span>, <span class="st">"#A0522D"</span>)) <span class="sc">+</span></span>
<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"mean_se"</span>, <span class="at">geom =</span> <span class="st">"errorbar"</span>, <span class="at">width =</span> .<span class="dv">1</span>,</span>
<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_dodge</span>(<span class="at">width =</span> <span class="fl">0.3</span>), <span class="at">na.rm =</span> T) <span class="sc">+</span></span>
<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span> <span class="fu">guides</span>(<span class="at">alpha =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="fu">guide_legend</span>(<span class="at">title=</span><span class="st">"Outcome"</span>)) <span class="sc">+</span> </span>
<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">size =</span> <span class="dv">1</span>) <span class="sc">+</span> </span>
<span id="cb9-14"><a href="#cb9-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>() <span class="sc">+</span></span>
<span id="cb9-15"><a href="#cb9-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_linedraw</span>() <span class="sc">+</span> </span>
<span id="cb9-16"><a href="#cb9-16" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Agent"</span>, </span>
<span id="cb9-17"><a href="#cb9-17" aria-hidden="true" tabindex="-1"></a><span class="co"># labels = c("Human Error", "Human Correct", "Humanoid Error", "Humanoid Correct", "Robotic Arm Error", "Robotic Arm Correct"), </span></span>
<span id="cb9-18"><a href="#cb9-18" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(.<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>)) <span class="sc">+</span></span>
<span id="cb9-19"><a href="#cb9-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">"Response time before seeing outcome (ms)"</span>, </span>
<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(.<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>),</span>
<span id="cb9-21"><a href="#cb9-21" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"1000"</span>, <span class="st">"500"</span>, <span class="st">"0"</span>, <span class="st">"500"</span>)</span>
<span id="cb9-22"><a href="#cb9-22" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb9-23"><a href="#cb9-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb9-24"><a href="#cb9-24" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb9-25"><a href="#cb9-25" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb9-26"><a href="#cb9-26" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="dv">3</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb9-27"><a href="#cb9-27" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text=</span><span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">12</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/unnamed-chunk-4-1.png" class="img-fluid" width="672"></p>
</div>
</div>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>plot_error_only <span class="ot"><-</span> plotting <span class="sc">|></span></span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">agent =</span> <span class="fu">case_when</span>(</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Human"</span>) <span class="sc">~</span> <span class="st">"Human"</span>, </span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Milo"</span>) <span class="sc">~</span> <span class="st">"Humanoid"</span>, </span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Theo"</span>) <span class="sc">~</span> <span class="st">"Robotic Arm"</span>, </span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span> </span>
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">motion_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Bio"</span>) <span class="sc">~</span> <span class="st">"Biological"</span>,</span>
<span id="cb10-9"><a href="#cb10-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Nonbio"</span>) <span class="sc">~</span> <span class="st">"Nonbiological"</span>, </span>
<span id="cb10-10"><a href="#cb10-10" aria-hidden="true" tabindex="-1"></a> )) <span class="sc">|></span></span>
<span id="cb10-11"><a href="#cb10-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">outcome_type =</span> <span class="fu">case_when</span>(</span>
<span id="cb10-12"><a href="#cb10-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Correct"</span>) <span class="sc">~</span> <span class="st">"Correct"</span>, </span>
<span id="cb10-13"><a href="#cb10-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_detect</span>(stimulus, <span class="st">"Spill"</span>) <span class="sc">~</span> <span class="st">"Error"</span>)) <span class="sc">|></span> </span>
<span id="cb10-14"><a href="#cb10-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(outcome_type <span class="sc">==</span> <span class="st">"Error"</span>)</span>
<span id="cb10-15"><a href="#cb10-15" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb10-16"><a href="#cb10-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-17"><a href="#cb10-17" aria-hidden="true" tabindex="-1"></a>plot_error_only <span class="sc">|></span> </span>
<span id="cb10-18"><a href="#cb10-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> stimulus, <span class="at">y =</span> <span class="sc">-</span>(mean_of_3_rounds), <span class="at">fill =</span> motion_type)) <span class="sc">+</span> </span>
<span id="cb10-19"><a href="#cb10-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_half_violin</span>(<span class="at">trim=</span><span class="cn">FALSE</span>, <span class="at">na.rm =</span> <span class="cn">TRUE</span>, <span class="at">width =</span> <span class="dv">1</span>, </span>
<span id="cb10-20"><a href="#cb10-20" aria-hidden="true" tabindex="-1"></a> <span class="at">position =</span> <span class="fu">position_nudge</span>(<span class="at">x =</span> <span class="sc">-</span>.<span class="dv">11</span>, <span class="at">y =</span> <span class="dv">0</span>)) <span class="sc">+</span> </span>
<span id="cb10-21"><a href="#cb10-21" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="at">fill =</span> <span class="st">"white"</span>, <span class="at">width =</span> .<span class="dv">15</span>,<span class="at">fatten =</span> <span class="dv">2</span>, <span class="at">na.rm =</span> T, <span class="at">alpha =</span> <span class="fl">0.6</span>) <span class="sc">+</span></span>
<span id="cb10-22"><a href="#cb10-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun =</span> <span class="st">"mean"</span>, <span class="at">geom =</span> <span class="st">"point"</span>, <span class="at">na.rm =</span> T) <span class="sc">+</span></span>
<span id="cb10-23"><a href="#cb10-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"darkgreen"</span>, <span class="st">"brown"</span>)) <span class="sc">+</span></span>
<span id="cb10-24"><a href="#cb10-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">fun.data =</span> <span class="st">"mean_se"</span>, <span class="at">geom =</span> <span class="st">"errorbar"</span>, <span class="at">width =</span> .<span class="dv">1</span>, <span class="at">na.rm =</span> T) <span class="sc">+</span></span>
<span id="cb10-25"><a href="#cb10-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span> </span>
<span id="cb10-26"><a href="#cb10-26" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">alpha =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb10-27"><a href="#cb10-27" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="fu">guide_legend</span>(<span class="at">title=</span><span class="st">"Outcome"</span>)) <span class="sc">+</span> </span>
<span id="cb10-28"><a href="#cb10-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="dv">0</span>, <span class="at">size =</span> <span class="dv">1</span>, <span class="at">color =</span> <span class="st">"#303030"</span>) <span class="sc">+</span> </span>
<span id="cb10-29"><a href="#cb10-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_linedraw</span>() <span class="sc">+</span> </span>
<span id="cb10-30"><a href="#cb10-30" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Conditions"</span>, </span>
<span id="cb10-31"><a href="#cb10-31" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Human"</span>, <span class="st">"Humanoid"</span>, <span class="st">"Robotic Arm"</span>), </span>
<span id="cb10-32"><a href="#cb10-32" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(.<span class="dv">15</span>, .<span class="dv">05</span>, .<span class="dv">35</span>, .<span class="dv">05</span>)) <span class="sc">+</span></span>
<span id="cb10-33"><a href="#cb10-33" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">"Response time before seeing outcome (ms)"</span>, </span>
<span id="cb10-34"><a href="#cb10-34" aria-hidden="true" tabindex="-1"></a> <span class="at">expand =</span> <span class="fu">c</span>(.<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>, .<span class="dv">05</span>), <span class="at">n.breaks =</span> <span class="dv">7</span>, </span>
<span id="cb10-35"><a href="#cb10-35" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"1000</span><span class="sc">\n</span><span class="st">before</span><span class="sc">\n</span><span class="st">pouring"</span>, <span class="st">"750"</span>, <span class="st">"500"</span>, <span class="st">"250"</span>, <span class="st">"0</span><span class="sc">\n</span><span class="st">outcome</span><span class="sc">\n</span><span class="st">shown"</span>, <span class="st">"-250"</span>, <span class="st">"-500"</span>),</span>
<span id="cb10-36"><a href="#cb10-36" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> <span class="fu">c</span>(<span class="sc">-</span><span class="dv">1000</span>, <span class="dv">500</span>)) <span class="sc">+</span></span>
<span id="cb10-37"><a href="#cb10-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb10-38"><a href="#cb10-38" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,.<span class="dv">5</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb10-39"><a href="#cb10-39" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb10-40"><a href="#cb10-40" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="dv">4</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb10-41"><a href="#cb10-41" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">12</span>), </span>
<span id="cb10-42"><a href="#cb10-42" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>, <span class="at">face =</span> <span class="st">"bold"</span>), </span>
<span id="cb10-43"><a href="#cb10-43" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.spacing =</span> <span class="fu">unit</span>(<span class="dv">2</span>, <span class="st">"lines"</span>), </span>
<span id="cb10-44"><a href="#cb10-44" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="st">"none"</span></span>
<span id="cb10-45"><a href="#cb10-45" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span> <span class="fu">facet_wrap</span>(<span class="sc">~</span>motion_type, <span class="at">scales =</span> <span class="st">"free"</span>, <span class="at">nrow=</span><span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/plot%20error%20only-1.png" class="img-fluid" width="864"></p>
</div>
</div>
</section>
<section id="interaction-plots" class="level2">
<h2 class="anchored" data-anchor-id="interaction-plots">Interaction plots</h2>
<section id="subset-by-agent" class="level3">
<h3 class="anchored" data-anchor-id="subset-by-agent">Subset by Agent</h3>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>iplot_arm <span class="ot"><-</span> </span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a> summary_statistics <span class="sc">|></span> </span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(agent <span class="sc">==</span> <span class="st">"Robotic Arm"</span>) <span class="sc">|></span></span>
<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> motion_type, <span class="at">y =</span> mean, <span class="at">group =</span> outcome_type, </span>
<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a> <span class="at">shape =</span> outcome_type, <span class="at">color =</span> outcome_type)) <span class="sc">+</span></span>
<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>(<span class="at">size =</span> <span class="dv">3</span>) <span class="sc">+</span></span>
<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">linetype =</span> outcome_type))<span class="sc">+</span></span>
<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Motion Type"</span>)<span class="sc">+</span></span>
<span id="cb11-9"><a href="#cb11-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">name =</span> <span class="st">"Response time </span><span class="sc">\n</span><span class="st">before outcome is shown (ms)"</span>, <span class="at">limits=</span><span class="fu">c</span>(<span class="dv">0</span>, <span class="dv">500</span>)) <span class="sc">+</span></span>
<span id="cb11-10"><a href="#cb11-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_classic</span>() <span class="sc">+</span> <span class="fu">scale_colour_brewer</span>(<span class="at">palette =</span> <span class="st">"Set1"</span>) <span class="sc">+</span> </span>
<span id="cb11-11"><a href="#cb11-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_colour_brewer</span>(<span class="at">palette =</span> <span class="st">"Set1"</span>, <span class="at">direction =</span> <span class="sc">-</span><span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb11-12"><a href="#cb11-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position=</span><span class="st">"none"</span>, </span>
<span id="cb11-13"><a href="#cb11-13" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb11-14"><a href="#cb11-14" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.6</span>, <span class="at">face =</span> <span class="st">"bold"</span>, <span class="at">size =</span> <span class="dv">16</span>), </span>
<span id="cb11-15"><a href="#cb11-15" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">+</span><span class="dv">3</span>, <span class="at">size =</span> <span class="dv">14</span>),</span>
<span id="cb11-16"><a href="#cb11-16" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="fl">1.5</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb11-17"><a href="#cb11-17" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span><span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">14</span>)) <span class="sc">+</span> </span>
<span id="cb11-18"><a href="#cb11-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggtitle</span>(<span class="st">"Robotic Arm"</span>)</span>
<span id="cb11-19"><a href="#cb11-19" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-20"><a href="#cb11-20" aria-hidden="true" tabindex="-1"></a>iplot_humanoid <span class="ot"><-</span> summary_statistics <span class="sc">|></span> </span>
<span id="cb11-21"><a href="#cb11-21" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(agent <span class="sc">==</span> <span class="st">"Humanoid"</span>) <span class="sc">|></span></span>
<span id="cb11-22"><a href="#cb11-22" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> motion_type, <span class="at">y =</span> mean, <span class="at">group =</span> outcome_type, </span>
<span id="cb11-23"><a href="#cb11-23" aria-hidden="true" tabindex="-1"></a> <span class="at">shape =</span> outcome_type, <span class="at">color =</span> outcome_type)) <span class="sc">+</span></span>
<span id="cb11-24"><a href="#cb11-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>(<span class="at">size =</span> <span class="dv">3</span>) <span class="sc">+</span></span>
<span id="cb11-25"><a href="#cb11-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">linetype =</span> outcome_type))<span class="sc">+</span></span>
<span id="cb11-26"><a href="#cb11-26" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Motion Type"</span>) <span class="sc">+</span> </span>
<span id="cb11-27"><a href="#cb11-27" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">limits=</span><span class="fu">c</span>(<span class="dv">0</span>, <span class="dv">500</span>)) <span class="sc">+</span></span>
<span id="cb11-28"><a href="#cb11-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_classic</span>() <span class="sc">+</span> <span class="fu">scale_colour_brewer</span>(<span class="at">palette =</span> <span class="st">"Set1"</span>, <span class="at">direction =</span> <span class="sc">-</span><span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb11-29"><a href="#cb11-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position=</span><span class="st">"none"</span>, </span>
<span id="cb11-30"><a href="#cb11-30" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb11-31"><a href="#cb11-31" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.6</span>, <span class="at">face =</span> <span class="st">"bold"</span>, <span class="at">size =</span> <span class="dv">16</span>), </span>
<span id="cb11-32"><a href="#cb11-32" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_blank</span>(), </span>
<span id="cb11-33"><a href="#cb11-33" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="fl">1.5</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb11-34"><a href="#cb11-34" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text=</span><span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">14</span>)) <span class="sc">+</span> </span>
<span id="cb11-35"><a href="#cb11-35" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggtitle</span>(<span class="st">"Humanoid"</span>)</span>
<span id="cb11-36"><a href="#cb11-36" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-37"><a href="#cb11-37" aria-hidden="true" tabindex="-1"></a>iplot_human <span class="ot"><-</span> summary_statistics <span class="sc">|></span> </span>
<span id="cb11-38"><a href="#cb11-38" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(agent <span class="sc">==</span> <span class="st">"Human"</span>) <span class="sc">|></span></span>
<span id="cb11-39"><a href="#cb11-39" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> motion_type, <span class="at">y =</span> mean, <span class="at">group =</span> outcome_type, </span>
<span id="cb11-40"><a href="#cb11-40" aria-hidden="true" tabindex="-1"></a> <span class="at">shape =</span> outcome_type, <span class="at">color =</span> outcome_type)) <span class="sc">+</span></span>
<span id="cb11-41"><a href="#cb11-41" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>(<span class="at">size =</span> <span class="dv">3</span>) <span class="sc">+</span></span>
<span id="cb11-42"><a href="#cb11-42" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">linetype =</span> outcome_type))<span class="sc">+</span></span>
<span id="cb11-43"><a href="#cb11-43" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">name =</span> <span class="st">"Motion Type"</span>)<span class="sc">+</span></span>
<span id="cb11-44"><a href="#cb11-44" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">limits=</span><span class="fu">c</span>(<span class="dv">0</span>, <span class="dv">500</span>)) <span class="sc">+</span></span>
<span id="cb11-45"><a href="#cb11-45" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_classic</span>() <span class="sc">+</span> <span class="fu">scale_colour_brewer</span>(<span class="at">palette =</span> <span class="st">"Set1"</span>, <span class="at">direction =</span> <span class="sc">-</span><span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb11-46"><a href="#cb11-46" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="fu">c</span>(<span class="fl">0.9</span>, <span class="fl">0.9</span>),</span>
<span id="cb11-47"><a href="#cb11-47" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.title =</span> <span class="fu">element_blank</span>(), </span>
<span id="cb11-48"><a href="#cb11-48" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">margin</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">1</span>, <span class="st">"cm"</span>), </span>
<span id="cb11-49"><a href="#cb11-49" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">face =</span> <span class="st">"bold"</span>, <span class="at">size =</span> <span class="dv">16</span>), </span>
<span id="cb11-50"><a href="#cb11-50" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_blank</span>(), </span>
<span id="cb11-51"><a href="#cb11-51" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">vjust =</span> <span class="sc">-</span><span class="dv">1</span>, <span class="at">size =</span> <span class="dv">14</span>), </span>
<span id="cb11-52"><a href="#cb11-52" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">size=</span><span class="dv">14</span>), </span>
<span id="cb11-53"><a href="#cb11-53" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">size =</span> <span class="dv">14</span>)) <span class="sc">+</span> </span>
<span id="cb11-54"><a href="#cb11-54" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggtitle</span>(<span class="st">"Human"</span>)</span>
<span id="cb11-55"><a href="#cb11-55" aria-hidden="true" tabindex="-1"></a>iplot_humanoid</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/interaction%20plots%20agent-1.png" class="img-fluid" width="672"></p>
</div>
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb12"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="co"># use ggplotify::as.grob to convert plots into grobs first</span></span>
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a>iplot_arm <span class="ot"><-</span> <span class="fu">as.grob</span>(iplot_arm)</span>
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a>iplot_humanoid <span class="ot"><-</span> <span class="fu">as.grob</span>(iplot_humanoid)</span>
<span id="cb12-4"><a href="#cb12-4" aria-hidden="true" tabindex="-1"></a>iplot_human <span class="ot"><-</span> <span class="fu">as.grob</span>(iplot_human)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>draw_label_theme <span class="ot"><-</span> <span class="cf">function</span>(label, <span class="at">theme =</span> <span class="cn">NULL</span>, <span class="at">element =</span> <span class="st">"text"</span>, ...) {</span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (<span class="fu">is.null</span>(theme)) {</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a> theme <span class="ot"><-</span> ggplot2<span class="sc">::</span><span class="fu">theme_get</span>()</span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (<span class="sc">!</span>element <span class="sc">%in%</span> <span class="fu">names</span>(theme)) {</span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(<span class="st">"Element must be a valid ggplot theme element name"</span>)</span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb13-8"><a href="#cb13-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb13-9"><a href="#cb13-9" aria-hidden="true" tabindex="-1"></a> elements <span class="ot"><-</span> ggplot2<span class="sc">::</span><span class="fu">calc_element</span>(element, theme)</span>
<span id="cb13-10"><a href="#cb13-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb13-11"><a href="#cb13-11" aria-hidden="true" tabindex="-1"></a> cowplot<span class="sc">::</span><span class="fu">draw_label</span>(label, </span>
<span id="cb13-12"><a href="#cb13-12" aria-hidden="true" tabindex="-1"></a> <span class="at">fontfamily =</span> elements<span class="sc">$</span>family,</span>
<span id="cb13-13"><a href="#cb13-13" aria-hidden="true" tabindex="-1"></a> <span class="at">fontface =</span> elements<span class="sc">$</span>face,</span>
<span id="cb13-14"><a href="#cb13-14" aria-hidden="true" tabindex="-1"></a> <span class="at">colour =</span> elements<span class="sc">$</span>color,</span>
<span id="cb13-15"><a href="#cb13-15" aria-hidden="true" tabindex="-1"></a> <span class="at">size =</span> elements<span class="sc">$</span>size,</span>
<span id="cb13-16"><a href="#cb13-16" aria-hidden="true" tabindex="-1"></a> ...</span>
<span id="cb13-17"><a href="#cb13-17" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb13-18"><a href="#cb13-18" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb13-19"><a href="#cb13-19" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb13-20"><a href="#cb13-20" aria-hidden="true" tabindex="-1"></a><span class="co"># set titles</span></span>
<span id="cb13-21"><a href="#cb13-21" aria-hidden="true" tabindex="-1"></a>iplot_agent_title <span class="ot"><-</span> <span class="fu">ggdraw</span>() <span class="sc">+</span></span>
<span id="cb13-22"><a href="#cb13-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">draw_label_theme</span>(<span class="st">"Interaction Plots by Agent"</span>, </span>
<span id="cb13-23"><a href="#cb13-23" aria-hidden="true" tabindex="-1"></a> <span class="at">element =</span> <span class="st">"plot.title"</span>,</span>
<span id="cb13-24"><a href="#cb13-24" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="fl">0.05</span>, <span class="at">hjust =</span> <span class="dv">0</span>, <span class="at">vjust =</span> <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb14"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="co"># arrange 3 interaction plots horizontally using cowplot::plot_grid</span></span>
<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a><span class="co"># remember to provide list() not vector </span></span>
<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a><span class="fu">plot_grid</span>(<span class="at">plotlist =</span> <span class="fu">list</span>(iplot_arm, iplot_humanoid, iplot_human), </span>
<span id="cb14-4"><a href="#cb14-4" aria-hidden="true" tabindex="-1"></a> <span class="at">align =</span> <span class="st">"h"</span>, <span class="at">nrow =</span> <span class="dv">1</span>, <span class="at">rel_widths =</span> <span class="fu">c</span>(<span class="fl">2.2</span>, <span class="dv">2</span>, <span class="fl">2.1</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="ReactionTimeAnalysis_files/figure-html/interaction%20plot%20grid%20by%20agents-1.png" class="img-fluid" width="1440"></p>
</div>
</div>
</section>
</section>
<section id="x2x2-anova" class="level2">
<h2 class="anchored" data-anchor-id="x2x2-anova">3x2x2 ANOVA</h2>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb15"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>mod_322 <span class="ot"><-</span> <span class="fu">aov_car</span>(<span class="at">formula =</span> mean_of_3_rounds<span class="sc">~</span> motion_type <span class="sc">*</span> outcome_type <span class="sc">*</span> agent <span class="sc">+</span> <span class="fu">Error</span>(participant<span class="sc">/</span>(motion_type <span class="sc">*</span> outcome_type <span class="sc">*</span> agent)),</span>
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a> <span class="at">dv =</span> <span class="st">"mean_of_3_rounds"</span>, </span>
<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a> <span class="at">es =</span> <span class="st">"pes"</span>, </span>
<span id="cb15-4"><a href="#cb15-4" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="dv">3</span>, </span>
<span id="cb15-5"><a href="#cb15-5" aria-hidden="true" tabindex="-1"></a> <span class="at">include_aov =</span> <span class="cn">TRUE</span>, </span>
<span id="cb15-6"><a href="#cb15-6" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> reactionTime)</span>
<span id="cb15-7"><a href="#cb15-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb15-8"><a href="#cb15-8" aria-hidden="true" tabindex="-1"></a><span class="fu">nice</span>(mod_322)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>Anova Table (Type 3 tests)
Response: mean_of_3_rounds
Effect df MSE F ges p.value
1 motion_type 1, 51 29443.17 234.63 *** .271 <.001
2 outcome_type 1, 51 19395.87 70.44 *** .068 <.001
3 agent 1.89, 96.57 23892.94 3.70 * .009 .031
4 motion_type:outcome_type 1, 51 22227.70 19.65 *** .023 <.001
5 motion_type:agent 1.94, 98.98 23181.09 84.80 *** .170 <.001
6 outcome_type:agent 1.86, 94.66 19772.50 4.67 * .009 .013
7 motion_type:outcome_type:agent 1.97, 100.55 17599.85 1.28 .002 .281
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Sphericity correction method: GG </code></pre>
</div>
</div>
</section>
<section id="anova-for-biological-action" class="level2">
<h2 class="anchored" data-anchor-id="anova-for-biological-action">ANOVA for biological action</h2>
<p><strong>3 x 1 repeated measures ANOVA</strong></p>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>subset_bio <span class="ot"><-</span> reactionTime <span class="sc">|></span> <span class="fu">filter</span>(motion_type <span class="sc">==</span><span class="st">"Biological"</span>)</span>
<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a>mod_bio <span class="ot"><-</span> <span class="fu">aov_car</span>(<span class="at">formula =</span> mean_of_3_rounds<span class="sc">~</span> outcome_type <span class="sc">*</span> agent <span class="sc">+</span> <span class="fu">Error</span>(participant<span class="sc">/</span>(outcome_type <span class="sc">*</span> agent)),</span>
<span id="cb17-4"><a href="#cb17-4" aria-hidden="true" tabindex="-1"></a> <span class="at">dv =</span> <span class="st">"mean_of_3_rounds"</span>, </span>
<span id="cb17-5"><a href="#cb17-5" aria-hidden="true" tabindex="-1"></a> <span class="at">es =</span> <span class="st">"pes"</span>, </span>
<span id="cb17-6"><a href="#cb17-6" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="dv">3</span>, </span>
<span id="cb17-7"><a href="#cb17-7" aria-hidden="true" tabindex="-1"></a> <span class="at">include_aov =</span> <span class="cn">TRUE</span>, </span>
<span id="cb17-8"><a href="#cb17-8" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> subset_bio)</span>
<span id="cb17-9"><a href="#cb17-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb17-10"><a href="#cb17-10" aria-hidden="true" tabindex="-1"></a><span class="fu">anova</span>(mod_bio)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>Anova Table (Type 3 tests)
Response: mean_of_3_rounds
num Df den Df MSE F ges Pr(>F)
outcome_type 1.0000 51.00 33065 50.6254 0.126902 3.580e-09 ***
agent 1.9180 97.82 26929 34.5154 0.134045 9.043e-12 ***
outcome_type:agent 1.8382 93.75 22858 0.6009 0.002188 0.5369
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre>
</div>
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb19"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Anova Table (Type 3 tests)</span></span>
<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a><span class="co"># </span></span>
<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a><span class="co"># Response: mean_of_3_rounds</span></span>
<span id="cb19-4"><a href="#cb19-4" aria-hidden="true" tabindex="-1"></a><span class="co"># num Df den Df MSE F ges Pr(>F) </span></span>
<span id="cb19-5"><a href="#cb19-5" aria-hidden="true" tabindex="-1"></a><span class="co"># outcome_type 1.0000 51.00 33065 50.6254 0.126902 3.580e-09 ***</span></span>
<span id="cb19-6"><a href="#cb19-6" aria-hidden="true" tabindex="-1"></a><span class="co"># agent 1.9180 97.82 26929 34.5154 0.134045 9.043e-12 ***</span></span>
<span id="cb19-7"><a href="#cb19-7" aria-hidden="true" tabindex="-1"></a><span class="co"># outcome_type:agent 1.8382 93.75 22858 0.6009 0.002188 0.5369 </span></span>
<span id="cb19-8"><a href="#cb19-8" aria-hidden="true" tabindex="-1"></a><span class="co"># ---</span></span>
<span id="cb19-9"><a href="#cb19-9" aria-hidden="true" tabindex="-1"></a><span class="co"># Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<section id="anova-for-nonbio-motion" class="level3">
<h3 class="anchored" data-anchor-id="anova-for-nonbio-motion">ANOVA for nonbio motion</h3>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a>subset_nonbio <span class="ot"><-</span> reactionTime <span class="sc">|></span> <span class="fu">filter</span>(motion_type <span class="sc">==</span><span class="st">"Nonbiological"</span>) </span>
<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a>mod_nonbio <span class="ot"><-</span> <span class="fu">aov_car</span>(<span class="at">formula =</span> mean_of_3_rounds<span class="sc">~</span> outcome_type <span class="sc">*</span> agent <span class="sc">+</span> <span class="fu">Error</span>(participant<span class="sc">/</span>(outcome_type <span class="sc">*</span> agent)),</span>
<span id="cb20-4"><a href="#cb20-4" aria-hidden="true" tabindex="-1"></a> <span class="at">dv =</span> <span class="st">"mean_of_3_rounds"</span>, </span>
<span id="cb20-5"><a href="#cb20-5" aria-hidden="true" tabindex="-1"></a> <span class="at">es =</span> <span class="st">"pes"</span>, </span>
<span id="cb20-6"><a href="#cb20-6" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="dv">3</span>, </span>
<span id="cb20-7"><a href="#cb20-7" aria-hidden="true" tabindex="-1"></a> <span class="at">include_aov =</span> <span class="cn">TRUE</span>, </span>
<span id="cb20-8"><a href="#cb20-8" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> subset_nonbio)</span>
<span id="cb20-9"><a href="#cb20-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb20-10"><a href="#cb20-10" aria-hidden="true" tabindex="-1"></a><span class="fu">anova</span>(mod_nonbio)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>Anova Table (Type 3 tests)
Response: mean_of_3_rounds
num Df den Df MSE F ges Pr(>F)
outcome_type 1.0000 51.000 8558.5 15.0734 0.017884 0.0002985 ***
agent 1.8346 93.565 21030.5 57.0182 0.236948 4.101e-16 ***
outcome_type:agent 1.9008 96.942 15456.7 6.4939 0.026225 0.0026538 **
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre>
</div>
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb22"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="fu">nice</span>(mod_nonbio)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>Anova Table (Type 3 tests)
Response: mean_of_3_rounds
Effect df MSE F ges p.value
1 outcome_type 1, 51 8558.53 15.07 *** .018 <.001
2 agent 1.83, 93.57 21030.51 57.02 *** .237 <.001
3 outcome_type:agent 1.90, 96.94 15456.72 6.49 ** .026 .003
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Sphericity correction method: GG </code></pre>
</div>
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb24"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Anova Table (Type 3 tests)</span></span>
<span id="cb24-2"><a href="#cb24-2" aria-hidden="true" tabindex="-1"></a><span class="co"># </span></span>
<span id="cb24-3"><a href="#cb24-3" aria-hidden="true" tabindex="-1"></a><span class="co"># Response: mean_of_3_rounds</span></span>
<span id="cb24-4"><a href="#cb24-4" aria-hidden="true" tabindex="-1"></a><span class="co"># num Df den Df MSE F ges Pr(>F) </span></span>
<span id="cb24-5"><a href="#cb24-5" aria-hidden="true" tabindex="-1"></a><span class="co"># outcome_type 1.0000 51.000 8558.5 15.0734 0.017884 0.0002985 ***</span></span>
<span id="cb24-6"><a href="#cb24-6" aria-hidden="true" tabindex="-1"></a><span class="co"># agent 1.8346 93.565 21030.5 57.0182 0.236948 4.101e-16 ***</span></span>
<span id="cb24-7"><a href="#cb24-7" aria-hidden="true" tabindex="-1"></a><span class="co"># outcome_type:agent 1.9008 96.942 15456.7 6.4939 0.026225 0.0026538 ** </span></span>
<span id="cb24-8"><a href="#cb24-8" aria-hidden="true" tabindex="-1"></a><span class="co"># ---</span></span>
<span id="cb24-9"><a href="#cb24-9" aria-hidden="true" tabindex="-1"></a><span class="co"># Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</section>
</section>
<section id="check-assumptions-for-anova" class="level2">
<h2 class="anchored" data-anchor-id="check-assumptions-for-anova">Check Assumptions for ANOVA</h2>
<section id="check-residuals-normal-distribution" class="level4">
<h4 class="anchored" data-anchor-id="check-residuals-normal-distribution">3. Check residuals normal distribution</h4>
<div class="cell">
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>plotting_reactionTime_bio <span class="ot"><-</span> plotting <span class="sc">|></span> </span>
<span id="cb25-2"><a href="#cb25-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(motion_type <span class="sc">==</span> <span class="st">"Biological"</span>)</span>
<span id="cb25-3"><a href="#cb25-3" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb25-4"><a href="#cb25-4" aria-hidden="true" tabindex="-1"></a>plotting_reactionTime_nonbio <span class="ot"><-</span> plotting <span class="sc">|></span> </span>
<span id="cb25-5"><a href="#cb25-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(motion_type <span class="sc">==</span> <span class="st">"Nonbiological"</span>)</span>
<span id="cb25-6"><a href="#cb25-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-7"><a href="#cb25-7" aria-hidden="true" tabindex="-1"></a><span class="co"># whole model</span></span>
<span id="cb25-8"><a href="#cb25-8" aria-hidden="true" tabindex="-1"></a>plot_model <span class="ot"><-</span> <span class="fu">aov_car</span>(<span class="at">formula =</span> mean_of_3_rounds<span class="sc">~</span> outcome_type <span class="sc">*</span> agent <span class="sc">+</span> <span class="fu">Error</span>(participant<span class="sc">/</span>(outcome_type <span class="sc">*</span> agent)),</span>
<span id="cb25-9"><a href="#cb25-9" aria-hidden="true" tabindex="-1"></a> <span class="at">dv =</span> <span class="st">"mean_of_3_rounds"</span>, </span>
<span id="cb25-10"><a href="#cb25-10" aria-hidden="true" tabindex="-1"></a> <span class="at">es =</span> <span class="st">"pes"</span>, </span>
<span id="cb25-11"><a href="#cb25-11" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="dv">3</span>, </span>
<span id="cb25-12"><a href="#cb25-12" aria-hidden="true" tabindex="-1"></a> <span class="at">include_aov =</span> <span class="cn">TRUE</span>, </span>
<span id="cb25-13"><a href="#cb25-13" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> plotting)</span>
<span id="cb25-14"><a href="#cb25-14" aria-hidden="true" tabindex="-1"></a><span class="co">#plotting</span></span>
<span id="cb25-15"><a href="#cb25-15" aria-hidden="true" tabindex="-1"></a><span class="co">#qqPlot(plot_model$lm$residuals)</span></span>
<span id="cb25-16"><a href="#cb25-16" aria-hidden="true" tabindex="-1"></a><span class="co">#check_normality(plot_model$lm$residuals)</span></span>
<span id="cb25-17"><a href="#cb25-17" aria-hidden="true" tabindex="-1"></a><span class="co">#plot(check_normality(plot_model), type = "qq")</span></span>
<span id="cb25-18"><a href="#cb25-18" aria-hidden="true" tabindex="-1"></a><span class="co">#shapiro.test(plot_model$lm$residuals)</span></span>
<span id="cb25-19"><a href="#cb25-19" aria-hidden="true" tabindex="-1"></a><span class="co"># Shapiro-Wilk normality test</span></span>
<span id="cb25-20"><a href="#cb25-20" aria-hidden="true" tabindex="-1"></a><span class="co"># </span></span>
<span id="cb25-21"><a href="#cb25-21" aria-hidden="true" tabindex="-1"></a><span class="co"># data: plot_model$lm$residuals</span></span>
<span id="cb25-22"><a href="#cb25-22" aria-hidden="true" tabindex="-1"></a><span class="co"># W = 0.98447, p-value = 0.1386</span></span>
<span id="cb25-23"><a href="#cb25-23" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-24"><a href="#cb25-24" aria-hidden="true" tabindex="-1"></a><span class="co"># bio only</span></span>
<span id="cb25-25"><a href="#cb25-25" aria-hidden="true" tabindex="-1"></a>model_bio <span class="ot"><-</span> <span class="fu">aov_car</span>(<span class="at">formula =</span> mean_of_3_rounds <span class="sc">~</span> outcome_type <span class="sc">*</span> agent <span class="sc">+</span> <span class="fu">Error</span>(participant<span class="sc">/</span>(outcome_type <span class="sc">*</span> agent)),</span>
<span id="cb25-26"><a href="#cb25-26" aria-hidden="true" tabindex="-1"></a> <span class="at">dv =</span> <span class="st">"mean_of_3_rounds"</span>, </span>
<span id="cb25-27"><a href="#cb25-27" aria-hidden="true" tabindex="-1"></a> <span class="at">es =</span> <span class="st">"pes"</span>, </span>
<span id="cb25-28"><a href="#cb25-28" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="dv">3</span>, </span>
<span id="cb25-29"><a href="#cb25-29" aria-hidden="true" tabindex="-1"></a> <span class="at">include_aov =</span> <span class="cn">TRUE</span>, </span>
<span id="cb25-30"><a href="#cb25-30" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> plotting)</span>
<span id="cb25-31"><a href="#cb25-31" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-32"><a href="#cb25-32" aria-hidden="true" tabindex="-1"></a><span class="co"># qqPlot(model_bio $lm$residuals)</span></span>
<span id="cb25-33"><a href="#cb25-33" aria-hidden="true" tabindex="-1"></a><span class="co"># check_normality(model_bio $lm$residuals)</span></span>
<span id="cb25-34"><a href="#cb25-34" aria-hidden="true" tabindex="-1"></a><span class="co"># check_sphericity(model_bio )</span></span>
<span id="cb25-35"><a href="#cb25-35" aria-hidden="true" tabindex="-1"></a><span class="co"># plot(check_normality(model_bio ), type = "qq")</span></span>
<span id="cb25-36"><a href="#cb25-36" aria-hidden="true" tabindex="-1"></a><span class="co"># shapiro.test(model_bio $lm$residuals)</span></span>
<span id="cb25-37"><a href="#cb25-37" aria-hidden="true" tabindex="-1"></a><span class="co"># Shapiro-Wilk normality test</span></span>
<span id="cb25-38"><a href="#cb25-38" aria-hidden="true" tabindex="-1"></a><span class="co"># </span></span>
<span id="cb25-39"><a href="#cb25-39" aria-hidden="true" tabindex="-1"></a><span class="co"># data: model_bio $lm$residuals</span></span>
<span id="cb25-40"><a href="#cb25-40" aria-hidden="true" tabindex="-1"></a><span class="co"># W = 0.99477, p-value = 0.6623</span></span>
<span id="cb25-41"><a href="#cb25-41" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb25-42"><a href="#cb25-42" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(model_bio)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>
Univariate Type III Repeated-Measures ANOVA Assuming Sphericity
Sum Sq num Df Error SS den Df F value Pr(>F)
(Intercept) 2448931 1 371279 6 39.5756 0.0007513 ***
outcome_type 150870 1 22748 6 39.7935 0.0007404 ***
agent 50584 2 74526 12 4.0725 0.0446777 *
outcome_type:agent 52289 2 226034 12 1.3880 0.2869107
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Mauchly Tests for Sphericity
Test statistic p-value
agent 0.29488 0.047218
outcome_type:agent 0.46774 0.149628
Greenhouse-Geisser and Huynh-Feldt Corrections
for Departure from Sphericity
GG eps Pr(>F[GG])
agent 0.58647 0.07977 .
outcome_type:agent 0.65263 0.28723
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
HF eps Pr(>F[HF])
agent 0.6433063 0.0736056
outcome_type:agent 0.7600888 0.2880767</code></pre>
</div>
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb27"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="co"># nonbio only</span></span>
<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a>plot_nonbio <span class="ot"><-</span> <span class="fu">aov_car</span>(<span class="at">formula =</span> mean_of_3_rounds <span class="sc">~</span> outcome_type <span class="sc">*</span> agent <span class="sc">+</span> <span class="fu">Error</span>(participant<span class="sc">/</span>(outcome_type <span class="sc">*</span> agent)),</span>
<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a> <span class="at">dv =</span> <span class="st">"mean_of_3_rounds"</span>, </span>
<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a> <span class="at">es =</span> <span class="st">"pes"</span>, </span>
<span id="cb27-5"><a href="#cb27-5" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="dv">3</span>, </span>
<span id="cb27-6"><a href="#cb27-6" aria-hidden="true" tabindex="-1"></a> <span class="at">include_aov =</span> <span class="cn">TRUE</span>, </span>
<span id="cb27-7"><a href="#cb27-7" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> plotting)</span>
<span id="cb27-8"><a href="#cb27-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb27-9"><a href="#cb27-9" aria-hidden="true" tabindex="-1"></a><span class="co">#qqPlot(plot_nonbio$lm$residuals)</span></span>
<span id="cb27-10"><a href="#cb27-10" aria-hidden="true" tabindex="-1"></a><span class="co">#check_normality(plot_nonbio$lm$residuals)</span></span>
<span id="cb27-11"><a href="#cb27-11" aria-hidden="true" tabindex="-1"></a><span class="fu">check_sphericity</span>(plot_nonbio)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>Warning: Sphericity violated for:
- agent (p = 0.047).</code></pre>
</div>
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb29"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="co">#plot(check_normality(plot_nonbio), type = "qq")</span></span>
<span id="cb29-2"><a href="#cb29-2" aria-hidden="true" tabindex="-1"></a><span class="fu">shapiro.test</span>(plot_nonbio<span class="sc">$</span>lm<span class="sc">$</span>residuals)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>
Shapiro-Wilk normality test
data: plot_nonbio$lm$residuals
W = 0.97524, p-value = 0.4864</code></pre>
</div>
<details open="">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb31"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Shapiro-Wilk normality test</span></span>
<span id="cb31-2"><a href="#cb31-2" aria-hidden="true" tabindex="-1"></a><span class="co"># </span></span>
<span id="cb31-3"><a href="#cb31-3" aria-hidden="true" tabindex="-1"></a><span class="co"># data: plot_nonbio$lm$residuals</span></span>
<span id="cb31-4"><a href="#cb31-4" aria-hidden="true" tabindex="-1"></a><span class="co"># W = 0.9776, p-value = 0.01838</span></span>
<span id="cb31-5"><a href="#cb31-5" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(plot_nonbio)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>
Univariate Type III Repeated-Measures ANOVA Assuming Sphericity
Sum Sq num Df Error SS den Df F value Pr(>F)
(Intercept) 2448931 1 371279 6 39.5756 0.0007513 ***
outcome_type 150870 1 22748 6 39.7935 0.0007404 ***
agent 50584 2 74526 12 4.0725 0.0446777 *
outcome_type:agent 52289 2 226034 12 1.3880 0.2869107