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<h1 class="title">Facets and a Lesson in Humility</h1>
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<p class="subtitle lead"></p><p>A look at Tableau for Healthcare Chapter 8. Table Lens graph.</p><p></p>
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<p><a href="https://kyleb.rbind.io/">Kyle Belanger</a> </p>
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<p class="date">January 29, 2020</p>
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<li><a href="#load-libraries" id="toc-load-libraries" class="nav-link active" data-scroll-target="#load-libraries">Load Libraries</a></li>
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<li><a href="#import-data" id="toc-import-data" class="nav-link" data-scroll-target="#import-data">Import Data</a></li>
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<li><a href="#clean-names-and-transform" id="toc-clean-names-and-transform" class="nav-link" data-scroll-target="#clean-names-and-transform">Clean Names and Transform</a></li>
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<p>Todays post is a lesson in Facets, as well as humility. The task this week was to replicate the graph in Chapter 8 of Tableau for Healthcare in R. The graph in question is called a Table Lens (This is the name the book uses, however I did have trouble finding this name in Google searches), it is a collection of charts with a common theme, this time looking at countries in various WHO regions and some statistics associated with mortality as well as health expenditure. I say this is a lesson in humiltiy as I have read through the excellent book <a href="https://r4ds.had.co.nz/">R for Data Science</a>, and yet the idea of faceting a ggplot graph slipped my mind. This ended with hours of trying to find a package in R to line up graphs, and way more time then I care to admit spent on getting things prefect. I did find such a package called cowplots, which can be found <a href="https://wilkelab.org/cowplot/index.html">here</a>. While this is an excellent package, its use was unecessary and I reverted back to using the excellent facet feature of GGplot, which can be seen below! <img src="WHO_LIFE.png" class="img-fluid"></p>
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<section id="load-libraries" class="level1">
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<h1>Load Libraries</h1>
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<div class="cell">
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<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>(magrittr) <span class="co">#pipes</span></span>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2) <span class="co">#ploting </span></span>
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<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
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<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyr)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</section>
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<section id="import-data" class="level1">
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<h1>Import Data</h1>
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<div class="cell">
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<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>ds <span class="ot"><-</span> readxl<span class="sc">::</span><span class="fu">read_xlsx</span>(<span class="at">path =</span> <span class="st">"../2020-01-04_my-start-to-r/Tableau 10 Training Practice Data.xlsx"</span></span>
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<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> ,<span class="at">sheet =</span> <span class="st">"03 - WHO Life Expect & Mort"</span></span>
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<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</section>
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<section id="clean-names-and-transform" class="level1">
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<h1>Clean Names and Transform</h1>
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<div class="cell">
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<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>varnames <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"who_region"</span>, <span class="st">"country"</span>, <span class="st">"year"</span> , <span class="st">"sex"</span> , <span class="st">"life_expect_birth"</span> , <span class="st">"neo_mort"</span></span>
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<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> ,<span class="st">"under_five_mort"</span> , <span class="st">"health_expenditure"</span>)</span>
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<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(ds) <span class="ot"><-</span> varnames</span>
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<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a><span class="co"># Order Countries based on Life Expectancy at Birth</span></span>
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<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a>ds<span class="sc">$</span>country <span class="ot"><-</span> <span class="fu">factor</span>(ds<span class="sc">$</span>country, <span class="at">levels =</span> ds<span class="sc">$</span>country[<span class="fu">order</span>(ds<span class="sc">$</span>life_expect_birth)]) </span>
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<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a><span class="co">#To "Long" Form</span></span>
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<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a>ds1 <span class="ot"><-</span> ds <span class="sc">%>%</span> <span class="fu">pivot_longer</span>(<span class="dv">5</span><span class="sc">:</span><span class="dv">8</span>)<span class="co">#select columns 5 throuh 8, leave new columns at default names</span></span>
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<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a><span class="co"># Set up labels for Facet, as well as function for Facet Labeller</span></span>
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<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a>facet_labels <span class="ot"><-</span> <span class="fu">list</span>(</span>
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<span id="cb3-16"><a href="#cb3-16" aria-hidden="true" tabindex="-1"></a><span class="st">"life_expect_birth"</span> <span class="ot">=</span> <span class="st">"Life Expectancy at Birth "</span> </span>
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<span id="cb3-17"><a href="#cb3-17" aria-hidden="true" tabindex="-1"></a>,<span class="st">"neo_mort"</span> <span class="ot">=</span> <span class="st">"Neonatal Mortality Rate"</span> </span>
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<span id="cb3-18"><a href="#cb3-18" aria-hidden="true" tabindex="-1"></a>,<span class="st">"under_five_mort"</span> <span class="ot">=</span> <span class="st">"Under-Five Mortality Rate"</span></span>
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<span id="cb3-19"><a href="#cb3-19" aria-hidden="true" tabindex="-1"></a>,<span class="st">"health_expenditure"</span> <span class="ot">=</span> <span class="st">"Health Expenditure per Capita (US$)"</span> )</span>
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<span id="cb3-20"><a href="#cb3-20" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-21"><a href="#cb3-21" aria-hidden="true" tabindex="-1"></a>variable_labeller <span class="ot"><-</span> <span class="cf">function</span>(variable,value){</span>
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<span id="cb3-22"><a href="#cb3-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">return</span>(facet_labels[value])</span>
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<span id="cb3-23"><a href="#cb3-23" aria-hidden="true" tabindex="-1"></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</section>
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<section id="graphs" class="level1">
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<h1>Graphs</h1>
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<div class="cell">
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<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>hightlight_countries <span class="ot"><-</span> (<span class="fu">c</span>(<span class="st">"Mauritania"</span>, <span class="st">"South Africa"</span>)) </span>
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<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>g1 <span class="ot"><-</span> ds1 <span class="sc">%>%</span> <span class="fu">filter</span>(who_region <span class="sc">==</span> <span class="st">"Africa"</span>) <span class="sc">%>%</span> </span>
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<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">name =</span> <span class="fu">factor</span>(name, <span class="at">levels =</span> <span class="fu">c</span>(<span class="st">"life_expect_birth"</span> , <span class="st">"neo_mort"</span></span>
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<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> ,<span class="st">"under_five_mort"</span> , <span class="st">"health_expenditure"</span>))</span>
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<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a> ,<span class="at">highlight =</span> country <span class="sc">%in%</span> hightlight_countries) <span class="sc">%>%</span> </span>
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<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> country, <span class="at">y =</span> value, <span class="at">fill =</span> highlight)) <span class="sc">+</span></span>
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<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_col</span>(<span class="at">show.legend =</span> <span class="cn">FALSE</span>) <span class="sc">+</span></span>
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<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span></span>
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<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(</span>
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<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"World Bank Life Expectancy, Neonatal & Under-Five Mortality Rates, and Health Expenditure Analysis"</span></span>
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<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a> ,<span class="at">x =</span> <span class="cn">NULL</span></span>
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<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a> ,<span class="at">y =</span> <span class="cn">NULL</span></span>
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<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
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<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">facet_grid</span>(<span class="sc">~</span>name, <span class="at">scales =</span> <span class="st">"free_x"</span>,<span class="at">labeller =</span> variable_labeller) <span class="sc">+</span></span>
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<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
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<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_text</span>(<span class="fu">aes</span>(<span class="at">label =</span> <span class="fu">round</span>(value, <span class="dv">0</span>)), <span class="at">hjust =</span> <span class="dv">0</span>) <span class="sc">+</span></span>
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<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">expand =</span> <span class="fu">expand_scale</span>(<span class="at">mult =</span> <span class="fu">c</span>(<span class="dv">0</span>,<span class="fl">0.2</span>))) <span class="sc">+</span></span>
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<span id="cb4-19"><a href="#cb4-19" 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">"TRUE"</span> <span class="ot">=</span> <span class="st">"#fc8d59"</span>, <span class="st">"FALSE"</span> <span class="ot">=</span> <span class="st">"#2b83ba"</span>))</span>
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<span id="cb4-20"><a href="#cb4-20" aria-hidden="true" tabindex="-1"></a>g1</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output-display">
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<div>
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<figure class="figure">
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<p><img src="facets-and-a-lesson-in-humility_files/figure-html/unnamed-chunk-4-1.png" class="img-fluid figure-img" width="1152"></p>
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</figure>
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</div>
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</div>
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</div>
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</section>
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<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" id="quarto-reuse"><h2 class="anchored quarto-appendix-heading">Reuse</h2><div class="quarto-appendix-contents"><div><a rel="license" href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a></div></div></section><section class="quarto-appendix-contents" id="quarto-citation"><h2 class="anchored quarto-appendix-heading">Citation</h2><div><div class="quarto-appendix-secondary-label">BibTeX citation:</div><pre class="sourceCode code-with-copy quarto-appendix-bibtex"><code class="sourceCode bibtex">@online{belanger2020,
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author = {Belanger, Kyle},
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title = {Facets and a {Lesson} in {Humility}},
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date = {2020-01-29},
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langid = {en}
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}
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</code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre><div class="quarto-appendix-secondary-label">For attribution, please cite this work as:</div><div id="ref-belanger2020" class="csl-entry quarto-appendix-citeas" role="listitem">
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Belanger, Kyle. 2020. <span>“Facets and a Lesson in Humility.”</span>
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January 29, 2020.
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