and build

docs/association.html

@@ -1266,7 +1266,7 @@ <h1 class="title">
 </div>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-correlation-pears-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-Figure&nbsp;16.3: <strong>Correlation between compactness and kernel width of wheat seeds</strong>. High quality images of the internal structure of wheat seeds were taken with a soft X-ray technique and the compactness and kernel width of the seeds were determined. There was a significant positive correlation (<span class="math inline">\(r\)</span> = 0.67) between compactness and kernel width (Pearson’s: <em>t</em> = 7.374; <em>df</em> = 68; <em>p</em>-value &lt; 0.0001). Note: axes do not start at 0. Data analysis was conducted in R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2023</a>)</span> with tidyverse packages <span class="citation" data-cites="tidyverse">(<a href="references.html#ref-tidyverse" role="doc-biblioref">Wickham et al. 2019</a>)</span>.
+Figure&nbsp;16.3: <strong>Correlation between compactness and kernel width of wheat seeds</strong>. High quality images of the internal structure of wheat seeds were taken with a soft X-ray technique and the compactness and kernel width of the seeds were determined. There was a significant positive correlation (<span class="math inline">\(r\)</span> = 0.67) between compactness and kernel width (Pearson’s: <em>t</em> = 7.374; <em>df</em> = 68; <em>p</em>-value &lt; 0.0001). Note: axes do not start at 0. Data analysis was conducted in R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2024</a>)</span> with tidyverse packages <span class="citation" data-cites="tidyverse">(<a href="references.html#ref-tidyverse" role="doc-biblioref">Wickham et al. 2019</a>)</span>.
 </figcaption></figure>
 </div>
 </section><section id="spearmans-rank-correlation-coefficient" class="level3" data-number="16.3.5"><h3 data-number="16.3.5" class="anchored" data-anchor-id="spearmans-rank-correlation-coefficient">
@@ -1385,7 +1385,7 @@ <h1 class="title">
 
 <div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list" style="display: none">
 <div id="ref-R-core" class="csl-entry" role="listitem">
-R Core Team. 2023. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
+R Core Team. 2024. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
 </div>
 <div id="ref-tidyverse" class="csl-entry" role="listitem">
 Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. <span>“Welcome to the <span></span>Tidyverse<span></span>”</span> 4: 1686. <a href="https://doi.org/10.21105/joss.01686">https://doi.org/10.21105/joss.01686</a>.

docs/confidence_intervals.html

@@ -549,7 +549,7 @@ <h1 class="title">
 </section><section id="large-samples" class="level2" data-number="10.6"><h2 data-number="10.6" class="anchored" data-anchor-id="large-samples">
 <span class="header-section-number">10.6</span> Large samples</h2>
 <p>A team of biomedical researchers is studying the concentration of Creatine Kinase (CK) in the blood of patients with muscle disorders. They collect a large random sample (n = 100) of blood samples from patients and measure the CK concentration in UL<sup>-1</sup> (units per litre).</p>
-<p>The goal is to estimate the average CK concentration in this patient population and calculate a 95% confidence interval for the mean concentration.</p>
+<p>The goal is to estimate the average CK concentration in this patient population and calculate a 95% confidence interval for the mean concentration. The data are in <a href="data-raw/ck_concen.csv">ck_concen.csv</a></p>
 <section id="import" class="level3" data-number="10.6.1"><h3 data-number="10.6.1" class="anchored" data-anchor-id="import">
 <span class="header-section-number">10.6.1</span> Import</h3>
 <div class="cell">
@@ -584,7 +584,7 @@ <h1 class="title">
 <span><span class="va">ucl</span> <span class="op">&lt;-</span> <span class="va">m</span> <span class="op">+</span> <span class="va">q</span> <span class="op">*</span> <span class="va">se</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>I used the names <code>lcl</code> and <code>ucl</code> to stand for “lower confidence limit” and “upper confidence limit” respectively.</p>
-<p><img src="images/do_in_R.png" class="img-fluid"> Print the values:</p>
+<p>Print the values:</p>
 <div class="cell">
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">lcl</span></span>
 <span><span class="co">## [1] 284.3891</span></span>

docs/data-raw/ck_concen.csv

@@ -0,0 +1,101 @@
+ck_conc
+213.15
+379.79
+322.64
+179.5
+253.71
+432.11
+105.87
+265.69
+401.27
+230.66
+245.69
+292.42
+419.31
+248.89
+264.48
+265.25
+476.47
+474.94
+380.32
+330.89
+358.99
+419.26
+225.13
+394.07
+199.69
+248.98
+372.57
+185.71
+288.79
+231.06
+279.55
+76.11
+158.28
+244.01
+374.2
+286.11
+300.23
+355.06
+229.64
+322.69
+235.57
+161.79
+268.73
+345.9
+327.09
+299.05
+491.39
+333.03
+378.3
+479.05
+196.47
+216.9
+439.5
+236.15
+302.37
+385.55
+371.26
+440.39
+419.65
+385.55
+238.18
+363.59
+325.14
+193.9
+413.38
+364.58
+303.64
+281.35
+204.14
+315.96
+337.48
+233.51
+392.98
+212.22
+130.15
+383.18
+267.73
+289.92
+233.0
+171.52
+400.42
+244.89
+432.88
+364.58
+274.82
+213.13
+241.4
+203.0
+466.97
+313.16
+392.02
+198.61
+314.48
+394.23
+273.2
+382.49
+213.23
+190.92
+330.35
+269.67

docs/index.html

@@ -314,7 +314,7 @@ <h1 class="title">Computational Analysis for Bioscientists</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">3 February, 2025</p>
+      <p class="date">10 February, 2025</p>
     </div>
   </div>
 

docs/intro.html

@@ -464,7 +464,7 @@ <h1 class="title">
 <p>Rand, E. (2023). Computational Analysis for Bioscientists (Version 0.1) https://3mmarand.github.io/comp4biosci/</p>
 </section><section id="credits" class="level2" data-number="1.10"><h2 data-number="1.10" class="anchored" data-anchor-id="credits">
 <span class="header-section-number">1.10</span> Credits</h2>
-<p>This book is written with R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2023</a>)</span>, Quarto <span class="citation" data-cites="allaire2022">(<a href="references.html#ref-allaire2022" role="doc-biblioref">Allaire et al. 2022</a>)</span>, <strong><code>knitr</code></strong> <span class="citation" data-cites="knitr">(<a href="references.html#ref-knitr" role="doc-biblioref">Xie 2022</a>)</span>, <strong><code>kableExtra</code></strong> <span class="citation" data-cites="kableExtra">(<a href="references.html#ref-kableExtra" role="doc-biblioref">Zhu 2021</a>)</span>. My R session information is shown below:</p>
+<p>This book is written with R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2024</a>)</span>, Quarto <span class="citation" data-cites="allaire2022">(<a href="references.html#ref-allaire2022" role="doc-biblioref">Allaire et al. 2022</a>)</span>, <strong><code>knitr</code></strong> <span class="citation" data-cites="knitr">(<a href="references.html#ref-knitr" role="doc-biblioref">Xie 2022</a>)</span>, <strong><code>kableExtra</code></strong> <span class="citation" data-cites="kableExtra">(<a href="references.html#ref-kableExtra" role="doc-biblioref">Zhu 2021</a>)</span>. My R session information is shown below:</p>
 <div class="cell">
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">## R version 4.4.2 (2024-10-31 ucrt)</span></span>
@@ -510,7 +510,7 @@ <h1 class="title">
 Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2022. <em>Quarto</em>. <a href="https://doi.org/10.5281/zenodo.5960048">https://doi.org/10.5281/zenodo.5960048</a>.
 </div>
 <div id="ref-R-core" class="csl-entry" role="listitem">
-R Core Team. 2023. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
+R Core Team. 2024. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
 </div>
 <div id="ref-ggplot2" class="csl-entry" role="listitem">
 Wickham, Hadley. 2016. <em>Ggplot2: Elegant Graphics for Data Analysis</em>. Springer-Verlag New York. <a href="https://ggplot2.tidyverse.org">https://ggplot2.tidyverse.org</a>.

docs/one_way_anova_and_kw.html

@@ -828,7 +828,7 @@ <h1 class="title">
 </div>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-culture-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-Figure&nbsp;14.5: <strong>Medium affects bacterial colony diameter</strong>. Ten replicate colonies were grown on three types of media: control, with sugar added and with both sugar and amino acids added. Error bars are means <span class="math inline">\(\pm\)</span> 1 standard error. There was a significant effect of media on the diameter of bacterial colonies (<em>F</em> = 6.11; <em>d.f.</em> = 2, 27; <em>p</em> = 0.006). Post-hoc testing with Tukey’s Honestly Significant Difference test <span class="citation" data-cites="tukey1949">(<a href="references.html#ref-tukey1949" role="doc-biblioref">Tukey 1949</a>)</span> revealed the colony diameters were significantly larger when grown with both sugar and amino acids than with neither or just sugar. Data analysis was conducted in R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2023</a>)</span> with tidyverse packages <span class="citation" data-cites="tidyverse">(<a href="references.html#ref-tidyverse" role="doc-biblioref">Wickham et al. 2019</a>)</span>.
+Figure&nbsp;14.5: <strong>Medium affects bacterial colony diameter</strong>. Ten replicate colonies were grown on three types of media: control, with sugar added and with both sugar and amino acids added. Error bars are means <span class="math inline">\(\pm\)</span> 1 standard error. There was a significant effect of media on the diameter of bacterial colonies (<em>F</em> = 6.11; <em>d.f.</em> = 2, 27; <em>p</em> = 0.006). Post-hoc testing with Tukey’s Honestly Significant Difference test <span class="citation" data-cites="tukey1949">(<a href="references.html#ref-tukey1949" role="doc-biblioref">Tukey 1949</a>)</span> revealed the colony diameters were significantly larger when grown with both sugar and amino acids than with neither or just sugar. Data analysis was conducted in R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2024</a>)</span> with tidyverse packages <span class="citation" data-cites="tidyverse">(<a href="references.html#ref-tidyverse" role="doc-biblioref">Wickham et al. 2019</a>)</span>.
 </figcaption></figure>
 </div>
 </section></section><section id="kruskal-wallis" class="level1" data-number="15"><h1 data-number="15">
@@ -922,7 +922,7 @@ <h1 class="title">
 </div>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-culture-kw-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-Figure&nbsp;15.1: <strong>Medium affects bacterial colony diameter</strong>. Ten replicate colonies were grown on three types of media: control, with sugar added and with both sugar and amino acids added. The heavy lines indicate median diameter, boxes indicate the interquartile range and whiskers the range. There was a significant effect of media on the diameter of bacterial colonies (Kruskal-Wallis: <em>chi-squared</em> = 6.34, <em>df</em> = 2, <em>p</em>-value = 0.042). Post-hoc testing with the Dunn test <span class="citation" data-cites="dunn1964">(<a href="references.html#ref-dunn1964" role="doc-biblioref">Dunn 1964</a>)</span> revealed the colony diameters were significantly larger when grown with both sugar and amino acids than with neither or just sugar. Data analysis was conducted in R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2023</a>)</span> with tidyverse packages <span class="citation" data-cites="tidyverse">(<a href="references.html#ref-tidyverse" role="doc-biblioref">Wickham et al. 2019</a>)</span>.
+Figure&nbsp;15.1: <strong>Medium affects bacterial colony diameter</strong>. Ten replicate colonies were grown on three types of media: control, with sugar added and with both sugar and amino acids added. The heavy lines indicate median diameter, boxes indicate the interquartile range and whiskers the range. There was a significant effect of media on the diameter of bacterial colonies (Kruskal-Wallis: <em>chi-squared</em> = 6.34, <em>df</em> = 2, <em>p</em>-value = 0.042). Post-hoc testing with the Dunn test <span class="citation" data-cites="dunn1964">(<a href="references.html#ref-dunn1964" role="doc-biblioref">Dunn 1964</a>)</span> revealed the colony diameters were significantly larger when grown with both sugar and amino acids than with neither or just sugar. Data analysis was conducted in R <span class="citation" data-cites="R-core">(<a href="references.html#ref-R-core" role="doc-biblioref">R Core Team 2024</a>)</span> with tidyverse packages <span class="citation" data-cites="tidyverse">(<a href="references.html#ref-tidyverse" role="doc-biblioref">Wickham et al. 2019</a>)</span>.
 </figcaption></figure>
 </div>
 </section></section><section id="summary" class="level1" data-number="16"><h1 data-number="16">
@@ -954,7 +954,7 @@ <h1 class="title">
 Ogle, Derek H., Jason C. Doll, A. Powell Wheeler, and Alexis Dinno. 2023. <span>“FSA: Simple Fisheries Stock Assessment Methods.”</span> <a href="https://CRAN.R-project.org/package=FSA">https://CRAN.R-project.org/package=FSA</a>.
 </div>
 <div id="ref-R-core" class="csl-entry" role="listitem">
-R Core Team. 2023. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
+R Core Team. 2024. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
 </div>
 <div id="ref-tukey1949" class="csl-entry" role="listitem">
 Tukey, John W. 1949. <span>“Comparing Individual Means in the Analysis of Variance.”</span> <em>Biometrics</em> 5 (2): 99–114. <a href="https://doi.org/10.2307/3001913">https://doi.org/10.2307/3001913</a>.

docs/references.html

@@ -367,7 +367,7 @@ <h1 class="title">References</h1>
 2023. <span>“FSA: Simple Fisheries Stock Assessment Methods.”</span> <a href="https://CRAN.R-project.org/package=FSA">https://CRAN.R-project.org/package=FSA</a>.
 </div>
 <div id="ref-R-core" class="csl-entry" role="listitem">
-R Core Team. 2023. <em>R: A Language and Environment for Statistical
+R Core Team. 2024. <em>R: A Language and Environment for Statistical
 Computing</em>. Vienna, Austria: R Foundation for Statistical Computing.
 <a href="https://www.R-project.org/">https://www.R-project.org/</a>.
 </div>