re-build HTML

_quarto.yml

@@ -171,8 +171,6 @@ format:
 
   # see: https://github.com/bgreenwell/quarto-crc for quarto and CRC press
   #      https://github.com/yihui/bookdown-crc        bookdown, CRC Press
-  pdf-engine-opt: 
-    interaction: nonstopmode
   pdf:
     documentclass: krantz
     classoption: [10pt, krantz2]
@@ -184,7 +182,8 @@ format:
     geometry:
       - top=20mm
       - left=25mm
-    code-block-bg: 'E8FFFF'  #'#f1f1f1'
+    code-block-bg: "dce8e7" # or #e6f2ee, not 'E8FFFF'  #'#f1f1f1'
+    interaction: nonstopmode
 
 
 

bib/pkgs.bib

@@ -186,6 +186,14 @@ @Manual{R-GGally
   url = {https://ggobi.github.io/ggally/},
 }
 
+@Manual{R-gganimate,
+  title = {gganimate: A Grammar of Animated Graphics},
+  author = {Thomas Lin Pedersen and David Robinson},
+  year = {2024},
+  note = {R package version 1.0.9},
+  url = {https://gganimate.com},
+}
+
 @Manual{R-ggbiplot,
   title = {ggbiplot: A Grammar of Graphics Implementation of Biplots},
   author = {Vincent Q. Vu and Michael Friendly},
@@ -301,7 +309,7 @@ @Manual{R-langevitour
 }
 
 @Manual{R-lattice,
-  title = {lattice: Trellis Graphics for {R}},
+  title = {lattice: Trellis Graphics for R},
   author = {Deepayan Sarkar},
   year = {2024},
   note = {R package version 0.22-6},

bib/pkgs.txt

@@ -76,6 +76,7 @@ car
 carData
 dplyr
 forcats
+gganimate
 ggplot2
 knitr
 matlib

docs/03-multivariate_plots.html

@@ -1863,7 +1863,7 @@ <h1 class="title"><span id="sec-multivariate_plots" class="quarto-section-identi
 <span><span class="fu"><a href="https://rdrr.io/r/graphics/lines.html">lines</a></span><span class="op">(</span><span class="va">axes.x</span>, <span class="va">axes.y</span>, col <span class="op">=</span> <span class="st">"grey"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="http://friendly.github.io/matlib/reference/vectors.html">vectors</a></span><span class="op">(</span><span class="va">P2</span>, labels <span class="op">=</span> <span class="va">labs</span>, cex.lab <span class="op">=</span> <span class="fl">1.8</span>, lwd <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html">par</a></span><span class="op">(</span><span class="va">op</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</details><div class="cell quarto-layout-panel" data-layout-align="center" data-layout-ncol="2">
+</details><div class="cell quarto-layout-panel" data-layout-ncol="2" data-layout-align="center">
 
 </div>
 <div class="cell" data-layout-align="center">
@@ -2344,7 +2344,7 @@ <h1 class="title"><span id="sec-multivariate_plots" class="quarto-section-identi
 Pineo, P. O., &amp; Porter, J. (2008). Occupational prestige in canada. <em>Canadian Review of Sociology</em>, <em>4</em>(1), 24–40. <a href="https://doi.org/10.1111/j.1755-618x.1967.tb00472.x">https://doi.org/10.1111/j.1755-618x.1967.tb00472.x</a>
 </div>
 <div id="ref-R-lattice" class="csl-entry" role="listitem">
-Sarkar, D. (2024). <em>Lattice: Trellis graphics for r</em>. <a href="https://lattice.r-forge.r-project.org/">https://lattice.r-forge.r-project.org/</a>
+Sarkar, D. (2024). <em>Lattice: Trellis graphics for <span>R</span></em>. <a href="https://lattice.r-forge.r-project.org/">https://lattice.r-forge.r-project.org/</a>
 </div>
 <div id="ref-R-GGally" class="csl-entry" role="listitem">
 Schloerke, B., Cook, D., Larmarange, J., Briatte, F., Marbach, M., Thoen, E., Elberg, A., &amp; Crowley, J. (2024). <em>GGally: Extension to ggplot2</em>. <a href="https://ggobi.github.io/ggally/">https://ggobi.github.io/ggally/</a>

docs/06-linear_models-plots.html

@@ -1704,8 +1704,6 @@ <h1 class="title"><span id="sec-linear-models-plots" class="quarto-section-ident
 
 
 
-
-
 ::: {.cell layout-align="center"}
 
 ```{.r .cell-code}
@@ -1727,8 +1725,6 @@ <h1 class="title"><span id="sec-linear-models-plots" class="quarto-section-ident
 
 
 
-
-
 -->
 <p>Because of the interaction with <code>type</code>, the fitted effects for <code>income</code> are calculated for the three types of occupation. It is easiest to compare these in the a single plot (using <code>multiline = TRUE</code>), rather than in separate panels as in <a href="#fig-prestige-allEffects" class="quarto-xref">Figure&nbsp;<span>6.17</span></a>. Income is represented as <code>log10(income)</code> in the model <code>prestige.mod3</code>, and it is also easier to understand the interaction by plotting income on a log scale, using the <code>axes</code> argument to specify a transformation of the <span class="math inline">\(x\)</span> axis. I use 68% confidence bands here to make the differences among type more apparent.</p>
 <div class="cell" data-layout-align="center">

docs/07-lin-mod-topics.html

@@ -353,7 +353,7 @@ <h1 class="title">
 
   <ul>
 <li>
-<a href="#sec:betaspace" id="toc-sec:betaspace" class="nav-link active" data-scroll-target="#sec\:betaspace"><span class="header-section-number">7.1</span> Ellipsoids in data space and <span class="math inline">\(\mathbf{\beta}\)</span> space</a>
+<a href="#sec-betaspace" id="toc-sec-betaspace" class="nav-link active" data-scroll-target="#sec-betaspace"><span class="header-section-number">7.1</span> Ellipsoids in data space and <span class="math inline">\(\mathbf{\beta}\)</span> space</a>
   <ul class="collapse">
 <li><a href="#coffee-stress-and-heart-disease" id="toc-coffee-stress-and-heart-disease" class="nav-link" data-scroll-target="#coffee-stress-and-heart-disease"><span class="header-section-number">7.1.1</span> Coffee, stress and heart disease</a></li>
   </ul>
@@ -379,9 +379,10 @@ <h1 class="title">
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://patchwork.data-imaginist.com">patchwork</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://r-forge.r-project.org/projects/car/">car</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/friendly/matlib">matlib</a></span><span class="op">)</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/">forcats</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://forcats.tidyverse.org/">forcats</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://gganimate.com">gganimate</a></span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
-<section id="sec:betaspace" class="level2" data-number="7.1"><h2 data-number="7.1" class="anchored" data-anchor-id="sec:betaspace">
+<section id="sec-betaspace" class="level2" data-number="7.1"><h2 data-number="7.1" class="anchored" data-anchor-id="sec-betaspace">
 <span class="header-section-number">7.1</span> Ellipsoids in data space and <span class="math inline">\(\mathbf{\beta}\)</span> space</h2>
 <p>It is most common to look at data and fitted models in “data space,” where axes correspond to variables, points represent observations, and fitted models are plotted as lines (or planes) in this space. As we’ve suggested, data ellipsoids provide informative summaries of relationships in data space. For linear models, particularly regression models with quantitative predictors, there is another space—“<span class="math inline">\(\mathbf{\beta}\)</span> space”—that provides deeper views of models and the relationships among them. This discussion extends <span class="citation" data-cites="Friendly-etal:ellipses:2013">Friendly et al. (<a href="95-references.html#ref-Friendly-etal:ellipses:2013" role="doc-biblioref">2013</a>)</span>, Sec. 4.6.</p>
 <p>In <span class="math inline">\(\mathbf{\beta}\)</span> space, the axes pertain to coefficients, for example <span class="math inline">\((\beta_0, \beta_1)\)</span> in a simple linear regression. Points in this space are models (true, hypothesized, fitted) whose coordinates represent values of these parameters. For example, one point <span class="math inline">\(\widehat{\mathbf{\beta}}_{\text{OLS}} = (\hat{\beta}_0, \hat{\beta}_1)\)</span> represents the least squares estimate; other points, <span class="math inline">\(\widehat{\mathbf{\beta}}_{\text{WLS}}\)</span> and <span class="math inline">\(\widehat{\mathbf{\beta}}_{\text{ML}}\)</span> would give weighted least squares and maximum likelihood estimates, and the line <span class="math inline">\(\beta_1 = 0\)</span> represents the null hypothesis that the slope is zero.</p>
@@ -665,7 +666,7 @@ <h1 class="title">
 <span>       color <span class="op">=</span> <span class="st">"Error on Y?"</span>,</span>
 <span>       shape <span class="op">=</span> <span class="st">"Error on Y?"</span>,</span>
 <span>       linetype <span class="op">=</span> <span class="st">"Error on Y?"</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">legend_inside</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0.2</span>, <span class="fl">0.9</span><span class="op">)</span><span class="op">)</span></span>
+<span>  <span class="fu">legend_inside</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0.25</span>, <span class="fl">0.8</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
 <span><span class="va">p2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span><span class="op">(</span>data<span class="op">=</span><span class="va">model_stats</span>, </span>
 <span>             <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">errX</span>, y <span class="op">=</span> <span class="va">sigma</span>, </span>
@@ -677,8 +678,7 @@ <h1 class="title">
 <span>       y <span class="op">=</span> <span class="st">"Model residual standard error"</span>,</span>
 <span>       color <span class="op">=</span> <span class="st">"Error on Y?"</span>,</span>
 <span>       shape <span class="op">=</span> <span class="st">"Error on Y?"</span>,</span>
-<span>       linetype <span class="op">=</span> <span class="st">"Error on Y?"</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">legend_inside</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0.8</span>, <span class="fl">0.9</span><span class="op">)</span><span class="op">)</span></span>
+<span>       linetype <span class="op">=</span> <span class="st">"Error on Y?"</span><span class="op">)</span> </span>
 <span></span>
 <span><span class="va">p1</span> <span class="op">+</span> <span class="va">p2</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
@@ -725,7 +725,7 @@ <h1 class="title">
 </div>
 <div class="cell" data-layout-align="center">
 <p><strong>Packages used here</strong>:</p>
-<p>9 packages used here: car, carData, dplyr, forcats, ggplot2, knitr, matlib, patchwork, tidyr</p>
+<p>10 packages used here: car, carData, dplyr, forcats, gganimate, ggplot2, knitr, matlib, patchwork, tidyr</p>
 </div>