website

vincentarelbundock · Oct 6, 2023 · 27e27b3 · 27e27b3
1 parent 0b0e8d9
commit 27e27b3
Show file tree

Hide file tree

Showing 89 changed files with 1,352 additions and 753 deletions.
diff --git a/docs/articles/alternative_software.html b/docs/articles/alternative_software.html
diff --git a/docs/articles/bootstrap.html b/docs/articles/bootstrap.html
diff --git a/docs/articles/bootstrap_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/bootstrap_files/figure-html/unnamed-chunk-13-1.png
diff --git a/docs/articles/brms.html b/docs/articles/brms.html
@@ -1078,8 +1078,8 @@ <h1 class="title">
 <span>    by <span class="op">=</span> <span class="st">"x"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;  x Estimate 2.5 % 97.5 %</span></span>
-<span><span class="co">#&gt;  0    0.450 0.343  0.565</span></span>
-<span><span class="co">#&gt;  1    0.549 0.441  0.664</span></span>
+<span><span class="co">#&gt;  0    0.454 0.338  0.565</span></span>
+<span><span class="co">#&gt;  1    0.552 0.436  0.664</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: x, estimate, conf.low, conf.high </span></span>
 <span><span class="co">#&gt; Type:  response</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -1093,7 +1093,7 @@ <h1 class="title">
 <span>    sample_new_levels <span class="op">=</span> <span class="st">"gaussian"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;  Term Contrast Estimate  2.5 % 97.5 %</span></span>
-<span><span class="co">#&gt;     x    1 - 0   0.0967 0.0465  0.162</span></span>
+<span><span class="co">#&gt;     x    1 - 0   0.0965 0.0494  0.162</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: term, contrast, estimate, conf.low, conf.high </span></span>
 <span><span class="co">#&gt; Type:  response</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -1111,7 +1111,7 @@ <h1 class="title">
 <span>  effects <span class="op">=</span> <span class="st">"integrateoutRE"</span><span class="op">)</span></span>
 <span><span class="va">bm</span><span class="op">$</span><span class="va">ContrastSummary</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt;            M        Mdn         LL        UL PercentROPE PercentMID   CI CIType ROPE  MID Label</span></span>
-<span><span class="co">#&gt; 1 0.09898374 0.09694253 0.04870074 0.1611877          NA         NA 0.95    ETI &lt;NA&gt; &lt;NA&gt; AME x</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="co">#&gt; 1 0.09864399 0.09651684 0.04835076 0.1610664          NA         NA 0.95    ETI &lt;NA&gt; &lt;NA&gt; AME x</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>See the <a href="alternative_software.html">alternative software vignette</a> for more information on <code>brmsmargins</code>.</p>
 </section></section><section id="multinomial-logit" class="level2" data-number="8.3"><h2 data-number="8.3" class="anchored" data-anchor-id="multinomial-logit">

diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-16-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-16-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-21-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-21-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-23-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-23-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-27-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-27-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-28-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-28-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-30-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-30-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-32-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-32-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-33-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-33-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-34-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-34-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-35-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-35-1.png
diff --git a/docs/articles/brms_files/figure-html/unnamed-chunk-66-1.png b/docs/articles/brms_files/figure-html/unnamed-chunk-66-1.png
diff --git a/docs/articles/categorical.html b/docs/articles/categorical.html
@@ -540,9 +540,9 @@ <h1 class="title">
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/marginaleffects/man/slopes.html">slopes</a></span><span class="op">(</span><span class="va">mod</span>, variables <span class="op">=</span> <span class="st">"mpg"</span>, newdata <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/marginaleffects/man/datagrid.html">datagrid</a></span><span class="op">(</span>mpg <span class="op">=</span> <span class="fl">25</span>, hp <span class="op">=</span> <span class="fl">110</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;  Group Term mpg  hp Estimate Std. Error       z Pr(&gt;|z|)    S    2.5 %  97.5 %</span></span>
-<span><span class="co">#&gt;      3  mpg  25 110 -0.06041     0.0169 -3.5802   &lt;0.001 11.5 -0.09348 -0.0273</span></span>
+<span><span class="co">#&gt;      3  mpg  25 110 -0.06041     0.0169 -3.5813   &lt;0.001 11.5 -0.09347 -0.0273</span></span>
 <span><span class="co">#&gt;      4  mpg  25 110 -0.00321     0.0335 -0.0958   0.9237  0.1 -0.06896  0.0625</span></span>
-<span><span class="co">#&gt;      5  mpg  25 110  0.06362     0.0301  2.1129   0.0346  4.9  0.00461  0.1226</span></span>
+<span><span class="co">#&gt;      5  mpg  25 110  0.06362     0.0301  2.1132   0.0346  4.9  0.00461  0.1226</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: rowid, term, group, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high, mpg, hp, predicted_lo, predicted_hi, predicted, gear </span></span>
 <span><span class="co">#&gt; Type:  probs</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -554,12 +554,12 @@ <h1 class="title">
 <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/pkg/marginaleffects/man/slopes.html">avg_slopes</a></span><span class="op">(</span><span class="va">mod</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;  Group Term Estimate Std. Error     z Pr(&gt;|z|)    S     2.5 %   97.5 %</span></span>
-<span><span class="co">#&gt;      3  hp  -0.00377   0.001514 -2.49  0.01285  6.3 -0.006735 -0.00080</span></span>
-<span><span class="co">#&gt;      3  mpg -0.07014   0.015484 -4.53  &lt; 0.001 17.4 -0.100488 -0.03979</span></span>
-<span><span class="co">#&gt;      4  hp   0.00201   0.000958  2.10  0.03555  4.8  0.000136  0.00389</span></span>
+<span><span class="co">#&gt;      3  hp  -0.00377   0.001514 -2.49  0.01284  6.3 -0.006735 -0.00080</span></span>
+<span><span class="co">#&gt;      3  mpg -0.07014   0.015485 -4.53  &lt; 0.001 17.4 -0.100490 -0.03979</span></span>
+<span><span class="co">#&gt;      4  hp   0.00201   0.000957  2.10  0.03553  4.8  0.000136  0.00389</span></span>
 <span><span class="co">#&gt;      4  mpg  0.03747   0.013861  2.70  0.00687  7.2  0.010303  0.06464</span></span>
 <span><span class="co">#&gt;      5  hp   0.00175   0.000833  2.11  0.03519  4.8  0.000122  0.00339</span></span>
-<span><span class="co">#&gt;      5  mpg  0.03267   0.009571  3.41  &lt; 0.001 10.6  0.013909  0.05143</span></span>
+<span><span class="co">#&gt;      5  mpg  0.03267   0.009572  3.41  &lt; 0.001 10.6  0.013907  0.05143</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: term, group, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high </span></span>
 <span><span class="co">#&gt; Type:  probs</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

diff --git a/docs/articles/comparisons_files/figure-html/unnamed-chunk-48-1.png b/docs/articles/comparisons_files/figure-html/unnamed-chunk-48-1.png
diff --git a/docs/articles/elasticity.html b/docs/articles/elasticity.html
@@ -530,7 +530,7 @@ <h1 class="title">
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;  Term Estimate Std. Error     z Pr(&gt;|z|)    S   2.5 %  97.5 %</span></span>
 <span><span class="co">#&gt;    hp  -0.0318    0.00903 -3.52   &lt;0.001 11.2 -0.0495 -0.0141</span></span>
-<span><span class="co">#&gt;    wt  -3.8778    0.63273 -6.13   &lt;0.001 30.1 -5.1180 -2.6377</span></span>
+<span><span class="co">#&gt;    wt  -3.8778    0.63276 -6.13   &lt;0.001 30.1 -5.1180 -2.6376</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: term, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high </span></span>
 <span><span class="co">#&gt; Type:  response</span></span>
@@ -548,7 +548,7 @@ <h1 class="title">
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;  Term Contrast Estimate Std. Error     z Pr(&gt;|z|)    S    2.5 %    97.5 %</span></span>
 <span><span class="co">#&gt;    hp    eY/dX -0.00173   0.000502 -3.46   &lt;0.001 10.8 -0.00272 -0.000751</span></span>
-<span><span class="co">#&gt;    wt    eY/dX -0.21165   0.037849 -5.59   &lt;0.001 25.4 -0.28583 -0.137464</span></span>
+<span><span class="co">#&gt;    wt    eY/dX -0.21165   0.037851 -5.59   &lt;0.001 25.4 -0.28583 -0.137461</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: term, contrast, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high </span></span>
 <span><span class="co">#&gt; Type:  response</span></span>

diff --git a/docs/articles/experiments.html b/docs/articles/experiments.html
@@ -534,7 +534,7 @@ <h1 class="title">
 <div class="cell">
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><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://tidyverse.tidyverse.org">tidyverse</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://marginaleffects.com/">marginaleffects</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://vincentarelbundock.github.io/modelsummary/">modelsummary</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://modelsummary.com">modelsummary</a></span><span class="op">)</span></span>
 <span></span>
 <span><span class="co">## See ?mtcars for variable definitions</span></span>
 <span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html">lm</a></span><span class="op">(</span><span class="va">mpg</span> <span class="op">~</span> <span class="va">vs</span> <span class="op">+</span> <span class="va">am</span> <span class="op">+</span> <span class="va">vs</span><span class="op">:</span><span class="va">am</span>, data<span class="op">=</span><span class="va">mtcars</span><span class="op">)</span> <span class="co"># equivalent to ~ vs*am</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

diff --git a/docs/articles/gam.html b/docs/articles/gam.html
@@ -600,11 +600,11 @@ <h1 class="title">
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;  Term Estimate Std. Error    z Pr(&gt;|z|)     S  2.5 % 97.5 %</span></span>
 <span><span class="co">#&gt;  Time   0.0261    0.00137 19.1   &lt;0.001 267.8 0.0234 0.0288</span></span>
-<span><span class="co">#&gt;  Time   0.0261    0.00136 19.2   &lt;0.001 270.3 0.0234 0.0288</span></span>
-<span><span class="co">#&gt;  Time   0.0261    0.00133 19.5   &lt;0.001 280.1 0.0235 0.0287</span></span>
-<span><span class="co">#&gt;  Time   0.0260    0.00128 20.3   &lt;0.001 301.1 0.0235 0.0285</span></span>
-<span><span class="co">#&gt;  Time   0.0259    0.00120 21.6   &lt;0.001 339.8 0.0235 0.0282</span></span>
-<span><span class="co">#&gt;  Time   0.0257    0.00109 23.5   &lt;0.001 404.6 0.0236 0.0279</span></span>
+<span><span class="co">#&gt;  Time   0.0261    0.00136 19.2   &lt;0.001 270.4 0.0234 0.0288</span></span>
+<span><span class="co">#&gt;  Time   0.0261    0.00133 19.5   &lt;0.001 280.0 0.0235 0.0287</span></span>
+<span><span class="co">#&gt;  Time   0.0260    0.00128 20.3   &lt;0.001 301.4 0.0235 0.0285</span></span>
+<span><span class="co">#&gt;  Time   0.0259    0.00120 21.6   &lt;0.001 340.0 0.0235 0.0282</span></span>
+<span><span class="co">#&gt;  Time   0.0257    0.00109 23.5   &lt;0.001 404.4 0.0236 0.0279</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: rowid, term, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high, predicted_lo, predicted_hi, predicted, Y, Group, Time, Subject </span></span>
 <span><span class="co">#&gt; Type:  response</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

diff --git a/docs/articles/gam_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/gam_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/gam_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/gam_files/figure-html/unnamed-chunk-7-1.png
diff --git a/docs/articles/gformula.html b/docs/articles/gformula.html
@@ -731,7 +731,7 @@ <h1 class="title">
 <span><span class="va">bootstrap</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>                           estimate std.error conf.low conf.high
-1 Treatment - No Treatment 3.517374  0.493746  2.54965  4.485099</code></pre>
+1 Treatment - No Treatment 3.517374 0.4765446 2.583364  4.451385</code></pre>
 </div>
 </div>
 <p>The results are close to those that we obtained with <code><a href="https://rdrr.io/pkg/marginaleffects/man/comparisons.html">comparisons()</a></code>, but the confidence interval differs slightly because of the difference between bootstrapping and the delta method.</p>

diff --git a/docs/articles/hypothesis.html b/docs/articles/hypothesis.html
@@ -744,8 +744,8 @@ <h1 class="title">
 <span>  hypothesis <span class="op">=</span> <span class="st">"median = mean"</span></span>
 <span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt;           Term  Estimate Std. Error      z Pr(&gt;|z|)   S   2.5 % 97.5 %</span></span>
-<span><span class="co">#&gt;  median = mean -0.000969    0.00702 -0.138     0.89 0.2 -0.0147 0.0128</span></span>
+<span><span class="co">#&gt;           Term Estimate Std. Error      z Pr(&gt;|z|)   S   2.5 % 97.5 %</span></span>
+<span><span class="co">#&gt;  median = mean  -0.0012    0.00594 -0.201    0.841 0.3 -0.0128 0.0104</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Columns: term, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>

diff --git a/docs/articles/logit.html b/docs/articles/logit.html
@@ -529,7 +529,7 @@ <h1 class="title">
 <p>Load libraries, data and fit a covariate-adjusted logistic regression model.</p>
 <div class="cell">
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><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://marginaleffects.com/">marginaleffects</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://vincentarelbundock.github.io/modelsummary/">modelsummary</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://modelsummary.com">modelsummary</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://ggplot2.tidyverse.org">ggplot2</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://hbiostat.org/R/rms/">rms</a></span><span class="op">)</span></span>
 <span></span>