From df58d85bc1aed263d52c460d787b70d4e467eec4 Mon Sep 17 00:00:00 2001
From: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Date: Sat, 16 Sep 2023 09:06:28 -0400
Subject: [PATCH] Issue #890

---
 book/articles/reference/comparisons.qmd      | 16 ++++++++--------
 book/articles/reference/datagrid.qmd         |  2 +-
 book/articles/reference/hypotheses.qmd       | 16 ++++++++--------
 book/articles/reference/inferences.qmd       |  2 +-
 book/articles/reference/marginal_means.qmd   | 16 ++++++++--------
 book/articles/reference/plot_comparisons.qmd |  2 +-
 book/articles/reference/plot_predictions.qmd |  2 +-
 book/articles/reference/plot_slopes.qmd      |  2 +-
 book/articles/reference/predictions.qmd      | 16 ++++++++--------
 book/articles/reference/slopes.qmd           | 20 ++++++++++----------
 book/utils/utils.R                           | 14 ++++++++++++--
 11 files changed, 59 insertions(+), 49 deletions(-)

diff --git a/book/articles/reference/comparisons.qmd b/book/articles/reference/comparisons.qmd
index 820eb1624..fee1a9c0f 100644
--- a/book/articles/reference/comparisons.qmd
+++ b/book/articles/reference/comparisons.qmd
@@ -770,19 +770,19 @@ posterior using the function supplied to the
 
 ## Equivalence, Inferiority, Superiority
 
-<p><code class="reqn">\theta</code> is an estimate, <code class="reqn">\sigma_\theta</code> its estimated standard error, and <code class="reqn">[a, b]</code> are the bounds of the interval supplied to the <code>equivalence</code> argument.
+<p>$\theta$ is an estimate, $\sigma_\theta$ its estimated standard error, and $[a, b]$ are the bounds of the interval supplied to the <code>equivalence</code> argument.
 </p>
 <p>Non-inferiority:
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \leq a</code>
+<li> <p>$H_0$: $\theta \leq a$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &gt; a</code>
+<li> <p>$H_1$: $\theta > a$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - a)/\sigma_\theta</code>
+<li> <p>$t=(\theta - a)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Upper-tail probability
@@ -793,13 +793,13 @@ posterior using the function supplied to the
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \geq b</code>
+<li> <p>$H_0$: $\theta \geq b$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &lt; b</code>
+<li> <p>$H_1$: $\theta < b$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - b)/\sigma_\theta</code>
+<li> <p>$t=(\theta - b)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Lower-tail probability
@@ -844,7 +844,7 @@ posterior using the function supplied to the
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 library(marginaleffects)
diff --git a/book/articles/reference/datagrid.qmd b/book/articles/reference/datagrid.qmd
index ea67e9920..6667eb7bb 100644
--- a/book/articles/reference/datagrid.qmd
+++ b/book/articles/reference/datagrid.qmd
@@ -135,7 +135,7 @@ explicitly defined are held at their mean or mode.
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 # The output only has 2 rows, and all the variables except `hp` are at their
diff --git a/book/articles/reference/hypotheses.qmd b/book/articles/reference/hypotheses.qmd
index 5091728fb..8b26771c6 100644
--- a/book/articles/reference/hypotheses.qmd
+++ b/book/articles/reference/hypotheses.qmd
@@ -250,19 +250,19 @@ For the Chi-squared test, the degrees of freedom are Q.
 
 ## Equivalence, Inferiority, Superiority
 
-<p><code class="reqn">\theta</code> is an estimate, <code class="reqn">\sigma_\theta</code> its estimated standard error, and <code class="reqn">[a, b]</code> are the bounds of the interval supplied to the <code>equivalence</code> argument.
+<p>$\theta$ is an estimate, $\sigma_\theta$ its estimated standard error, and $[a, b]$ are the bounds of the interval supplied to the <code>equivalence</code> argument.
 </p>
 <p>Non-inferiority:
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \leq a</code>
+<li> <p>$H_0$: $\theta \leq a$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &gt; a</code>
+<li> <p>$H_1$: $\theta > a$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - a)/\sigma_\theta</code>
+<li> <p>$t=(\theta - a)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Upper-tail probability
@@ -273,13 +273,13 @@ For the Chi-squared test, the degrees of freedom are Q.
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \geq b</code>
+<li> <p>$H_0$: $\theta \geq b$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &lt; b</code>
+<li> <p>$H_1$: $\theta < b$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - b)/\sigma_\theta</code>
+<li> <p>$t=(\theta - b)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Lower-tail probability
@@ -299,7 +299,7 @@ For the Chi-squared test, the degrees of freedom are Q.
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 library(marginaleffects)
diff --git a/book/articles/reference/inferences.qmd b/book/articles/reference/inferences.qmd
index 9e6c8642b..8c8df0f73 100644
--- a/book/articles/reference/inferences.qmd
+++ b/book/articles/reference/inferences.qmd
@@ -168,7 +168,7 @@
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 library(marginaleffects)
diff --git a/book/articles/reference/marginal_means.qmd b/book/articles/reference/marginal_means.qmd
index 9f27ff15f..eb2ea1875 100644
--- a/book/articles/reference/marginal_means.qmd
+++ b/book/articles/reference/marginal_means.qmd
@@ -431,19 +431,19 @@ posterior using the function supplied to the
 
 ## Equivalence, Inferiority, Superiority
 
-<p><code class="reqn">\theta</code> is an estimate, <code class="reqn">\sigma_\theta</code> its estimated standard error, and <code class="reqn">[a, b]</code> are the bounds of the interval supplied to the <code>equivalence</code> argument.
+<p>$\theta$ is an estimate, $\sigma_\theta$ its estimated standard error, and $[a, b]$ are the bounds of the interval supplied to the <code>equivalence</code> argument.
 </p>
 <p>Non-inferiority:
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \leq a</code>
+<li> <p>$H_0$: $\theta \leq a$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &gt; a</code>
+<li> <p>$H_1$: $\theta > a$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - a)/\sigma_\theta</code>
+<li> <p>$t=(\theta - a)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Upper-tail probability
@@ -454,13 +454,13 @@ posterior using the function supplied to the
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \geq b</code>
+<li> <p>$H_0$: $\theta \geq b$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &lt; b</code>
+<li> <p>$H_1$: $\theta < b$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - b)/\sigma_\theta</code>
+<li> <p>$t=(\theta - b)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Lower-tail probability
@@ -505,7 +505,7 @@ posterior using the function supplied to the
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 library(marginaleffects)
diff --git a/book/articles/reference/plot_comparisons.qmd b/book/articles/reference/plot_comparisons.qmd
index 16e289a98..e41766791 100644
--- a/book/articles/reference/plot_comparisons.qmd
+++ b/book/articles/reference/plot_comparisons.qmd
@@ -315,7 +315,7 @@ the table below.
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 mod <- lm(mpg ~ hp * drat * factor(am), data = mtcars)
diff --git a/book/articles/reference/plot_predictions.qmd b/book/articles/reference/plot_predictions.qmd
index 8b7bf2fe6..43e74afbb 100644
--- a/book/articles/reference/plot_predictions.qmd
+++ b/book/articles/reference/plot_predictions.qmd
@@ -275,7 +275,7 @@ the table below.
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 mod <- lm(mpg ~ hp + wt, data = mtcars)
diff --git a/book/articles/reference/plot_slopes.qmd b/book/articles/reference/plot_slopes.qmd
index e2968a367..6cfb11a68 100644
--- a/book/articles/reference/plot_slopes.qmd
+++ b/book/articles/reference/plot_slopes.qmd
@@ -304,7 +304,7 @@ the table below.
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 library(marginaleffects)
diff --git a/book/articles/reference/predictions.qmd b/book/articles/reference/predictions.qmd
index 623b190f5..05a285bde 100644
--- a/book/articles/reference/predictions.qmd
+++ b/book/articles/reference/predictions.qmd
@@ -574,19 +574,19 @@ posterior using the function supplied to the
 
 ## Equivalence, Inferiority, Superiority
 
-<p><code class="reqn">\theta</code> is an estimate, <code class="reqn">\sigma_\theta</code> its estimated standard error, and <code class="reqn">[a, b]</code> are the bounds of the interval supplied to the <code>equivalence</code> argument.
+<p>$\theta$ is an estimate, $\sigma_\theta$ its estimated standard error, and $[a, b]$ are the bounds of the interval supplied to the <code>equivalence</code> argument.
 </p>
 <p>Non-inferiority:
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \leq a</code>
+<li> <p>$H_0$: $\theta \leq a$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &gt; a</code>
+<li> <p>$H_1$: $\theta > a$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - a)/\sigma_\theta</code>
+<li> <p>$t=(\theta - a)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Upper-tail probability
@@ -597,13 +597,13 @@ posterior using the function supplied to the
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \geq b</code>
+<li> <p>$H_0$: $\theta \geq b$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &lt; b</code>
+<li> <p>$H_1$: $\theta < b$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - b)/\sigma_\theta</code>
+<li> <p>$t=(\theta - b)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Lower-tail probability
@@ -648,7 +648,7 @@ posterior using the function supplied to the
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 # Adjusted Prediction for every row of the original dataset
diff --git a/book/articles/reference/slopes.qmd b/book/articles/reference/slopes.qmd
index 5f1f9fb1a..e61533842 100644
--- a/book/articles/reference/slopes.qmd
+++ b/book/articles/reference/slopes.qmd
@@ -375,9 +375,9 @@ including non-linear models with transformations (e.g., polynomials).
 Uncertainty estimates are computed using the delta method.
 </p>
 <p>Numerical derivatives for the <code>slopes</code> function are calculated
-using a simple epsilon difference approach: <code class="reqn">\partial Y / \partial X = (f(X + \varepsilon/2) - f(X-\varepsilon/2)) / \varepsilon</code>,
+using a simple epsilon difference approach: $\partial Y / \partial X = (f(X + \varepsilon/2) - f(X-\varepsilon/2)) / \varepsilon$,
 where f is the <code>predict()</code> method associated with the model class, and
-<code class="reqn">\varepsilon</code> is determined by the <code>eps</code> argument.
+$\varepsilon$ is determined by the <code>eps</code> argument.
 </p>
 
 
@@ -556,19 +556,19 @@ posterior using the function supplied to the
 
 ## Equivalence, Inferiority, Superiority
 
-<p><code class="reqn">\theta</code> is an estimate, <code class="reqn">\sigma_\theta</code> its estimated standard error, and <code class="reqn">[a, b]</code> are the bounds of the interval supplied to the <code>equivalence</code> argument.
+<p>$\theta$ is an estimate, $\sigma_\theta$ its estimated standard error, and $[a, b]$ are the bounds of the interval supplied to the <code>equivalence</code> argument.
 </p>
 <p>Non-inferiority:
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \leq a</code>
+<li> <p>$H_0$: $\theta \leq a$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &gt; a</code>
+<li> <p>$H_1$: $\theta > a$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - a)/\sigma_\theta</code>
+<li> <p>$t=(\theta - a)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Upper-tail probability
@@ -579,13 +579,13 @@ posterior using the function supplied to the
 </p>
 
 <ul>
-<li> <p><code class="reqn">H_0</code>: <code class="reqn">\theta \geq b</code>
+<li> <p>$H_0$: $\theta \geq b$
 </p>
 </li>
-<li> <p><code class="reqn">H_1</code>: <code class="reqn">\theta &lt; b</code>
+<li> <p>$H_1$: $\theta < b$
 </p>
 </li>
-<li> <p><code class="reqn">t=(\theta - b)/\sigma_\theta</code>
+<li> <p>$t=(\theta - b)/\sigma_\theta$
 </p>
 </li>
 <li><p> p: Lower-tail probability
@@ -630,7 +630,7 @@ posterior using the function supplied to the
 
 
 ## Examples
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(marginaleffects)
 
 
diff --git a/book/utils/utils.R b/book/utils/utils.R
index 7ad5012c9..3578ca138 100644
--- a/book/utils/utils.R
+++ b/book/utils/utils.R
@@ -85,7 +85,6 @@ rd2qmd = function(src) {
 
   # superfluous header and footer
   tmp = readLines(tmp_html)
-  tmp = gsub("\\eqn\\{.*\\}\\{.*\\}", "\\$\\1\\$", tmp)
   tmp = tmp[(grep("</table>$", tmp)[1] + 1):length(tmp)]
   tmp = tmp[seq_len(which("</div>" == tmp) - 3)]
 
@@ -107,9 +106,20 @@ rd2qmd = function(src) {
     ex = gsub("&gt;", ">", ex)
     ex = ex[!grepl("## Not run:", ex)]
     ex = ex[!grepl("## End", ex)]
-    tmp = c(tmp[2:idx], "```{r}", "library(marginaleffects)", ex, "```")
+    tmp = c(tmp[2:idx], "```{r, warning=FALSE, message=FALSE}", "library(marginaleffects)", ex, "```")
   }
 
+  # cleanup equations
+  tmp <- gsub(
+    '<code class="reqn">(.*?)&gt;(.*?)</code>',
+    '<code class="reqn">\\1>\\2</code>',
+     tmp)
+  tmp <- gsub(
+    '<code class="reqn">(.*?)&lt;(.*?)</code>',
+    '<code class="reqn">\\1<\\2</code>',
+     tmp)
+  tmp <- gsub('<code class="reqn">(.*?)</code>', '\\$\\1\\$', tmp)
+
   # title
   funname = tools::file_path_sans_ext(basename(src))
   if (!is.null(title)) {