jabenninghoff · jabenninghoff · Mar 10, 2024 · Mar 10, 2024 · Mar 10, 2024 · Mar 10, 2024
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rtraining
 Title: R Training
-Version: 1.1.9
+Version: 1.1.10
 Authors@R:
     person("John", "Benninghoff", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6230-4742"))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# rtraining 1.1.10
+
+* Maintenance updates
+
 # rtraining 1.1.9
 
 * Maintenance updates

diff --git a/README.Rmd b/README.Rmd
@@ -36,7 +36,7 @@ Feel free to use and/or fork this project!
 Notebooks in this package:
 
 ```{r notebooks, echo = FALSE, results = 'asis'}
-notebooks <- dir_ls("analysis", glob = "*.Rmd") |>
+notebooks <- dir_ls("analysis", regexp = "[.][Rq]md$") |>
   map_dfr(rmd_metadata) |>
   mutate(bullet = paste0("- [", title, "](", url, ") (", date, "): ", description)) |>
   pull(bullet)

diff --git a/_freeze/analysis/FaultTree/execute-results/html.json b/_freeze/analysis/FaultTree/execute-results/html.json
diff --git a/_freeze/analysis/advanced-r-1/execute-results/html.json b/_freeze/analysis/advanced-r-1/execute-results/html.json
diff --git a/_freeze/analysis/advanced-r-2/execute-results/html.json b/_freeze/analysis/advanced-r-2/execute-results/html.json
diff --git a/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-11-1.png b/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-11-1.png
diff --git a/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-12-1.png b/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-12-1.png
diff --git a/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-58-1.png b/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-58-1.png
diff --git a/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-58-2.png b/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-58-2.png
diff --git a/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-58-3.png b/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-58-3.png
diff --git a/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-59-1.png b/_freeze/analysis/advanced-r-2/figure-html/unnamed-chunk-59-1.png
diff --git a/_freeze/analysis/advanced-r-3/execute-results/html.json b/_freeze/analysis/advanced-r-3/execute-results/html.json
diff --git a/_freeze/analysis/advanced-r-4/execute-results/html.json b/_freeze/analysis/advanced-r-4/execute-results/html.json
diff --git a/_freeze/analysis/ggplot2-1/execute-results/html.json b/_freeze/analysis/ggplot2-1/execute-results/html.json
diff --git a/_freeze/analysis/ggplot2-1/figure-html/unnamed-chunk-19-1.png b/_freeze/analysis/ggplot2-1/figure-html/unnamed-chunk-19-1.png
diff --git a/_freeze/analysis/ggplot2-2/execute-results/html.json b/_freeze/analysis/ggplot2-2/execute-results/html.json
diff --git a/_freeze/analysis/ggplot2-3/execute-results/html.json b/_freeze/analysis/ggplot2-3/execute-results/html.json
diff --git a/_freeze/analysis/ggplot2-4/execute-results/html.json b/_freeze/analysis/ggplot2-4/execute-results/html.json
diff --git a/_freeze/analysis/ggplot2-4/figure-html/unnamed-chunk-2-1.png b/_freeze/analysis/ggplot2-4/figure-html/unnamed-chunk-2-1.png
diff --git a/_freeze/analysis/ggplot2-4/figure-html/unnamed-chunk-3-1.png b/_freeze/analysis/ggplot2-4/figure-html/unnamed-chunk-3-1.png
diff --git a/_freeze/analysis/ggplot2-5/execute-results/html.json b/_freeze/analysis/ggplot2-5/execute-results/html.json
diff --git a/_freeze/analysis/r-books/execute-results/html.json b/_freeze/analysis/r-books/execute-results/html.json
diff --git a/_freeze/analysis/r-setup-log/execute-results/html.json b/_freeze/analysis/r-setup-log/execute-results/html.json
diff --git a/_freeze/analysis/r-training-log/execute-results/html.json b/_freeze/analysis/r-training-log/execute-results/html.json
diff --git a/_freeze/analysis/using-Rcpp/execute-results/html.json b/_freeze/analysis/using-Rcpp/execute-results/html.json
diff --git a/analysis/FaultTree.Rmd b/analysis/FaultTree.Rmd
@@ -2,7 +2,7 @@
 title: "FaultTree.widget Test"
 author: "John Benninghoff"
 date: '2021-09-30'
-file-modified: '2022-01-12'
+date-modified: '2022-01-12'
 categories: notes
 order: 103
 output:

diff --git a/analysis/advanced-r-1.Rmd b/analysis/advanced-r-1.Rmd
@@ -2,7 +2,7 @@
 title: "Advanced R (Foundations)"
 author: "John Benninghoff"
 date: '2022-06-12'
-file-modified: '2022-07-31'
+date-modified: '2022-07-31'
 categories: [exercises, advanced-r]
 order: 201
 output:

diff --git a/analysis/advanced-r-2.Rmd b/analysis/advanced-r-2.Rmd
@@ -2,7 +2,7 @@
 title: "Advanced R (Functional programming)"
 author: "John Benninghoff"
 date: '2022-07-31'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, advanced-r]
 order: 202
 output:

diff --git a/analysis/advanced-r-3.Rmd b/analysis/advanced-r-3.Rmd
@@ -2,7 +2,7 @@
 title: "Advanced R (Object-oriented programming)"
 author: "John Benninghoff"
 date: '2022-08-15'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, advanced-r]
 order: 203
 output:

diff --git a/analysis/advanced-r-4.Rmd b/analysis/advanced-r-4.Rmd
@@ -2,7 +2,7 @@
 title: "Advanced R (Metaprogramming)"
 author: "John Benninghoff"
 date: '2023-02-19'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, advanced-r]
 order: 204
 output:

diff --git a/analysis/ggplot2-1.Rmd b/analysis/ggplot2-1.Rmd
@@ -2,7 +2,7 @@
 title: "ggplot2 (Getting started)"
 author: "John Benninghoff"
 date: '2022-11-20'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, ggplot2]
 order: 301
 output:

diff --git a/analysis/ggplot2-2.Rmd b/analysis/ggplot2-2.Rmd
@@ -2,7 +2,7 @@
 title: "ggplot2 (Layers)"
 author: "John Benninghoff"
 date: '2022-11-20'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, ggplot2]
 order: 302
 output:

diff --git a/analysis/ggplot2-3.Rmd b/analysis/ggplot2-3.Rmd
@@ -2,7 +2,7 @@
 title: "ggplot2 (Scales)"
 author: "John Benninghoff"
 date: '2022-12-03'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, ggplot2]
 order: 303
 output:

diff --git a/analysis/ggplot2-4.Rmd b/analysis/ggplot2-4.Rmd
@@ -2,7 +2,7 @@
 title: "ggplot2 (Grammar)"
 author: "John Benninghoff"
 date: '2022-12-09'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, ggplot2]
 order: 304
 output:

diff --git a/analysis/ggplot2-5.Rmd b/analysis/ggplot2-5.Rmd
@@ -2,7 +2,7 @@
 title: "ggplot2 (Extending)"
 author: "John Benninghoff"
 date: '2022-12-18'
-file-modified: '2023-11-11'
+date-modified: '2023-11-11'
 categories: [exercises, ggplot2]
 order: 305
 output:

diff --git a/analysis/r-books.Rmd b/analysis/r-books.Rmd
@@ -2,7 +2,7 @@
 title: "R Books"
 author: "John Benninghoff"
 date: '2023-11-17'
-file-modified: '2023-12-29'
+date-modified: '2024-01-01'
 categories: reading
 order: 1
 output:

diff --git a/analysis/r-setup-log.Rmd b/analysis/r-setup-log.Rmd
@@ -2,7 +2,7 @@
 title: "R Setup Log"
 author: "John Benninghoff"
 date: '2020-12-30'
-file-modified: '2023-11-17'
+date-modified: '2024-02-24'
 categories: notes
 order: 102
 output:

diff --git a/analysis/r-training-log.Rmd b/analysis/r-training-log.Rmd
@@ -2,7 +2,7 @@
 title: "R Training Log"
 author: "John Benninghoff"
 date: '2020-12-02'
-file-modified: '2023-12-08'
+date-modified: '2023-12-08'
 categories: notes
 order: 101
 output:

diff --git a/analysis/using-Rcpp.Rmd b/analysis/using-Rcpp.Rmd
@@ -2,7 +2,7 @@
 title: "Using Rcpp"
 author: "John Benninghoff"
 date: '2023-12-21'
-file-modified: '2023-12-31'
+date-modified: '2024-03-10'
 categories: notes
 order: 104
 output:
@@ -122,7 +122,7 @@ that calls `phevaluator::EvaluateCards()` and returns a string based on `Rank.ca
 [`cpp_example.cc`](https://github.com/HenryRLee/PokerHandEvaluator/blob/master/cpp/examples/cpp_example.cc). A more complete implementation would use
 [Rcpp Modules](https://CRAN.R-project.org/package=Rcpp/vignettes/Rcpp-modules.pdf) to expose
 the C++ classes and methods in PH Evaluator, with help from the
-[RcppStudent](https://github.com/coatless-r-n-d/rcpp-modules-student) R package.
+[RcppStudent](https://github.com/coatless-rd-rcpp/rcpp-modules-student) R package.
 
 Additional examples implementing C++ libraries in Rcpp I found include
 [RcppAnnoy](https://github.com/eddelbuettel/rcppannoy), written by Rcpp author and maintainer Dirk
@@ -284,9 +284,9 @@ reading a tidyverse blog post on
 I learned that the R C++ standard was now C++17, so I technically did not need that line in the
 `Makevars` file, but I decided to keep it as it was an upstream requirement.
 
-I also discovered an example [package](https://github.com/coatless-r-n-d/rcpp-headers-subdirs) that
-explained how to put code in a subdirectory of `src/`, which I plan to use for the second version
-using Rcpp Modules.
+I also discovered an example [package](https://github.com/coatless-rd-rcpp/rcpp-headers-subdirs)
+that explained how to put code in a subdirectory of `src/`, which I plan to use for the second
+version using Rcpp Modules.
 
 I later added a script to copy (or update) the PH Evaluator source and header files to the cards
 package, to automate future updates if needed.
@@ -298,4 +298,4 @@ I am inclined to use a simple approach to creating a "phevaluator" package, copy
 files into `src/` (with a shell script for reproducibility), use a minimal `Makevars` file, and use
 [Rcpp Modules](https://CRAN.R-project.org/package=Rcpp/vignettes/Rcpp-modules.pdf) to expose
 the C++ classes and methods in PH Evaluator, following the approach used by the
-[RcppStudent](https://github.com/coatless-r-n-d/rcpp-modules-student) R package.
+[RcppStudent](https://github.com/coatless-rd-rcpp/rcpp-modules-student) R package.
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.550">
+<meta name="generator" content="quarto-1.4.551">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -461,6 +461,24 @@ <h1>MIT License</h1>
     // clear code selection
     e.clearSelection();
   });
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp("https:\/\/jabenninghoff\.github\.io\/rtraining\/");
+    var isInternal = (href) => {
+        return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+    }
+    // Inspect non-navigation links and adorn them if external
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+    for (var i=0; i<links.length; i++) {
+      const link = links[i];
+      if (!isInternal(link.href)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
+      }
+    }
   function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
@@ -495,7 +513,11 @@ <h1>MIT License</h1>
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
     });
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');

diff --git a/docs/NEWS.html b/docs/NEWS.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.550">
+<meta name="generator" content="quarto-1.4.551">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -217,7 +217,8 @@
     <h2 id="toc-title">On this page</h2>
 
   <ul>
-  <li><a href="#rtraining-1.1.9" id="toc-rtraining-1.1.9" class="nav-link active" data-scroll-target="#rtraining-1.1.9">rtraining 1.1.9</a></li>
+  <li><a href="#rtraining-1.1.10" id="toc-rtraining-1.1.10" class="nav-link active" data-scroll-target="#rtraining-1.1.10">rtraining 1.1.10</a></li>
+  <li><a href="#rtraining-1.1.9" id="toc-rtraining-1.1.9" class="nav-link" data-scroll-target="#rtraining-1.1.9">rtraining 1.1.9</a></li>
   <li><a href="#rtraining-1.1.8" id="toc-rtraining-1.1.8" class="nav-link" data-scroll-target="#rtraining-1.1.8">rtraining 1.1.8</a></li>
   <li><a href="#rtraining-1.1.7" id="toc-rtraining-1.1.7" class="nav-link" data-scroll-target="#rtraining-1.1.7">rtraining 1.1.7</a></li>
   <li><a href="#rtraining-1.1.6" id="toc-rtraining-1.1.6" class="nav-link" data-scroll-target="#rtraining-1.1.6">rtraining 1.1.6</a></li>
@@ -301,6 +302,12 @@ <h2 id="toc-title">On this page</h2>
 
 
 
+<section id="rtraining-1.1.10" class="level1">
+<h1>rtraining 1.1.10</h1>
+<ul>
+<li>Maintenance updates</li>
+</ul>
+</section>
 <section id="rtraining-1.1.9" class="level1">
 <h1>rtraining 1.1.9</h1>
 <ul>
@@ -951,6 +958,24 @@ <h2 class="anchored" data-anchor-id="new-contentfeatures-2">New Content/Features
     // clear code selection
     e.clearSelection();
   });
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp("https:\/\/jabenninghoff\.github\.io\/rtraining\/");
+    var isInternal = (href) => {
+        return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+    }
+    // Inspect non-navigation links and adorn them if external
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+    for (var i=0; i<links.length; i++) {
+      const link = links[i];
+      if (!isInternal(link.href)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
+      }
+    }
   function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
@@ -985,7 +1010,11 @@ <h2 class="anchored" data-anchor-id="new-contentfeatures-2">New Content/Features
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
     });
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');

diff --git a/docs/TODO.html b/docs/TODO.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.550">
+<meta name="generator" content="quarto-1.4.551">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -521,6 +521,24 @@ <h2 class="anchored" data-anchor-id="github">GitHub</h2>
     // clear code selection
     e.clearSelection();
   });
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp("https:\/\/jabenninghoff\.github\.io\/rtraining\/");
+    var isInternal = (href) => {
+        return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+    }
+    // Inspect non-navigation links and adorn them if external
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+    for (var i=0; i<links.length; i++) {
+      const link = links[i];
+      if (!isInternal(link.href)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
+      }
+    }
   function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
@@ -555,7 +573,11 @@ <h2 class="anchored" data-anchor-id="github">GitHub</h2>
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
     });
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');