update version.

gorkang · May 7, 2024 · a464032 · a464032
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diff --git a/.Rprofile b/.Rprofile
@@ -1,9 +1,10 @@
+options(repos = c(CRAN = "https://packagemanager.posit.co/all/__linux__/jammy/latest"))
 # Sys.getenv("R_LIBS_USER")
 
 # .libPaths(c( Sys.getenv("R_LIBS_USER") , .libPaths()))
 # .libPaths(Sys.getenv("R_LIBS_USER"))
 R_LIBS_SITE=Sys.getenv("R_LIBS_USER") # Install packages on local user library
-options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/jammy/latest"))
+options(repos = c(CRAN = "https://packagemanager.posit.co/all/__linux__/jammy/latest"))
 
 # TO avoid error: Error: Input files not all in same directory, please supply
 # explicit wd

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: jsPsychR
 Title: Create experimental paradigms with jsPsych, simulate participants and standardize the data preparation and analysis
-Version: 0.2.7
-Date: 2023-09-11
+Version: 0.3.5.900
+Date: 2024-05-07
 Authors@R: 
   c(person("Gorka", "Navarrete", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7678-8656")),
   person("Herman", "Valencia", email = "[email protected]", role = c("aut"), comment = c(ORCID = "")))

diff --git a/README.md b/README.md
@@ -13,3 +13,8 @@ We have three main tools:
 -   [jsPsychHelpeR](https://github.com/gorkang/jsPsychHelpeR): Standardize and automatize data preparation, analysis and reporting of [jsPsych](https://www.jspsych.org/) experiments created with [jsPsychMaker](#jsPsychMaker)
 
 ![](img/jsPsych-trinity.png)
+
+
+## How to cite jsPSychR
+
+Navarrete, G., & Valencia, H. (2023). Create experimental paradigms with jsPsych: Simulate Participants and Standardize the Data Preparation and Analysis, 1, 73. https://gorkang.github.io/jsPsychRmanual/, 10.5281/zenodo.8296995
diff --git a/docs/index.html b/docs/index.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.515">
+<meta name="generator" content="quarto-1.4.553">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Gorka Navarrete">
-<meta name="dcterms.date" content="2023-12-04">
+<meta name="dcterms.date" content="2024-05-01">
 
 <title>jsPsychR manual</title>
 <style>
@@ -63,6 +63,7 @@
     "search-more-match-text": "more match in this document",
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
+    "search-text-placeholder": "",
     "search-detached-cancel-button-title": "Cancel",
     "search-submit-button-title": "Submit",
     "search-label": "Search"
@@ -226,7 +227,7 @@ <h1 class="title">jsPsychR manual</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">December 4, 2023</p>
+      <p class="date">May 1, 2024</p>
     </div>
   </div>
 
@@ -287,7 +288,7 @@ <h2 class="anchored" data-anchor-id="papers-published-using-jspsychr">Papers pub
 <p>So far, the following papers using jsPsychR have been published or submitted:</p>
 <ul>
 <li><p>Neely-Prado, A., van Elk, M., Navarrete, G., Hola, F., &amp; Huepe, D. (2021). Social Adaptation in Context: The Differential Role of Religiosity and Self-Esteem in Vulnerable vs.&nbsp;Non-vulnerable Populations–A Registered Report Study. Frontiers in Psychology, 12, 5257. <a href="https://doi.org/10.3389/fpsyg.2021.519623">https://doi.org/10.3389/fpsyg.2021.519623</a></p></li>
-<li><p>Juan-Pablo Morales, Brenda E. Ryan, Vince Polito, Gorka Navarrete, Mayte Vergara, David Huepe. (Submitted). Can beliefs improve mental health? A dive into resilience during pandemic times in South America</p></li>
+<li><p>Morales, Juan Pablo and Ryan, Brenda and Polito, Vince and Vergara, Mayte and Navarrete, Gorka and Huepe, David, Can Beliefs Improve Mental Health? A Dive into Resilience During Pandemic Times in South America. <a href="http://dx.doi.org/10.2139/ssrn.4634882">http://dx.doi.org/10.2139/ssrn.4634882</a></p></li>
 </ul>
 
 
@@ -374,6 +375,24 @@ <h2 class="anchored" data-anchor-id="papers-published-using-jspsychr">Papers pub
     // clear code selection
     e.clearSelection();
   });
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp('/' + window.location.host + '/');
+    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,
@@ -408,7 +427,11 @@ <h2 class="anchored" data-anchor-id="papers-published-using-jspsychr">Papers pub
       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');
@@ -423,27 +446,6 @@ <h2 class="anchored" data-anchor-id="papers-published-using-jspsychr">Papers pub
       }
     }
     stripColumnClz(note)
-    const typesetMath = (el) => {
-      if (window.MathJax) {
-        // MathJax Typeset
-        window.MathJax.typeset([el]);
-      } else if (window.katex) {
-        // KaTeX Render
-        var mathElements = el.getElementsByClassName("math");
-        var macros = [];
-        for (var i = 0; i < mathElements.length; i++) {
-          var texText = mathElements[i].firstChild;
-          if (mathElements[i].tagName == "SPAN") {
-            window.katex.render(texText.data, mathElements[i], {
-              displayMode: mathElements[i].classList.contains('display'),
-              throwOnError: false,
-              macros: macros,
-              fleqn: false
-            });
-          }
-        }
-      }
-    }
     if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
@@ -458,10 +460,14 @@ <h2 class="anchored" data-anchor-id="papers-published-using-jspsychr">Papers pub
             break;
           }
         }
-        typesetMath(container);
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(container);
+        }
         return container.innerHTML
       } else {
-        typesetMath(note);
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(note);
+        }
         return note.innerHTML;
       }
     } else {
@@ -470,8 +476,15 @@ <h2 class="anchored" data-anchor-id="papers-published-using-jspsychr">Papers pub
       if (anchorLink) {
         anchorLink.remove();
       }
-      typesetMath(note);
-      return note.innerHTML;
+      if (window.Quarto?.typesetMath) {
+        window.Quarto.typesetMath(note);
+      }
+      // TODO in 1.5, we should make sure this works without a callout special case
+      if (note.classList.contains("callout")) {
+        return note.outerHTML;
+      } else {
+        return note.innerHTML;
+      }
     }
   }
   for (var i=0; i<xrefs.length; i++) {
@@ -696,7 +709,7 @@ <h2 class="anchored" data-anchor-id="papers-published-using-jspsychr">Papers pub
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./qmd/01-intro.html" class="pagination-link" aria-label="<span class='chapter-number'>1</span>&nbsp; <span class='chapter-title'>Reproducible experiments</span>">
+      <a href="./qmd/01-intro.html" class="pagination-link" aria-label="Reproducible experiments">
         <span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Reproducible experiments</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>

diff --git a/docs/jsPsychR-manual.pdf b/docs/jsPsychR-manual.pdf
diff --git a/docs/qmd/01-intro.html b/docs/qmd/01-intro.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-1.4.515">
+<meta name="generator" content="quarto-1.4.553">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -82,6 +82,7 @@
     "search-more-match-text": "more match in this document",
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
+    "search-text-placeholder": "",
     "search-detached-cancel-button-title": "Cancel",
     "search-submit-button-title": "Submit",
     "search-label": "Search"
@@ -363,6 +364,24 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="automatization"><span cla
     // clear code selection
     e.clearSelection();
   });
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp('/' + window.location.host + '/');
+    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,
@@ -397,7 +416,11 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="automatization"><span cla
       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');
@@ -412,27 +435,6 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="automatization"><span cla
       }
     }
     stripColumnClz(note)
-    const typesetMath = (el) => {
-      if (window.MathJax) {
-        // MathJax Typeset
-        window.MathJax.typeset([el]);
-      } else if (window.katex) {
-        // KaTeX Render
-        var mathElements = el.getElementsByClassName("math");
-        var macros = [];
-        for (var i = 0; i < mathElements.length; i++) {
-          var texText = mathElements[i].firstChild;
-          if (mathElements[i].tagName == "SPAN") {
-            window.katex.render(texText.data, mathElements[i], {
-              displayMode: mathElements[i].classList.contains('display'),
-              throwOnError: false,
-              macros: macros,
-              fleqn: false
-            });
-          }
-        }
-      }
-    }
     if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
@@ -447,10 +449,14 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="automatization"><span cla
             break;
           }
         }
-        typesetMath(container);
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(container);
+        }
         return container.innerHTML
       } else {
-        typesetMath(note);
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(note);
+        }
         return note.innerHTML;
       }
     } else {
@@ -459,8 +465,15 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="automatization"><span cla
       if (anchorLink) {
         anchorLink.remove();
       }
-      typesetMath(note);
-      return note.innerHTML;
+      if (window.Quarto?.typesetMath) {
+        window.Quarto.typesetMath(note);
+      }
+      // TODO in 1.5, we should make sure this works without a callout special case
+      if (note.classList.contains("callout")) {
+        return note.outerHTML;
+      } else {
+        return note.innerHTML;
+      }
     }
   }
   for (var i=0; i<xrefs.length; i++) {
@@ -683,12 +696,12 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="automatization"><span cla
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../index.html" class="pagination-link  aria-label=" what="" is="" jspsychr?"="">
+      <a href="../index.html" class="pagination-link" aria-label="What is jsPsychR?">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">What is jsPsychR?</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../qmd/02-QuickGuide.html" class="pagination-link" aria-label="<span class='chapter-number'>2</span>&nbsp; <span class='chapter-title'>Quick Guide</span>">
+      <a href="../qmd/02-QuickGuide.html" class="pagination-link" aria-label="Quick Guide">
         <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Quick Guide</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>