Add flow diagram

protocol/.gitignore

@@ -0,0 +1 @@
+.qualtrics.yml

protocol/master-protocol.Rmd

@@ -130,6 +130,34 @@ The process of scheduling participants involves the following steps:
 
 # Data processing
 
+The following diagram depicts the post-study data processing workflow.
+
+```{r}
+library(DiagrammeR)
+
+DiagrammeR::grViz("digraph {
+graph [layout = dot, rankdir = LR]
+
+# define the global styles of the nodes. We can override these in box if we wish
+node [shape = rectangle, style = filled, fillcolor = Linen]
+
+murray [label = 'Murray', shape = folder, fillcolor = Beige]
+abramov [label = 'Abramov', shape = folder, fillcolor = Beige]
+survey [label = 'Qualtrics']
+test_computer [label = 'Task\ncomputer']
+survey_computer [label ='Survey\ncomputer']
+other_computer [label = 'Unspecified\ncomputer']
+flash_drive [label='Flash\ndrive']
+unspecified_process [label='TBD']
+box [label = 'Box.com' fillcolor = White]
+qualtrics_server [label = 'Qualtrics\nServer' fillcolor = White]
+
+# edge definitions with the node IDs
+{murray abramov} -> test_computer -> flash_drive -> other_computer -> box
+survey -> survey_computer -> qualtrics_server -> unspecified_process -> box
+}")
+```
+
 ## Gathering
 
 ### Retrieve Behavioral Data

protocol/master-protocol.html

@@ -28,6 +28,10 @@
 <script src="master-protocol_files/navigation-1.1/codefolding.js"></script>
 <link href="master-protocol_files/highlightjs-9.12.0/default.css" rel="stylesheet" />
 <script src="master-protocol_files/highlightjs-9.12.0/highlight.js"></script>
+<script src="master-protocol_files/htmlwidgets-1.3/htmlwidgets.js"></script>
+<script src="master-protocol_files/viz-0.3/viz.js"></script>
+<link href="master-protocol_files/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
+<script src="master-protocol_files/grViz-binding-1.0.1/grViz.js"></script>
 
 <style type="text/css">code{white-space: pre;}</style>
 <style type="text/css">
@@ -261,7 +265,8 @@
 
 <h1 class="title toc-ignore">Individual differences in visual perception in adults</h1>
 <h4 class="author">Rick Gilmore, Yiming Qian, &amp; Andrea Seisler</h4>
-<h4 class="date">2019-11-06 08:29:56</h4>
+<h4 class="date">2019-11-06 10:06:04</h4>
+
 
 </div>
 
@@ -938,6 +943,32 @@ <h3>Clean-up</h3>
 </div>
 <div id="data-processing" class="section level1">
 <h1>Data processing</h1>
+<p>The following diagram depicts the post-study data processing workflow.</p>
+<pre class="r"><code>library(DiagrammeR)
+
+DiagrammeR::grViz(&quot;digraph {
+graph [layout = dot, rankdir = LR]
+
+# define the global styles of the nodes. We can override these in box if we wish
+node [shape = rectangle, style = filled, fillcolor = Linen]
+
+murray [label = &#39;Murray&#39;, shape = folder, fillcolor = Beige]
+abramov [label = &#39;Abramov&#39;, shape = folder, fillcolor = Beige]
+survey [label = &#39;Qualtrics&#39;]
+test_computer [label = &#39;Task\ncomputer&#39;]
+survey_computer [label =&#39;Survey\ncomputer&#39;]
+other_computer [label = &#39;Unspecified\ncomputer&#39;]
+flash_drive [label=&#39;Flash\ndrive&#39;]
+unspecified_process [label=&#39;TBD&#39;]
+box [label = &#39;Box.com&#39; fillcolor = White]
+qualtrics_server [label = &#39;Qualtrics\nServer&#39; fillcolor = White]
+
+# edge definitions with the node IDs
+{murray abramov} -&gt; test_computer -&gt; flash_drive -&gt; other_computer -&gt; box
+survey -&gt; survey_computer -&gt; qualtrics_server -&gt; unspecified_process -&gt; box
+}&quot;)</code></pre>
+<div id="htmlwidget-46a250b15bbc3050180a" style="width:672px;height:480px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-46a250b15bbc3050180a">{"x":{"diagram":"digraph {\ngraph [layout = dot, rankdir = LR]\n\n# define the global styles of the nodes. We can override these in box if we wish\nnode [shape = rectangle, style = filled, fillcolor = Linen]\n\nmurray [label = \"Murray\", shape = folder, fillcolor = Beige]\nabramov [label = \"Abramov\", shape = folder, fillcolor = Beige]\nsurvey [label = \"Qualtrics\"]\ntest_computer [label = \"Task\ncomputer\"]\nsurvey_computer [label =\"Survey\ncomputer\"]\nother_computer [label = \"Unspecified\ncomputer\"]\nflash_drive [label=\"Flash\ndrive\"]\nunspecified_process [label=\"TBD\"]\nbox [label = \"Box.com\" fillcolor = White]\nqualtrics_server [label = \"Qualtrics\nServer\" fillcolor = White]\n\n# edge definitions with the node IDs\n{murray abramov} -> test_computer -> flash_drive -> other_computer -> box\nsurvey -> survey_computer -> qualtrics_server -> unspecified_process -> box\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <div id="gathering" class="section level2">
 <h2>Gathering</h2>
 <div id="retrieve-behavioral-data" class="section level3">

protocol/master-protocol_files/DiagrammeR-styles-0.2/styles.css

@@ -0,0 +1,14 @@
+.DiagrammeR,.grViz pre {
+  white-space: pre-wrap;       /* CSS 3 */
+  white-space: -moz-pre-wrap;  /* Mozilla, since 1999 */
+  white-space: -pre-wrap;      /* Opera 4-6 */
+  white-space: -o-pre-wrap;    /* Opera 7 */
+  word-wrap: break-word;       /* Internet Explorer 5.5+ */
+}
+
+.DiagrammeR g .label {
+  font-family: Helvetica;
+  font-size: 14px;
+  color: #333333;
+}
+

protocol/master-protocol_files/grViz-binding-1.0.1/grViz.js

@@ -0,0 +1,71 @@
+HTMLWidgets.widget({
+
+  name: 'grViz',
+
+  type: 'output',
+
+  initialize: function(el, width, height) {
+
+    return {
+      // TODO: add instance fields as required
+    }
+
+  },
+
+  renderValue: function(el, x, instance) {
+    // use this to sort of make our diagram responsive
+    //  or at a minimum fit within the bounds set by htmlwidgets
+    //  for the parent container
+    function makeResponsive(el){
+       var svg = el.getElementsByTagName("svg")[0];
+       if(svg){
+        if(svg.width) {svg.removeAttribute("width")};
+        if(svg.height) {svg.removeAttribute("height")};
+        svg.style.width = "100%";
+        svg.style.height = "100%";
+       }
+    };
+
+    if ( x.diagram != "" ) {
+
+      if ( typeof x.config === "undefined" ){
+        x.config = {};
+        x.config.engine = "dot";
+        x.config.options = {};
+      }
+
+      try {
+        el.innerHTML = Viz( x.diagram, format="svg", engine=x.config.engine, options=x.config.options );
+
+        makeResponsive(el);
+
+        // set up a container for tasks to perform after completion
+        //  one example would be add callbacks for event handling
+        //  styling
+        if (!(typeof x.tasks === "undefined") ){
+          if ( (typeof x.tasks.length === "undefined") ||
+           (typeof x.tasks === "function" ) ) {
+             // handle a function not enclosed in array
+             // should be able to remove once using jsonlite
+             x.tasks = [x.tasks];
+          }
+          x.tasks.map(function(t){
+            // for each tasks add it to the mermaid.tasks with el
+            t.call(el);
+          })
+        }        
+      } catch(e){
+        var p = document.createElement("pre")
+        p.innerText = e;
+        el.appendChild(p);
+      }
+    }
+
+  },
+
+  resize: function(el, width, height, instance) {
+
+  }
+
+
+});