fixed some bugs in the vignette

DESCRIPTION

@@ -35,6 +35,6 @@ VignetteBuilder: knitr
 License: GPL (>=2)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Depends: 
     R (>= 3.5.0)

R/AnophelesModel_db_query.R

@@ -201,7 +201,7 @@ get_net_types = function() {
 #'
 #'
 #' @examples
-#' net_insecticide_types = get_net_insecticide_types()
+#' net_insecticide_types = get_net_insecticides()
 #' print(net_insecticide_types)
 #'
 #' @export
@@ -285,8 +285,6 @@ get_net_decay = function(net_type, country, insecticide_type, n_ips, duration){
 #' @references TO DO
 #'
 #' @examples
-#' net_surv = get_net_survival_and_holed_area()
-#' print(net_surv)
 #'
 #' @export
 #'

README.md

@@ -10,6 +10,8 @@ To install the package:
 ```{r}
 devtools::install_github("SwissTPH/AnophelesModel", build_vignettes = TRUE)
 ```
+IMPORTANT: To be able to build the vignette during package installation, you need to have the following packages installed: DiagrammeR, ggpubr, and Hmisc.
+
 A documentation describing the package use cases and functions is available [here](https://swisstph.github.io/AnophelesModel/articles/AnophelesModel.html) and can also be accessed using the following R command:
 ```{r}
 browseVignettes(AnophelesModel)

docs/articles/AnophelesModel_files/grViz-binding-1.0.10/grViz.js

@@ -0,0 +1,91 @@
+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);
+
+        if (HTMLWidgets.shinyMode) {
+          // Get widget id
+          var id = el.id;
+
+          $("#" + id + " .node").click(function(e) {
+            // Get node id
+            var nodeid = e.currentTarget.id;
+            // Get node text object and make an array
+            var node_texts = $("#" + id + " #" + nodeid + " text");
+            //var node_path = $("#" + nodeid + " path")[0];
+            var text_array = node_texts.map(function() {return $(this).text(); }).toArray();
+            // Build return object *obj* with node-id, node text values and node fill
+            var obj = {
+              id: nodeid,
+              //fill: node_path.attributes.fill.nodeValue,
+              //outerHMTL: node_path.outerHTML,
+              nodeValues: text_array
+            };
+            // Send *obj* to Shiny's inputs (input$[id]+_click  e.g.: input$vtree_click))
+            Shiny.setInputValue(id + "_click", obj, {priority: "event"});
+          });
+        }
+
+        // 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) {
+  }
+});