").addClass(errClass).css("position", "absolute")
+ .css("top", el.offsetTop)
+ .css("left", el.offsetLeft)
+ // setting width can push out the page size, forcing otherwise
+ // unnecessary scrollbars to appear and making it impossible for
+ // the element to shrink; so use max-width instead
+ .css("maxWidth", el.offsetWidth)
+ .css("height", el.offsetHeight);
+ errorDiv.text(err.message);
+ $el.after(errorDiv);
+
+ // Really dumb way to keep the size/position of the error in sync with
+ // the parent element as the window is resized or whatever.
+ var intId = setInterval(function() {
+ if (!errorDiv[0].parentElement) {
+ clearInterval(intId);
+ return;
+ }
+ errorDiv
+ .css("top", el.offsetTop)
+ .css("left", el.offsetLeft)
+ .css("maxWidth", el.offsetWidth)
+ .css("height", el.offsetHeight);
+ }, 500);
+ }
+ }
+ },
+ clearError: function(el) {
+ var $el = $(el);
+ var display = $el.data("restore-display-mode");
+ $el.data("restore-display-mode", null);
+
+ if (display === "inline" || display === "inline-block") {
+ if (display)
+ $el.css("display", display);
+ $(el.nextSibling).filter(".htmlwidgets-error").remove();
+ } else if (display === "block"){
+ $el.css("visibility", "inherit");
+ $(el.nextSibling).filter(".htmlwidgets-error").remove();
+ }
+ },
+ sizing: {}
+ };
+
+ // Called by widget bindings to register a new type of widget. The definition
+ // object can contain the following properties:
+ // - name (required) - A string indicating the binding name, which will be
+ // used by default as the CSS classname to look for.
+ // - initialize (optional) - A function(el) that will be called once per
+ // widget element; if a value is returned, it will be passed as the third
+ // value to renderValue.
+ // - renderValue (required) - A function(el, data, initValue) that will be
+ // called with data. Static contexts will cause this to be called once per
+ // element; Shiny apps will cause this to be called multiple times per
+ // element, as the data changes.
+ window.HTMLWidgets.widget = function(definition) {
+ if (!definition.name) {
+ throw new Error("Widget must have a name");
+ }
+ if (!definition.type) {
+ throw new Error("Widget must have a type");
+ }
+ // Currently we only support output widgets
+ if (definition.type !== "output") {
+ throw new Error("Unrecognized widget type '" + definition.type + "'");
+ }
+ // TODO: Verify that .name is a valid CSS classname
+
+ // Support new-style instance-bound definitions. Old-style class-bound
+ // definitions have one widget "object" per widget per type/class of
+ // widget; the renderValue and resize methods on such widget objects
+ // take el and instance arguments, because the widget object can't
+ // store them. New-style instance-bound definitions have one widget
+ // object per widget instance; the definition that's passed in doesn't
+ // provide renderValue or resize methods at all, just the single method
+ // factory(el, width, height)
+ // which returns an object that has renderValue(x) and resize(w, h).
+ // This enables a far more natural programming style for the widget
+ // author, who can store per-instance state using either OO-style
+ // instance fields or functional-style closure variables (I guess this
+ // is in contrast to what can only be called C-style pseudo-OO which is
+ // what we required before).
+ if (definition.factory) {
+ definition = createLegacyDefinitionAdapter(definition);
+ }
+
+ if (!definition.renderValue) {
+ throw new Error("Widget must have a renderValue function");
+ }
+
+ // For static rendering (non-Shiny), use a simple widget registration
+ // scheme. We also use this scheme for Shiny apps/documents that also
+ // contain static widgets.
+ window.HTMLWidgets.widgets = window.HTMLWidgets.widgets || [];
+ // Merge defaults into the definition; don't mutate the original definition.
+ var staticBinding = extend({}, defaults, definition);
+ overrideMethod(staticBinding, "find", function(superfunc) {
+ return function(scope) {
+ var results = superfunc(scope);
+ // Filter out Shiny outputs, we only want the static kind
+ return filterByClass(results, "html-widget-output", false);
+ };
+ });
+ window.HTMLWidgets.widgets.push(staticBinding);
+
+ if (shinyMode) {
+ // Shiny is running. Register the definition with an output binding.
+ // The definition itself will not be the output binding, instead
+ // we will make an output binding object that delegates to the
+ // definition. This is because we foolishly used the same method
+ // name (renderValue) for htmlwidgets definition and Shiny bindings
+ // but they actually have quite different semantics (the Shiny
+ // bindings receive data that includes lots of metadata that it
+ // strips off before calling htmlwidgets renderValue). We can't
+ // just ignore the difference because in some widgets it's helpful
+ // to call this.renderValue() from inside of resize(), and if
+ // we're not delegating, then that call will go to the Shiny
+ // version instead of the htmlwidgets version.
+
+ // Merge defaults with definition, without mutating either.
+ var bindingDef = extend({}, defaults, definition);
+
+ // This object will be our actual Shiny binding.
+ var shinyBinding = new Shiny.OutputBinding();
+
+ // With a few exceptions, we'll want to simply use the bindingDef's
+ // version of methods if they are available, otherwise fall back to
+ // Shiny's defaults. NOTE: If Shiny's output bindings gain additional
+ // methods in the future, and we want them to be overrideable by
+ // HTMLWidget binding definitions, then we'll need to add them to this
+ // list.
+ delegateMethod(shinyBinding, bindingDef, "getId");
+ delegateMethod(shinyBinding, bindingDef, "onValueChange");
+ delegateMethod(shinyBinding, bindingDef, "onValueError");
+ delegateMethod(shinyBinding, bindingDef, "renderError");
+ delegateMethod(shinyBinding, bindingDef, "clearError");
+ delegateMethod(shinyBinding, bindingDef, "showProgress");
+
+ // The find, renderValue, and resize are handled differently, because we
+ // want to actually decorate the behavior of the bindingDef methods.
+
+ shinyBinding.find = function(scope) {
+ var results = bindingDef.find(scope);
+
+ // Only return elements that are Shiny outputs, not static ones
+ var dynamicResults = results.filter(".html-widget-output");
+
+ // It's possible that whatever caused Shiny to think there might be
+ // new dynamic outputs, also caused there to be new static outputs.
+ // Since there might be lots of different htmlwidgets bindings, we
+ // schedule execution for later--no need to staticRender multiple
+ // times.
+ if (results.length !== dynamicResults.length)
+ scheduleStaticRender();
+
+ return dynamicResults;
+ };
+
+ // Wrap renderValue to handle initialization, which unfortunately isn't
+ // supported natively by Shiny at the time of this writing.
+
+ shinyBinding.renderValue = function(el, data) {
+ Shiny.renderDependencies(data.deps);
+ // Resolve strings marked as javascript literals to objects
+ if (!(data.evals instanceof Array)) data.evals = [data.evals];
+ for (var i = 0; data.evals && i < data.evals.length; i++) {
+ window.HTMLWidgets.evaluateStringMember(data.x, data.evals[i]);
+ }
+ if (!bindingDef.renderOnNullValue) {
+ if (data.x === null) {
+ el.style.visibility = "hidden";
+ return;
+ } else {
+ el.style.visibility = "inherit";
+ }
+ }
+ if (!elementData(el, "initialized")) {
+ initSizing(el);
+
+ elementData(el, "initialized", true);
+ if (bindingDef.initialize) {
+ var rect = el.getBoundingClientRect();
+ var result = bindingDef.initialize(el, rect.width, rect.height);
+ elementData(el, "init_result", result);
+ }
+ }
+ bindingDef.renderValue(el, data.x, elementData(el, "init_result"));
+ evalAndRun(data.jsHooks.render, elementData(el, "init_result"), [el, data.x]);
+ };
+
+ // Only override resize if bindingDef implements it
+ if (bindingDef.resize) {
+ shinyBinding.resize = function(el, width, height) {
+ // Shiny can call resize before initialize/renderValue have been
+ // called, which doesn't make sense for widgets.
+ if (elementData(el, "initialized")) {
+ bindingDef.resize(el, width, height, elementData(el, "init_result"));
+ }
+ };
+ }
+
+ Shiny.outputBindings.register(shinyBinding, bindingDef.name);
+ }
+ };
+
+ var scheduleStaticRenderTimerId = null;
+ function scheduleStaticRender() {
+ if (!scheduleStaticRenderTimerId) {
+ scheduleStaticRenderTimerId = setTimeout(function() {
+ scheduleStaticRenderTimerId = null;
+ window.HTMLWidgets.staticRender();
+ }, 1);
+ }
+ }
+
+ // Render static widgets after the document finishes loading
+ // Statically render all elements that are of this widget's class
+ window.HTMLWidgets.staticRender = function() {
+ var bindings = window.HTMLWidgets.widgets || [];
+ forEach(bindings, function(binding) {
+ var matches = binding.find(document.documentElement);
+ forEach(matches, function(el) {
+ var sizeObj = initSizing(el, binding);
+
+ var getSize = function(el) {
+ if (sizeObj) {
+ return {w: sizeObj.getWidth(), h: sizeObj.getHeight()}
+ } else {
+ var rect = el.getBoundingClientRect();
+ return {w: rect.width, h: rect.height}
+ }
+ };
+
+ if (hasClass(el, "html-widget-static-bound"))
+ return;
+ el.className = el.className + " html-widget-static-bound";
+
+ var initResult;
+ if (binding.initialize) {
+ var size = getSize(el);
+ initResult = binding.initialize(el, size.w, size.h);
+ elementData(el, "init_result", initResult);
+ }
+
+ if (binding.resize) {
+ var lastSize = getSize(el);
+ var resizeHandler = function(e) {
+ var size = getSize(el);
+ if (size.w === 0 && size.h === 0)
+ return;
+ if (size.w === lastSize.w && size.h === lastSize.h)
+ return;
+ lastSize = size;
+ binding.resize(el, size.w, size.h, initResult);
+ };
+
+ on(window, "resize", resizeHandler);
+
+ // This is needed for cases where we're running in a Shiny
+ // app, but the widget itself is not a Shiny output, but
+ // rather a simple static widget. One example of this is
+ // an rmarkdown document that has runtime:shiny and widget
+ // that isn't in a render function. Shiny only knows to
+ // call resize handlers for Shiny outputs, not for static
+ // widgets, so we do it ourselves.
+ if (window.jQuery) {
+ window.jQuery(document).on(
+ "shown.htmlwidgets shown.bs.tab.htmlwidgets shown.bs.collapse.htmlwidgets",
+ resizeHandler
+ );
+ window.jQuery(document).on(
+ "hidden.htmlwidgets hidden.bs.tab.htmlwidgets hidden.bs.collapse.htmlwidgets",
+ resizeHandler
+ );
+ }
+
+ // This is needed for the specific case of ioslides, which
+ // flips slides between display:none and display:block.
+ // Ideally we would not have to have ioslide-specific code
+ // here, but rather have ioslides raise a generic event,
+ // but the rmarkdown package just went to CRAN so the
+ // window to getting that fixed may be long.
+ if (window.addEventListener) {
+ // It's OK to limit this to window.addEventListener
+ // browsers because ioslides itself only supports
+ // such browsers.
+ on(document, "slideenter", resizeHandler);
+ on(document, "slideleave", resizeHandler);
+ }
+ }
+
+ var scriptData = document.querySelector("script[data-for='" + el.id + "'][type='application/json']");
+ if (scriptData) {
+ var data = JSON.parse(scriptData.textContent || scriptData.text);
+ // Resolve strings marked as javascript literals to objects
+ if (!(data.evals instanceof Array)) data.evals = [data.evals];
+ for (var k = 0; data.evals && k < data.evals.length; k++) {
+ window.HTMLWidgets.evaluateStringMember(data.x, data.evals[k]);
+ }
+ binding.renderValue(el, data.x, initResult);
+ evalAndRun(data.jsHooks.render, initResult, [el, data.x]);
+ }
+ });
+ });
+
+ invokePostRenderHandlers();
+ }
+
+
+ function has_jQuery3() {
+ if (!window.jQuery) {
+ return false;
+ }
+ var $version = window.jQuery.fn.jquery;
+ var $major_version = parseInt($version.split(".")[0]);
+ return $major_version >= 3;
+ }
+
+ /*
+ / Shiny 1.4 bumped jQuery from 1.x to 3.x which means jQuery's
+ / on-ready handler (i.e., $(fn)) is now asyncronous (i.e., it now
+ / really means $(setTimeout(fn)).
+ / https://jquery.com/upgrade-guide/3.0/#breaking-change-document-ready-handlers-are-now-asynchronous
+ /
+ / Since Shiny uses $() to schedule initShiny, shiny>=1.4 calls initShiny
+ / one tick later than it did before, which means staticRender() is
+ / called renderValue() earlier than (advanced) widget authors might be expecting.
+ / https://github.com/rstudio/shiny/issues/2630
+ /
+ / For a concrete example, leaflet has some methods (e.g., updateBounds)
+ / which reference Shiny methods registered in initShiny (e.g., setInputValue).
+ / Since leaflet is privy to this life-cycle, it knows to use setTimeout() to
+ / delay execution of those methods (until Shiny methods are ready)
+ / https://github.com/rstudio/leaflet/blob/18ec981/javascript/src/index.js#L266-L268
+ /
+ / Ideally widget authors wouldn't need to use this setTimeout() hack that
+ / leaflet uses to call Shiny methods on a staticRender(). In the long run,
+ / the logic initShiny should be broken up so that method registration happens
+ / right away, but binding happens later.
+ */
+ function maybeStaticRenderLater() {
+ if (shinyMode && has_jQuery3()) {
+ window.jQuery(window.HTMLWidgets.staticRender);
+ } else {
+ window.HTMLWidgets.staticRender();
+ }
+ }
+
+ if (document.addEventListener) {
+ document.addEventListener("DOMContentLoaded", function() {
+ document.removeEventListener("DOMContentLoaded", arguments.callee, false);
+ maybeStaticRenderLater();
+ }, false);
+ } else if (document.attachEvent) {
+ document.attachEvent("onreadystatechange", function() {
+ if (document.readyState === "complete") {
+ document.detachEvent("onreadystatechange", arguments.callee);
+ maybeStaticRenderLater();
+ }
+ });
+ }
+
+
+ window.HTMLWidgets.getAttachmentUrl = function(depname, key) {
+ // If no key, default to the first item
+ if (typeof(key) === "undefined")
+ key = 1;
+
+ var link = document.getElementById(depname + "-" + key + "-attachment");
+ if (!link) {
+ throw new Error("Attachment " + depname + "/" + key + " not found in document");
+ }
+ return link.getAttribute("href");
+ };
+
+ window.HTMLWidgets.dataframeToD3 = function(df) {
+ var names = [];
+ var length;
+ for (var name in df) {
+ if (df.hasOwnProperty(name))
+ names.push(name);
+ if (typeof(df[name]) !== "object" || typeof(df[name].length) === "undefined") {
+ throw new Error("All fields must be arrays");
+ } else if (typeof(length) !== "undefined" && length !== df[name].length) {
+ throw new Error("All fields must be arrays of the same length");
+ }
+ length = df[name].length;
+ }
+ var results = [];
+ var item;
+ for (var row = 0; row < length; row++) {
+ item = {};
+ for (var col = 0; col < names.length; col++) {
+ item[names[col]] = df[names[col]][row];
+ }
+ results.push(item);
+ }
+ return results;
+ };
+
+ window.HTMLWidgets.transposeArray2D = function(array) {
+ if (array.length === 0) return array;
+ var newArray = array[0].map(function(col, i) {
+ return array.map(function(row) {
+ return row[i]
+ })
+ });
+ return newArray;
+ };
+ // Split value at splitChar, but allow splitChar to be escaped
+ // using escapeChar. Any other characters escaped by escapeChar
+ // will be included as usual (including escapeChar itself).
+ function splitWithEscape(value, splitChar, escapeChar) {
+ var results = [];
+ var escapeMode = false;
+ var currentResult = "";
+ for (var pos = 0; pos < value.length; pos++) {
+ if (!escapeMode) {
+ if (value[pos] === splitChar) {
+ results.push(currentResult);
+ currentResult = "";
+ } else if (value[pos] === escapeChar) {
+ escapeMode = true;
+ } else {
+ currentResult += value[pos];
+ }
+ } else {
+ currentResult += value[pos];
+ escapeMode = false;
+ }
+ }
+ if (currentResult !== "") {
+ results.push(currentResult);
+ }
+ return results;
+ }
+ // Function authored by Yihui/JJ Allaire
+ window.HTMLWidgets.evaluateStringMember = function(o, member) {
+ var parts = splitWithEscape(member, '.', '\\');
+ for (var i = 0, l = parts.length; i < l; i++) {
+ var part = parts[i];
+ // part may be a character or 'numeric' member name
+ if (o !== null && typeof o === "object" && part in o) {
+ if (i == (l - 1)) { // if we are at the end of the line then evalulate
+ if (typeof o[part] === "string")
+ o[part] = tryEval(o[part]);
+ } else { // otherwise continue to next embedded object
+ o = o[part];
+ }
+ }
+ }
+ };
+
+ // Retrieve the HTMLWidget instance (i.e. the return value of an
+ // HTMLWidget binding's initialize() or factory() function)
+ // associated with an element, or null if none.
+ window.HTMLWidgets.getInstance = function(el) {
+ return elementData(el, "init_result");
+ };
+
+ // Finds the first element in the scope that matches the selector,
+ // and returns the HTMLWidget instance (i.e. the return value of
+ // an HTMLWidget binding's initialize() or factory() function)
+ // associated with that element, if any. If no element matches the
+ // selector, or the first matching element has no HTMLWidget
+ // instance associated with it, then null is returned.
+ //
+ // The scope argument is optional, and defaults to window.document.
+ window.HTMLWidgets.find = function(scope, selector) {
+ if (arguments.length == 1) {
+ selector = scope;
+ scope = document;
+ }
+
+ var el = scope.querySelector(selector);
+ if (el === null) {
+ return null;
+ } else {
+ return window.HTMLWidgets.getInstance(el);
+ }
+ };
+
+ // Finds all elements in the scope that match the selector, and
+ // returns the HTMLWidget instances (i.e. the return values of
+ // an HTMLWidget binding's initialize() or factory() function)
+ // associated with the elements, in an array. If elements that
+ // match the selector don't have an associated HTMLWidget
+ // instance, the returned array will contain nulls.
+ //
+ // The scope argument is optional, and defaults to window.document.
+ window.HTMLWidgets.findAll = function(scope, selector) {
+ if (arguments.length == 1) {
+ selector = scope;
+ scope = document;
+ }
+
+ var nodes = scope.querySelectorAll(selector);
+ var results = [];
+ for (var i = 0; i < nodes.length; i++) {
+ results.push(window.HTMLWidgets.getInstance(nodes[i]));
+ }
+ return results;
+ };
+
+ var postRenderHandlers = [];
+ function invokePostRenderHandlers() {
+ while (postRenderHandlers.length) {
+ var handler = postRenderHandlers.shift();
+ if (handler) {
+ handler();
+ }
+ }
+ }
+
+ // Register the given callback function to be invoked after the
+ // next time static widgets are rendered.
+ window.HTMLWidgets.addPostRenderHandler = function(callback) {
+ postRenderHandlers.push(callback);
+ };
+
+ // Takes a new-style instance-bound definition, and returns an
+ // old-style class-bound definition. This saves us from having
+ // to rewrite all the logic in this file to accomodate both
+ // types of definitions.
+ function createLegacyDefinitionAdapter(defn) {
+ var result = {
+ name: defn.name,
+ type: defn.type,
+ initialize: function(el, width, height) {
+ return defn.factory(el, width, height);
+ },
+ renderValue: function(el, x, instance) {
+ return instance.renderValue(x);
+ },
+ resize: function(el, width, height, instance) {
+ return instance.resize(width, height);
+ }
+ };
+
+ if (defn.find)
+ result.find = defn.find;
+ if (defn.renderError)
+ result.renderError = defn.renderError;
+ if (defn.clearError)
+ result.clearError = defn.clearError;
+
+ return result;
+ }
+})();
diff --git a/docs/reference/libs/plotly-binding-4.10.1/plotly.js b/docs/reference/libs/plotly-binding-4.10.1/plotly.js
new file mode 100644
index 00000000..1155269d
--- /dev/null
+++ b/docs/reference/libs/plotly-binding-4.10.1/plotly.js
@@ -0,0 +1,939 @@
+
+HTMLWidgets.widget({
+ name: "plotly",
+ type: "output",
+
+ initialize: function(el, width, height) {
+ return {};
+ },
+
+ resize: function(el, width, height, instance) {
+ if (instance.autosize) {
+ var width = instance.width || width;
+ var height = instance.height || height;
+ Plotly.relayout(el.id, {width: width, height: height});
+ }
+ },
+
+ renderValue: function(el, x, instance) {
+
+ // Plotly.relayout() mutates the plot input object, so make sure to
+ // keep a reference to the user-supplied width/height *before*
+ // we call Plotly.plot();
+ var lay = x.layout || {};
+ instance.width = lay.width;
+ instance.height = lay.height;
+ instance.autosize = lay.autosize || true;
+
+ /*
+ / 'inform the world' about highlighting options this is so other
+ / crosstalk libraries have a chance to respond to special settings
+ / such as persistent selection.
+ / AFAIK, leaflet is the only library with such intergration
+ / https://github.com/rstudio/leaflet/pull/346/files#diff-ad0c2d51ce5fdf8c90c7395b102f4265R154
+ */
+ var ctConfig = crosstalk.var('plotlyCrosstalkOpts').set(x.highlight);
+
+ if (typeof(window) !== "undefined") {
+ // make sure plots don't get created outside the network (for on-prem)
+ window.PLOTLYENV = window.PLOTLYENV || {};
+ window.PLOTLYENV.BASE_URL = x.base_url;
+
+ // Enable persistent selection when shift key is down
+ // https://stackoverflow.com/questions/1828613/check-if-a-key-is-down
+ var persistOnShift = function(e) {
+ if (!e) window.event;
+ if (e.shiftKey) {
+ x.highlight.persistent = true;
+ x.highlight.persistentShift = true;
+ } else {
+ x.highlight.persistent = false;
+ x.highlight.persistentShift = false;
+ }
+ };
+
+ // Only relevant if we haven't forced persistent mode at command line
+ if (!x.highlight.persistent) {
+ window.onmousemove = persistOnShift;
+ }
+ }
+
+ var graphDiv = document.getElementById(el.id);
+
+ // TODO: move the control panel injection strategy inside here...
+ HTMLWidgets.addPostRenderHandler(function() {
+
+ // lower the z-index of the modebar to prevent it from highjacking hover
+ // (TODO: do this via CSS?)
+ // https://github.com/ropensci/plotly/issues/956
+ // https://www.w3schools.com/jsref/prop_style_zindex.asp
+ var modebars = document.querySelectorAll(".js-plotly-plot .plotly .modebar");
+ for (var i = 0; i < modebars.length; i++) {
+ modebars[i].style.zIndex = 1;
+ }
+ });
+
+ // inject a "control panel" holding selectize/dynamic color widget(s)
+ if ((x.selectize || x.highlight.dynamic) && !instance.plotly) {
+ var flex = document.createElement("div");
+ flex.class = "plotly-crosstalk-control-panel";
+ flex.style = "display: flex; flex-wrap: wrap";
+
+ // inject the colourpicker HTML container into the flexbox
+ if (x.highlight.dynamic) {
+ var pickerDiv = document.createElement("div");
+
+ var pickerInput = document.createElement("input");
+ pickerInput.id = el.id + "-colourpicker";
+ pickerInput.placeholder = "asdasd";
+
+ var pickerLabel = document.createElement("label");
+ pickerLabel.for = pickerInput.id;
+ pickerLabel.innerHTML = "Brush color ";
+
+ pickerDiv.appendChild(pickerLabel);
+ pickerDiv.appendChild(pickerInput);
+ flex.appendChild(pickerDiv);
+ }
+
+ // inject selectize HTML containers (one for every crosstalk group)
+ if (x.selectize) {
+ var ids = Object.keys(x.selectize);
+
+ for (var i = 0; i < ids.length; i++) {
+ var container = document.createElement("div");
+ container.id = ids[i];
+ container.style = "width: 80%; height: 10%";
+ container.class = "form-group crosstalk-input-plotly-highlight";
+
+ var label = document.createElement("label");
+ label.for = ids[i];
+ label.innerHTML = x.selectize[ids[i]].group;
+ label.class = "control-label";
+
+ var selectDiv = document.createElement("div");
+ var select = document.createElement("select");
+ select.multiple = true;
+
+ selectDiv.appendChild(select);
+ container.appendChild(label);
+ container.appendChild(selectDiv);
+ flex.appendChild(container);
+ }
+ }
+
+ // finally, insert the flexbox inside the htmlwidget container,
+ // but before the plotly graph div
+ graphDiv.parentElement.insertBefore(flex, graphDiv);
+
+ if (x.highlight.dynamic) {
+ var picker = $("#" + pickerInput.id);
+ var colors = x.highlight.color || [];
+ // TODO: let users specify options?
+ var opts = {
+ value: colors[0],
+ showColour: "both",
+ palette: "limited",
+ allowedCols: colors.join(" "),
+ width: "20%",
+ height: "10%"
+ };
+ picker.colourpicker({changeDelay: 0});
+ picker.colourpicker("settings", opts);
+ picker.colourpicker("value", opts.value);
+ // inform crosstalk about a change in the current selection colour
+ var grps = x.highlight.ctGroups || [];
+ for (var i = 0; i < grps.length; i++) {
+ crosstalk.group(grps[i]).var('plotlySelectionColour')
+ .set(picker.colourpicker('value'));
+ }
+ picker.on("change", function() {
+ for (var i = 0; i < grps.length; i++) {
+ crosstalk.group(grps[i]).var('plotlySelectionColour')
+ .set(picker.colourpicker('value'));
+ }
+ });
+ }
+ }
+
+ // if no plot exists yet, create one with a particular configuration
+ if (!instance.plotly) {
+
+ var plot = Plotly.newPlot(graphDiv, x);
+ instance.plotly = true;
+
+ } else if (x.layout.transition) {
+
+ var plot = Plotly.react(graphDiv, x);
+
+ } else {
+
+ // this is essentially equivalent to Plotly.newPlot(), but avoids creating
+ // a new webgl context
+ // https://github.com/plotly/plotly.js/blob/2b24f9def901831e61282076cf3f835598d56f0e/src/plot_api/plot_api.js#L531-L532
+
+ // TODO: restore crosstalk selections?
+ Plotly.purge(graphDiv);
+ // TODO: why is this necessary to get crosstalk working?
+ graphDiv.data = undefined;
+ graphDiv.layout = undefined;
+ var plot = Plotly.newPlot(graphDiv, x);
+ }
+
+ // Trigger plotly.js calls defined via `plotlyProxy()`
+ plot.then(function() {
+ if (HTMLWidgets.shinyMode) {
+ Shiny.addCustomMessageHandler("plotly-calls", function(msg) {
+ var gd = document.getElementById(msg.id);
+ if (!gd) {
+ throw new Error("Couldn't find plotly graph with id: " + msg.id);
+ }
+ // This isn't an official plotly.js method, but it's the only current way to
+ // change just the configuration of a plot
+ // https://community.plot.ly/t/update-config-function/9057
+ if (msg.method == "reconfig") {
+ Plotly.react(gd, gd.data, gd.layout, msg.args);
+ return;
+ }
+ if (!Plotly[msg.method]) {
+ throw new Error("Unknown method " + msg.method);
+ }
+ var args = [gd].concat(msg.args);
+ Plotly[msg.method].apply(null, args);
+ });
+ }
+
+ // plotly's mapbox API doesn't currently support setting bounding boxes
+ // https://www.mapbox.com/mapbox-gl-js/example/fitbounds/
+ // so we do this manually...
+ // TODO: make sure this triggers on a redraw and relayout as well as on initial draw
+ var mapboxIDs = graphDiv._fullLayout._subplots.mapbox || [];
+ for (var i = 0; i < mapboxIDs.length; i++) {
+ var id = mapboxIDs[i];
+ var mapOpts = x.layout[id] || {};
+ var args = mapOpts._fitBounds || {};
+ if (!args) {
+ continue;
+ }
+ var mapObj = graphDiv._fullLayout[id]._subplot.map;
+ mapObj.fitBounds(args.bounds, args.options);
+ }
+
+ });
+
+ // Attach attributes (e.g., "key", "z") to plotly event data
+ function eventDataWithKey(eventData) {
+ if (eventData === undefined || !eventData.hasOwnProperty("points")) {
+ return null;
+ }
+ return eventData.points.map(function(pt) {
+ var obj = {
+ curveNumber: pt.curveNumber,
+ pointNumber: pt.pointNumber,
+ x: pt.x,
+ y: pt.y
+ };
+
+ // If 'z' is reported with the event data, then use it!
+ if (pt.hasOwnProperty("z")) {
+ obj.z = pt.z;
+ }
+
+ if (pt.hasOwnProperty("customdata")) {
+ obj.customdata = pt.customdata;
+ }
+
+ /*
+ TL;DR: (I think) we have to select the graph div (again) to attach keys...
+
+ Why? Remember that crosstalk will dynamically add/delete traces
+ (see traceManager.prototype.updateSelection() below)
+ For this reason, we can't simply grab keys from x.data (like we did previously)
+ Moreover, we can't use _fullData, since that doesn't include
+ unofficial attributes. It's true that click/hover events fire with
+ pt.data, but drag events don't...
+ */
+ var gd = document.getElementById(el.id);
+ var trace = gd.data[pt.curveNumber];
+
+ if (!trace._isSimpleKey) {
+ var attrsToAttach = ["key"];
+ } else {
+ // simple keys fire the whole key
+ obj.key = trace.key;
+ var attrsToAttach = [];
+ }
+
+ for (var i = 0; i < attrsToAttach.length; i++) {
+ var attr = trace[attrsToAttach[i]];
+ if (Array.isArray(attr)) {
+ if (typeof pt.pointNumber === "number") {
+ obj[attrsToAttach[i]] = attr[pt.pointNumber];
+ } else if (Array.isArray(pt.pointNumber)) {
+ obj[attrsToAttach[i]] = attr[pt.pointNumber[0]][pt.pointNumber[1]];
+ } else if (Array.isArray(pt.pointNumbers)) {
+ obj[attrsToAttach[i]] = pt.pointNumbers.map(function(idx) { return attr[idx]; });
+ }
+ }
+ }
+ return obj;
+ });
+ }
+
+
+ var legendEventData = function(d) {
+ // if legendgroup is not relevant just return the trace
+ var trace = d.data[d.curveNumber];
+ if (!trace.legendgroup) return trace;
+
+ // if legendgroup was specified, return all traces that match the group
+ var legendgrps = d.data.map(function(trace){ return trace.legendgroup; });
+ var traces = [];
+ for (i = 0; i < legendgrps.length; i++) {
+ if (legendgrps[i] == trace.legendgroup) {
+ traces.push(d.data[i]);
+ }
+ }
+
+ return traces;
+ };
+
+
+ // send user input event data to shiny
+ if (HTMLWidgets.shinyMode && Shiny.setInputValue) {
+
+ // Some events clear other input values
+ // TODO: always register these?
+ var eventClearMap = {
+ plotly_deselect: ["plotly_selected", "plotly_selecting", "plotly_brushed", "plotly_brushing", "plotly_click"],
+ plotly_unhover: ["plotly_hover"],
+ plotly_doubleclick: ["plotly_click"]
+ };
+
+ Object.keys(eventClearMap).map(function(evt) {
+ graphDiv.on(evt, function() {
+ var inputsToClear = eventClearMap[evt];
+ inputsToClear.map(function(input) {
+ Shiny.setInputValue(input + "-" + x.source, null, {priority: "event"});
+ });
+ });
+ });
+
+ var eventDataFunctionMap = {
+ plotly_click: eventDataWithKey,
+ plotly_sunburstclick: eventDataWithKey,
+ plotly_hover: eventDataWithKey,
+ plotly_unhover: eventDataWithKey,
+ // If 'plotly_selected' has already been fired, and you click
+ // on the plot afterwards, this event fires `undefined`?!?
+ // That might be considered a plotly.js bug, but it doesn't make
+ // sense for this input change to occur if `d` is falsy because,
+ // even in the empty selection case, `d` is truthy (an object),
+ // and the 'plotly_deselect' event will reset this input
+ plotly_selected: function(d) { if (d) { return eventDataWithKey(d); } },
+ plotly_selecting: function(d) { if (d) { return eventDataWithKey(d); } },
+ plotly_brushed: function(d) {
+ if (d) { return d.range ? d.range : d.lassoPoints; }
+ },
+ plotly_brushing: function(d) {
+ if (d) { return d.range ? d.range : d.lassoPoints; }
+ },
+ plotly_legendclick: legendEventData,
+ plotly_legenddoubleclick: legendEventData,
+ plotly_clickannotation: function(d) { return d.fullAnnotation }
+ };
+
+ var registerShinyValue = function(event) {
+ var eventDataPreProcessor = eventDataFunctionMap[event] || function(d) { return d ? d : el.id };
+ // some events are unique to the R package
+ var plotlyJSevent = (event == "plotly_brushed") ? "plotly_selected" : (event == "plotly_brushing") ? "plotly_selecting" : event;
+ // register the event
+ graphDiv.on(plotlyJSevent, function(d) {
+ Shiny.setInputValue(
+ event + "-" + x.source,
+ JSON.stringify(eventDataPreProcessor(d)),
+ {priority: "event"}
+ );
+ });
+ }
+
+ var shinyEvents = x.shinyEvents || [];
+ shinyEvents.map(registerShinyValue);
+ }
+
+ // Given an array of {curveNumber: x, pointNumber: y} objects,
+ // return a hash of {
+ // set1: {value: [key1, key2, ...], _isSimpleKey: false},
+ // set2: {value: [key3, key4, ...], _isSimpleKey: false}
+ // }
+ function pointsToKeys(points) {
+ var keysBySet = {};
+ for (var i = 0; i < points.length; i++) {
+
+ var trace = graphDiv.data[points[i].curveNumber];
+ if (!trace.key || !trace.set) {
+ continue;
+ }
+
+ // set defaults for this keySet
+ // note that we don't track the nested property (yet) since we always
+ // emit the union -- http://cpsievert.github.io/talks/20161212b/#21
+ keysBySet[trace.set] = keysBySet[trace.set] || {
+ value: [],
+ _isSimpleKey: trace._isSimpleKey
+ };
+
+ // Use pointNumber by default, but aggregated traces should emit pointNumbers
+ var ptNum = points[i].pointNumber;
+ var hasPtNum = typeof ptNum === "number";
+ var ptNum = hasPtNum ? ptNum : points[i].pointNumbers;
+
+ // selecting a point of a "simple" trace means: select the
+ // entire key attached to this trace, which is useful for,
+ // say clicking on a fitted line to select corresponding observations
+ var key = trace._isSimpleKey ? trace.key : Array.isArray(ptNum) ? ptNum.map(function(idx) { return trace.key[idx]; }) : trace.key[ptNum];
+ // http://stackoverflow.com/questions/10865025/merge-flatten-an-array-of-arrays-in-javascript
+ var keyFlat = trace._isNestedKey ? [].concat.apply([], key) : key;
+
+ // TODO: better to only add new values?
+ keysBySet[trace.set].value = keysBySet[trace.set].value.concat(keyFlat);
+ }
+
+ return keysBySet;
+ }
+
+
+ x.highlight.color = x.highlight.color || [];
+ // make sure highlight color is an array
+ if (!Array.isArray(x.highlight.color)) {
+ x.highlight.color = [x.highlight.color];
+ }
+
+ var traceManager = new TraceManager(graphDiv, x.highlight);
+
+ // Gather all *unique* sets.
+ var allSets = [];
+ for (var curveIdx = 0; curveIdx < x.data.length; curveIdx++) {
+ var newSet = x.data[curveIdx].set;
+ if (newSet) {
+ if (allSets.indexOf(newSet) === -1) {
+ allSets.push(newSet);
+ }
+ }
+ }
+
+ // register event listeners for all sets
+ for (var i = 0; i < allSets.length; i++) {
+
+ var set = allSets[i];
+ var selection = new crosstalk.SelectionHandle(set);
+ var filter = new crosstalk.FilterHandle(set);
+
+ var filterChange = function(e) {
+ removeBrush(el);
+ traceManager.updateFilter(set, e.value);
+ };
+ filter.on("change", filterChange);
+
+
+ var selectionChange = function(e) {
+
+ // Workaround for 'plotly_selected' now firing previously selected
+ // points (in addition to new ones) when holding shift key. In our case,
+ // we just want the new keys
+ if (x.highlight.on === "plotly_selected" && x.highlight.persistentShift) {
+ // https://stackoverflow.com/questions/1187518/how-to-get-the-difference-between-two-arrays-in-javascript
+ Array.prototype.diff = function(a) {
+ return this.filter(function(i) {return a.indexOf(i) < 0;});
+ };
+ e.value = e.value.diff(e.oldValue);
+ }
+
+ // array of "event objects" tracking the selection history
+ // this is used to avoid adding redundant selections
+ var selectionHistory = crosstalk.var("plotlySelectionHistory").get() || [];
+
+ // Construct an event object "defining" the current event.
+ var event = {
+ receiverID: traceManager.gd.id,
+ plotlySelectionColour: crosstalk.group(set).var("plotlySelectionColour").get()
+ };
+ event[set] = e.value;
+ // TODO: is there a smarter way to check object equality?
+ if (selectionHistory.length > 0) {
+ var ev = JSON.stringify(event);
+ for (var i = 0; i < selectionHistory.length; i++) {
+ var sel = JSON.stringify(selectionHistory[i]);
+ if (sel == ev) {
+ return;
+ }
+ }
+ }
+
+ // accumulate history for persistent selection
+ if (!x.highlight.persistent) {
+ selectionHistory = [event];
+ } else {
+ selectionHistory.push(event);
+ }
+ crosstalk.var("plotlySelectionHistory").set(selectionHistory);
+
+ // do the actual updating of traces, frames, and the selectize widget
+ traceManager.updateSelection(set, e.value);
+ // https://github.com/selectize/selectize.js/blob/master/docs/api.md#methods_items
+ if (x.selectize) {
+ if (!x.highlight.persistent || e.value === null) {
+ selectize.clear(true);
+ }
+ selectize.addItems(e.value, true);
+ selectize.close();
+ }
+ }
+ selection.on("change", selectionChange);
+
+ // Set a crosstalk variable selection value, triggering an update
+ var turnOn = function(e) {
+ if (e) {
+ var selectedKeys = pointsToKeys(e.points);
+ // Keys are group names, values are array of selected keys from group.
+ for (var set in selectedKeys) {
+ if (selectedKeys.hasOwnProperty(set)) {
+ selection.set(selectedKeys[set].value, {sender: el});
+ }
+ }
+ }
+ };
+ if (x.highlight.debounce > 0) {
+ turnOn = debounce(turnOn, x.highlight.debounce);
+ }
+ graphDiv.on(x.highlight.on, turnOn);
+
+ graphDiv.on(x.highlight.off, function turnOff(e) {
+ // remove any visual clues
+ removeBrush(el);
+ // remove any selection history
+ crosstalk.var("plotlySelectionHistory").set(null);
+ // trigger the actual removal of selection traces
+ selection.set(null, {sender: el});
+ });
+
+ // register a callback for selectize so that there is bi-directional
+ // communication between the widget and direct manipulation events
+ if (x.selectize) {
+ var selectizeID = Object.keys(x.selectize)[i];
+ var items = x.selectize[selectizeID].items;
+ var first = [{value: "", label: "(All)"}];
+ var opts = {
+ options: first.concat(items),
+ searchField: "label",
+ valueField: "value",
+ labelField: "label",
+ maxItems: 50
+ };
+ var select = $("#" + selectizeID).find("select")[0];
+ var selectize = $(select).selectize(opts)[0].selectize;
+ // NOTE: this callback is triggered when *directly* altering
+ // dropdown items
+ selectize.on("change", function() {
+ var currentItems = traceManager.groupSelections[set] || [];
+ if (!x.highlight.persistent) {
+ removeBrush(el);
+ for (var i = 0; i < currentItems.length; i++) {
+ selectize.removeItem(currentItems[i], true);
+ }
+ }
+ var newItems = selectize.items.filter(function(idx) {
+ return currentItems.indexOf(idx) < 0;
+ });
+ if (newItems.length > 0) {
+ traceManager.updateSelection(set, newItems);
+ } else {
+ // Item has been removed...
+ // TODO: this logic won't work for dynamically changing palette
+ traceManager.updateSelection(set, null);
+ traceManager.updateSelection(set, selectize.items);
+ }
+ });
+ }
+ } // end of selectionChange
+
+ } // end of renderValue
+}); // end of widget definition
+
+/**
+ * @param graphDiv The Plotly graph div
+ * @param highlight An object with options for updating selection(s)
+ */
+function TraceManager(graphDiv, highlight) {
+ // The Plotly graph div
+ this.gd = graphDiv;
+
+ // Preserve the original data.
+ // TODO: try using Lib.extendFlat() as done in
+ // https://github.com/plotly/plotly.js/pull/1136
+ this.origData = JSON.parse(JSON.stringify(graphDiv.data));
+
+ // avoid doing this over and over
+ this.origOpacity = [];
+ for (var i = 0; i < this.origData.length; i++) {
+ this.origOpacity[i] = this.origData[i].opacity === 0 ? 0 : (this.origData[i].opacity || 1);
+ }
+
+ // key: group name, value: null or array of keys representing the
+ // most recently received selection for that group.
+ this.groupSelections = {};
+
+ // selection parameters (e.g., transient versus persistent selection)
+ this.highlight = highlight;
+}
+
+TraceManager.prototype.close = function() {
+ // TODO: Unhook all event handlers
+};
+
+TraceManager.prototype.updateFilter = function(group, keys) {
+
+ if (typeof(keys) === "undefined" || keys === null) {
+
+ this.gd.data = JSON.parse(JSON.stringify(this.origData));
+
+ } else {
+
+ var traces = [];
+ for (var i = 0; i < this.origData.length; i++) {
+ var trace = this.origData[i];
+ if (!trace.key || trace.set !== group) {
+ continue;
+ }
+ var matchFunc = getMatchFunc(trace);
+ var matches = matchFunc(trace.key, keys);
+
+ if (matches.length > 0) {
+ if (!trace._isSimpleKey) {
+ // subsetArrayAttrs doesn't mutate trace (it makes a modified clone)
+ trace = subsetArrayAttrs(trace, matches);
+ }
+ traces.push(trace);
+ }
+ }
+ this.gd.data = traces;
+ }
+
+ Plotly.redraw(this.gd);
+
+ // NOTE: we purposely do _not_ restore selection(s), since on filter,
+ // axis likely will update, changing the pixel -> data mapping, leading
+ // to a likely mismatch in the brush outline and highlighted marks
+
+};
+
+TraceManager.prototype.updateSelection = function(group, keys) {
+
+ if (keys !== null && !Array.isArray(keys)) {
+ throw new Error("Invalid keys argument; null or array expected");
+ }
+
+ // if selection has been cleared, or if this is transient
+ // selection, delete the "selection traces"
+ var nNewTraces = this.gd.data.length - this.origData.length;
+ if (keys === null || !this.highlight.persistent && nNewTraces > 0) {
+ var tracesToRemove = [];
+ for (var i = 0; i < this.gd.data.length; i++) {
+ if (this.gd.data[i]._isCrosstalkTrace) tracesToRemove.push(i);
+ }
+ Plotly.deleteTraces(this.gd, tracesToRemove);
+ this.groupSelections[group] = keys;
+ } else {
+ // add to the groupSelection, rather than overwriting it
+ // TODO: can this be removed?
+ this.groupSelections[group] = this.groupSelections[group] || [];
+ for (var i = 0; i < keys.length; i++) {
+ var k = keys[i];
+ if (this.groupSelections[group].indexOf(k) < 0) {
+ this.groupSelections[group].push(k);
+ }
+ }
+ }
+
+ if (keys === null) {
+
+ Plotly.restyle(this.gd, {"opacity": this.origOpacity});
+
+ } else if (keys.length >= 1) {
+
+ // placeholder for new "selection traces"
+ var traces = [];
+ // this variable is set in R/highlight.R
+ var selectionColour = crosstalk.group(group).var("plotlySelectionColour").get() ||
+ this.highlight.color[0];
+
+ for (var i = 0; i < this.origData.length; i++) {
+ // TODO: try using Lib.extendFlat() as done in
+ // https://github.com/plotly/plotly.js/pull/1136
+ var trace = JSON.parse(JSON.stringify(this.gd.data[i]));
+ if (!trace.key || trace.set !== group) {
+ continue;
+ }
+ // Get sorted array of matching indices in trace.key
+ var matchFunc = getMatchFunc(trace);
+ var matches = matchFunc(trace.key, keys);
+
+ if (matches.length > 0) {
+ // If this is a "simple" key, that means select the entire trace
+ if (!trace._isSimpleKey) {
+ trace = subsetArrayAttrs(trace, matches);
+ }
+ // reach into the full trace object so we can properly reflect the
+ // selection attributes in every view
+ var d = this.gd._fullData[i];
+
+ /*
+ / Recursively inherit selection attributes from various sources,
+ / in order of preference:
+ / (1) official plotly.js selected attribute
+ / (2) highlight(selected = attrs_selected(...))
+ */
+ // TODO: it would be neat to have a dropdown to dynamically specify these!
+ $.extend(true, trace, this.highlight.selected);
+
+ // if it is defined, override color with the "dynamic brush color""
+ if (d.marker) {
+ trace.marker = trace.marker || {};
+ trace.marker.color = selectionColour || trace.marker.color || d.marker.color;
+ }
+ if (d.line) {
+ trace.line = trace.line || {};
+ trace.line.color = selectionColour || trace.line.color || d.line.color;
+ }
+ if (d.textfont) {
+ trace.textfont = trace.textfont || {};
+ trace.textfont.color = selectionColour || trace.textfont.color || d.textfont.color;
+ }
+ if (d.fillcolor) {
+ // TODO: should selectionColour inherit alpha from the existing fillcolor?
+ trace.fillcolor = selectionColour || trace.fillcolor || d.fillcolor;
+ }
+ // attach a sensible name/legendgroup
+ trace.name = trace.name || keys.join("
");
+ trace.legendgroup = trace.legendgroup || keys.join("
");
+
+ // keep track of mapping between this new trace and the trace it targets
+ // (necessary for updating frames to reflect the selection traces)
+ trace._originalIndex = i;
+ trace._newIndex = this.gd._fullData.length + traces.length;
+ trace._isCrosstalkTrace = true;
+ traces.push(trace);
+ }
+ }
+
+ if (traces.length > 0) {
+
+ Plotly.addTraces(this.gd, traces).then(function(gd) {
+ // incrementally add selection traces to frames
+ // (this is heavily inspired by Plotly.Plots.modifyFrames()
+ // in src/plots/plots.js)
+ var _hash = gd._transitionData._frameHash;
+ var _frames = gd._transitionData._frames || [];
+
+ for (var i = 0; i < _frames.length; i++) {
+
+ // add to _frames[i].traces *if* this frame references selected trace(s)
+ var newIndices = [];
+ for (var j = 0; j < traces.length; j++) {
+ var tr = traces[j];
+ if (_frames[i].traces.indexOf(tr._originalIndex) > -1) {
+ newIndices.push(tr._newIndex);
+ _frames[i].traces.push(tr._newIndex);
+ }
+ }
+
+ // nothing to do...
+ if (newIndices.length === 0) {
+ continue;
+ }
+
+ var ctr = 0;
+ var nFrameTraces = _frames[i].data.length;
+
+ for (var j = 0; j < nFrameTraces; j++) {
+ var frameTrace = _frames[i].data[j];
+ if (!frameTrace.key || frameTrace.set !== group) {
+ continue;
+ }
+
+ var matchFunc = getMatchFunc(frameTrace);
+ var matches = matchFunc(frameTrace.key, keys);
+
+ if (matches.length > 0) {
+ if (!trace._isSimpleKey) {
+ frameTrace = subsetArrayAttrs(frameTrace, matches);
+ }
+ var d = gd._fullData[newIndices[ctr]];
+ if (d.marker) {
+ frameTrace.marker = d.marker;
+ }
+ if (d.line) {
+ frameTrace.line = d.line;
+ }
+ if (d.textfont) {
+ frameTrace.textfont = d.textfont;
+ }
+ ctr = ctr + 1;
+ _frames[i].data.push(frameTrace);
+ }
+ }
+
+ // update gd._transitionData._frameHash
+ _hash[_frames[i].name] = _frames[i];
+ }
+
+ });
+
+ // dim traces that have a set matching the set of selection sets
+ var tracesToDim = [],
+ opacities = [],
+ sets = Object.keys(this.groupSelections),
+ n = this.origData.length;
+
+ for (var i = 0; i < n; i++) {
+ var opacity = this.origOpacity[i] || 1;
+ // have we already dimmed this trace? Or is this even worth doing?
+ if (opacity !== this.gd._fullData[i].opacity || this.highlight.opacityDim === 1) {
+ continue;
+ }
+ // is this set an element of the set of selection sets?
+ var matches = findMatches(sets, [this.gd.data[i].set]);
+ if (matches.length) {
+ tracesToDim.push(i);
+ opacities.push(opacity * this.highlight.opacityDim);
+ }
+ }
+
+ if (tracesToDim.length > 0) {
+ Plotly.restyle(this.gd, {"opacity": opacities}, tracesToDim);
+ // turn off the selected/unselected API
+ Plotly.restyle(this.gd, {"selectedpoints": null});
+ }
+
+ }
+
+ }
+};
+
+/*
+Note: in all of these match functions, we assume needleSet (i.e. the selected keys)
+is a 1D (or flat) array. The real difference is the meaning of haystack.
+findMatches() does the usual thing you'd expect for
+linked brushing on a scatterplot matrix. findSimpleMatches() returns a match iff
+haystack is a subset of the needleSet. findNestedMatches() returns
+*/
+
+function getMatchFunc(trace) {
+ return (trace._isNestedKey) ? findNestedMatches :
+ (trace._isSimpleKey) ? findSimpleMatches : findMatches;
+}
+
+// find matches for "flat" keys
+function findMatches(haystack, needleSet) {
+ var matches = [];
+ haystack.forEach(function(obj, i) {
+ if (obj === null || needleSet.indexOf(obj) >= 0) {
+ matches.push(i);
+ }
+ });
+ return matches;
+}
+
+// find matches for "simple" keys
+function findSimpleMatches(haystack, needleSet) {
+ var match = haystack.every(function(val) {
+ return val === null || needleSet.indexOf(val) >= 0;
+ });
+ // yes, this doesn't make much sense other than conforming
+ // to the output type of the other match functions
+ return (match) ? [0] : []
+}
+
+// find matches for a "nested" haystack (2D arrays)
+function findNestedMatches(haystack, needleSet) {
+ var matches = [];
+ for (var i = 0; i < haystack.length; i++) {
+ var hay = haystack[i];
+ var match = hay.every(function(val) {
+ return val === null || needleSet.indexOf(val) >= 0;
+ });
+ if (match) {
+ matches.push(i);
+ }
+ }
+ return matches;
+}
+
+function isPlainObject(obj) {
+ return (
+ Object.prototype.toString.call(obj) === '[object Object]' &&
+ Object.getPrototypeOf(obj) === Object.prototype
+ );
+}
+
+function subsetArrayAttrs(obj, indices) {
+ var newObj = {};
+ Object.keys(obj).forEach(function(k) {
+ var val = obj[k];
+
+ if (k.charAt(0) === "_") {
+ newObj[k] = val;
+ } else if (k === "transforms" && Array.isArray(val)) {
+ newObj[k] = val.map(function(transform) {
+ return subsetArrayAttrs(transform, indices);
+ });
+ } else if (k === "colorscale" && Array.isArray(val)) {
+ newObj[k] = val;
+ } else if (isPlainObject(val)) {
+ newObj[k] = subsetArrayAttrs(val, indices);
+ } else if (Array.isArray(val)) {
+ newObj[k] = subsetArray(val, indices);
+ } else {
+ newObj[k] = val;
+ }
+ });
+ return newObj;
+}
+
+function subsetArray(arr, indices) {
+ var result = [];
+ for (var i = 0; i < indices.length; i++) {
+ result.push(arr[indices[i]]);
+ }
+ return result;
+}
+
+// Convenience function for removing plotly's brush
+function removeBrush(el) {
+ var outlines = el.querySelectorAll(".select-outline");
+ for (var i = 0; i < outlines.length; i++) {
+ outlines[i].remove();
+ }
+}
+
+
+// https://davidwalsh.name/javascript-debounce-function
+
+// Returns a function, that, as long as it continues to be invoked, will not
+// be triggered. The function will be called after it stops being called for
+// N milliseconds. If `immediate` is passed, trigger the function on the
+// leading edge, instead of the trailing.
+function debounce(func, wait, immediate) {
+ var timeout;
+ return function() {
+ var context = this, args = arguments;
+ var later = function() {
+ timeout = null;
+ if (!immediate) func.apply(context, args);
+ };
+ var callNow = immediate && !timeout;
+ clearTimeout(timeout);
+ timeout = setTimeout(later, wait);
+ if (callNow) func.apply(context, args);
+ };
+};
diff --git a/docs/reference/libs/plotly-binding-4.10.3/plotly.js b/docs/reference/libs/plotly-binding-4.10.3/plotly.js
new file mode 100644
index 00000000..7a2a143b
--- /dev/null
+++ b/docs/reference/libs/plotly-binding-4.10.3/plotly.js
@@ -0,0 +1,941 @@
+
+HTMLWidgets.widget({
+ name: "plotly",
+ type: "output",
+
+ initialize: function(el, width, height) {
+ return {};
+ },
+
+ resize: function(el, width, height, instance) {
+ if (instance.autosize) {
+ var width = instance.width || width;
+ var height = instance.height || height;
+ Plotly.relayout(el.id, {width: width, height: height});
+ }
+ },
+
+ renderValue: function(el, x, instance) {
+
+ // Plotly.relayout() mutates the plot input object, so make sure to
+ // keep a reference to the user-supplied width/height *before*
+ // we call Plotly.plot();
+ var lay = x.layout || {};
+ instance.width = lay.width;
+ instance.height = lay.height;
+ instance.autosize = lay.autosize || true;
+
+ /*
+ / 'inform the world' about highlighting options this is so other
+ / crosstalk libraries have a chance to respond to special settings
+ / such as persistent selection.
+ / AFAIK, leaflet is the only library with such intergration
+ / https://github.com/rstudio/leaflet/pull/346/files#diff-ad0c2d51ce5fdf8c90c7395b102f4265R154
+ */
+ var ctConfig = crosstalk.var('plotlyCrosstalkOpts').set(x.highlight);
+
+ if (typeof(window) !== "undefined") {
+ // make sure plots don't get created outside the network (for on-prem)
+ window.PLOTLYENV = window.PLOTLYENV || {};
+ window.PLOTLYENV.BASE_URL = x.base_url;
+
+ // Enable persistent selection when shift key is down
+ // https://stackoverflow.com/questions/1828613/check-if-a-key-is-down
+ var persistOnShift = function(e) {
+ if (!e) window.event;
+ if (e.shiftKey) {
+ x.highlight.persistent = true;
+ x.highlight.persistentShift = true;
+ } else {
+ x.highlight.persistent = false;
+ x.highlight.persistentShift = false;
+ }
+ };
+
+ // Only relevant if we haven't forced persistent mode at command line
+ if (!x.highlight.persistent) {
+ window.onmousemove = persistOnShift;
+ }
+ }
+
+ var graphDiv = document.getElementById(el.id);
+
+ // TODO: move the control panel injection strategy inside here...
+ HTMLWidgets.addPostRenderHandler(function() {
+
+ // lower the z-index of the modebar to prevent it from highjacking hover
+ // (TODO: do this via CSS?)
+ // https://github.com/ropensci/plotly/issues/956
+ // https://www.w3schools.com/jsref/prop_style_zindex.asp
+ var modebars = document.querySelectorAll(".js-plotly-plot .plotly .modebar");
+ for (var i = 0; i < modebars.length; i++) {
+ modebars[i].style.zIndex = 1;
+ }
+ });
+
+ // inject a "control panel" holding selectize/dynamic color widget(s)
+ if ((x.selectize || x.highlight.dynamic) && !instance.plotly) {
+ var flex = document.createElement("div");
+ flex.class = "plotly-crosstalk-control-panel";
+ flex.style = "display: flex; flex-wrap: wrap";
+
+ // inject the colourpicker HTML container into the flexbox
+ if (x.highlight.dynamic) {
+ var pickerDiv = document.createElement("div");
+
+ var pickerInput = document.createElement("input");
+ pickerInput.id = el.id + "-colourpicker";
+ pickerInput.placeholder = "asdasd";
+
+ var pickerLabel = document.createElement("label");
+ pickerLabel.for = pickerInput.id;
+ pickerLabel.innerHTML = "Brush color ";
+
+ pickerDiv.appendChild(pickerLabel);
+ pickerDiv.appendChild(pickerInput);
+ flex.appendChild(pickerDiv);
+ }
+
+ // inject selectize HTML containers (one for every crosstalk group)
+ if (x.selectize) {
+ var ids = Object.keys(x.selectize);
+
+ for (var i = 0; i < ids.length; i++) {
+ var container = document.createElement("div");
+ container.id = ids[i];
+ container.style = "width: 80%; height: 10%";
+ container.class = "form-group crosstalk-input-plotly-highlight";
+
+ var label = document.createElement("label");
+ label.for = ids[i];
+ label.innerHTML = x.selectize[ids[i]].group;
+ label.class = "control-label";
+
+ var selectDiv = document.createElement("div");
+ var select = document.createElement("select");
+ select.multiple = true;
+
+ selectDiv.appendChild(select);
+ container.appendChild(label);
+ container.appendChild(selectDiv);
+ flex.appendChild(container);
+ }
+ }
+
+ // finally, insert the flexbox inside the htmlwidget container,
+ // but before the plotly graph div
+ graphDiv.parentElement.insertBefore(flex, graphDiv);
+
+ if (x.highlight.dynamic) {
+ var picker = $("#" + pickerInput.id);
+ var colors = x.highlight.color || [];
+ // TODO: let users specify options?
+ var opts = {
+ value: colors[0],
+ showColour: "both",
+ palette: "limited",
+ allowedCols: colors.join(" "),
+ width: "20%",
+ height: "10%"
+ };
+ picker.colourpicker({changeDelay: 0});
+ picker.colourpicker("settings", opts);
+ picker.colourpicker("value", opts.value);
+ // inform crosstalk about a change in the current selection colour
+ var grps = x.highlight.ctGroups || [];
+ for (var i = 0; i < grps.length; i++) {
+ crosstalk.group(grps[i]).var('plotlySelectionColour')
+ .set(picker.colourpicker('value'));
+ }
+ picker.on("change", function() {
+ for (var i = 0; i < grps.length; i++) {
+ crosstalk.group(grps[i]).var('plotlySelectionColour')
+ .set(picker.colourpicker('value'));
+ }
+ });
+ }
+ }
+
+ // if no plot exists yet, create one with a particular configuration
+ if (!instance.plotly) {
+
+ var plot = Plotly.newPlot(graphDiv, x);
+ instance.plotly = true;
+
+ } else if (x.layout.transition) {
+
+ var plot = Plotly.react(graphDiv, x);
+
+ } else {
+
+ // this is essentially equivalent to Plotly.newPlot(), but avoids creating
+ // a new webgl context
+ // https://github.com/plotly/plotly.js/blob/2b24f9def901831e61282076cf3f835598d56f0e/src/plot_api/plot_api.js#L531-L532
+
+ // TODO: restore crosstalk selections?
+ Plotly.purge(graphDiv);
+ // TODO: why is this necessary to get crosstalk working?
+ graphDiv.data = undefined;
+ graphDiv.layout = undefined;
+ var plot = Plotly.newPlot(graphDiv, x);
+ }
+
+ // Trigger plotly.js calls defined via `plotlyProxy()`
+ plot.then(function() {
+ if (HTMLWidgets.shinyMode) {
+ Shiny.addCustomMessageHandler("plotly-calls", function(msg) {
+ var gd = document.getElementById(msg.id);
+ if (!gd) {
+ throw new Error("Couldn't find plotly graph with id: " + msg.id);
+ }
+ // This isn't an official plotly.js method, but it's the only current way to
+ // change just the configuration of a plot
+ // https://community.plot.ly/t/update-config-function/9057
+ if (msg.method == "reconfig") {
+ Plotly.react(gd, gd.data, gd.layout, msg.args);
+ return;
+ }
+ if (!Plotly[msg.method]) {
+ throw new Error("Unknown method " + msg.method);
+ }
+ var args = [gd].concat(msg.args);
+ Plotly[msg.method].apply(null, args);
+ });
+ }
+
+ // plotly's mapbox API doesn't currently support setting bounding boxes
+ // https://www.mapbox.com/mapbox-gl-js/example/fitbounds/
+ // so we do this manually...
+ // TODO: make sure this triggers on a redraw and relayout as well as on initial draw
+ var mapboxIDs = graphDiv._fullLayout._subplots.mapbox || [];
+ for (var i = 0; i < mapboxIDs.length; i++) {
+ var id = mapboxIDs[i];
+ var mapOpts = x.layout[id] || {};
+ var args = mapOpts._fitBounds || {};
+ if (!args) {
+ continue;
+ }
+ var mapObj = graphDiv._fullLayout[id]._subplot.map;
+ mapObj.fitBounds(args.bounds, args.options);
+ }
+
+ });
+
+ // Attach attributes (e.g., "key", "z") to plotly event data
+ function eventDataWithKey(eventData) {
+ if (eventData === undefined || !eventData.hasOwnProperty("points")) {
+ return null;
+ }
+ return eventData.points.map(function(pt) {
+ var obj = {
+ curveNumber: pt.curveNumber,
+ pointNumber: pt.pointNumber,
+ x: pt.x,
+ y: pt.y
+ };
+
+ // If 'z' is reported with the event data, then use it!
+ if (pt.hasOwnProperty("z")) {
+ obj.z = pt.z;
+ }
+
+ if (pt.hasOwnProperty("customdata")) {
+ obj.customdata = pt.customdata;
+ }
+
+ /*
+ TL;DR: (I think) we have to select the graph div (again) to attach keys...
+
+ Why? Remember that crosstalk will dynamically add/delete traces
+ (see traceManager.prototype.updateSelection() below)
+ For this reason, we can't simply grab keys from x.data (like we did previously)
+ Moreover, we can't use _fullData, since that doesn't include
+ unofficial attributes. It's true that click/hover events fire with
+ pt.data, but drag events don't...
+ */
+ var gd = document.getElementById(el.id);
+ var trace = gd.data[pt.curveNumber];
+
+ if (!trace._isSimpleKey) {
+ var attrsToAttach = ["key"];
+ } else {
+ // simple keys fire the whole key
+ obj.key = trace.key;
+ var attrsToAttach = [];
+ }
+
+ for (var i = 0; i < attrsToAttach.length; i++) {
+ var attr = trace[attrsToAttach[i]];
+ if (Array.isArray(attr)) {
+ if (typeof pt.pointNumber === "number") {
+ obj[attrsToAttach[i]] = attr[pt.pointNumber];
+ } else if (Array.isArray(pt.pointNumber)) {
+ obj[attrsToAttach[i]] = attr[pt.pointNumber[0]][pt.pointNumber[1]];
+ } else if (Array.isArray(pt.pointNumbers)) {
+ obj[attrsToAttach[i]] = pt.pointNumbers.map(function(idx) { return attr[idx]; });
+ }
+ }
+ }
+ return obj;
+ });
+ }
+
+
+ var legendEventData = function(d) {
+ // if legendgroup is not relevant just return the trace
+ var trace = d.data[d.curveNumber];
+ if (!trace.legendgroup) return trace;
+
+ // if legendgroup was specified, return all traces that match the group
+ var legendgrps = d.data.map(function(trace){ return trace.legendgroup; });
+ var traces = [];
+ for (i = 0; i < legendgrps.length; i++) {
+ if (legendgrps[i] == trace.legendgroup) {
+ traces.push(d.data[i]);
+ }
+ }
+
+ return traces;
+ };
+
+
+ // send user input event data to shiny
+ if (HTMLWidgets.shinyMode && Shiny.setInputValue) {
+
+ // Some events clear other input values
+ // TODO: always register these?
+ var eventClearMap = {
+ plotly_deselect: ["plotly_selected", "plotly_selecting", "plotly_brushed", "plotly_brushing", "plotly_click"],
+ plotly_unhover: ["plotly_hover"],
+ plotly_doubleclick: ["plotly_click"]
+ };
+
+ Object.keys(eventClearMap).map(function(evt) {
+ graphDiv.on(evt, function() {
+ var inputsToClear = eventClearMap[evt];
+ inputsToClear.map(function(input) {
+ Shiny.setInputValue(input + "-" + x.source, null, {priority: "event"});
+ });
+ });
+ });
+
+ var eventDataFunctionMap = {
+ plotly_click: eventDataWithKey,
+ plotly_sunburstclick: eventDataWithKey,
+ plotly_hover: eventDataWithKey,
+ plotly_unhover: eventDataWithKey,
+ // If 'plotly_selected' has already been fired, and you click
+ // on the plot afterwards, this event fires `undefined`?!?
+ // That might be considered a plotly.js bug, but it doesn't make
+ // sense for this input change to occur if `d` is falsy because,
+ // even in the empty selection case, `d` is truthy (an object),
+ // and the 'plotly_deselect' event will reset this input
+ plotly_selected: function(d) { if (d) { return eventDataWithKey(d); } },
+ plotly_selecting: function(d) { if (d) { return eventDataWithKey(d); } },
+ plotly_brushed: function(d) {
+ if (d) { return d.range ? d.range : d.lassoPoints; }
+ },
+ plotly_brushing: function(d) {
+ if (d) { return d.range ? d.range : d.lassoPoints; }
+ },
+ plotly_legendclick: legendEventData,
+ plotly_legenddoubleclick: legendEventData,
+ plotly_clickannotation: function(d) { return d.fullAnnotation }
+ };
+
+ var registerShinyValue = function(event) {
+ var eventDataPreProcessor = eventDataFunctionMap[event] || function(d) { return d ? d : el.id };
+ // some events are unique to the R package
+ var plotlyJSevent = (event == "plotly_brushed") ? "plotly_selected" : (event == "plotly_brushing") ? "plotly_selecting" : event;
+ // register the event
+ graphDiv.on(plotlyJSevent, function(d) {
+ Shiny.setInputValue(
+ event + "-" + x.source,
+ JSON.stringify(eventDataPreProcessor(d)),
+ {priority: "event"}
+ );
+ });
+ }
+
+ var shinyEvents = x.shinyEvents || [];
+ shinyEvents.map(registerShinyValue);
+ }
+
+ // Given an array of {curveNumber: x, pointNumber: y} objects,
+ // return a hash of {
+ // set1: {value: [key1, key2, ...], _isSimpleKey: false},
+ // set2: {value: [key3, key4, ...], _isSimpleKey: false}
+ // }
+ function pointsToKeys(points) {
+ var keysBySet = {};
+ for (var i = 0; i < points.length; i++) {
+
+ var trace = graphDiv.data[points[i].curveNumber];
+ if (!trace.key || !trace.set) {
+ continue;
+ }
+
+ // set defaults for this keySet
+ // note that we don't track the nested property (yet) since we always
+ // emit the union -- http://cpsievert.github.io/talks/20161212b/#21
+ keysBySet[trace.set] = keysBySet[trace.set] || {
+ value: [],
+ _isSimpleKey: trace._isSimpleKey
+ };
+
+ // Use pointNumber by default, but aggregated traces should emit pointNumbers
+ var ptNum = points[i].pointNumber;
+ var hasPtNum = typeof ptNum === "number";
+ var ptNum = hasPtNum ? ptNum : points[i].pointNumbers;
+
+ // selecting a point of a "simple" trace means: select the
+ // entire key attached to this trace, which is useful for,
+ // say clicking on a fitted line to select corresponding observations
+ var key = trace._isSimpleKey ? trace.key : Array.isArray(ptNum) ? ptNum.map(function(idx) { return trace.key[idx]; }) : trace.key[ptNum];
+ // http://stackoverflow.com/questions/10865025/merge-flatten-an-array-of-arrays-in-javascript
+ var keyFlat = trace._isNestedKey ? [].concat.apply([], key) : key;
+
+ // TODO: better to only add new values?
+ keysBySet[trace.set].value = keysBySet[trace.set].value.concat(keyFlat);
+ }
+
+ return keysBySet;
+ }
+
+
+ x.highlight.color = x.highlight.color || [];
+ // make sure highlight color is an array
+ if (!Array.isArray(x.highlight.color)) {
+ x.highlight.color = [x.highlight.color];
+ }
+
+ var traceManager = new TraceManager(graphDiv, x.highlight);
+
+ // Gather all *unique* sets.
+ var allSets = [];
+ for (var curveIdx = 0; curveIdx < x.data.length; curveIdx++) {
+ var newSet = x.data[curveIdx].set;
+ if (newSet) {
+ if (allSets.indexOf(newSet) === -1) {
+ allSets.push(newSet);
+ }
+ }
+ }
+
+ // register event listeners for all sets
+ for (var i = 0; i < allSets.length; i++) {
+
+ var set = allSets[i];
+ var selection = new crosstalk.SelectionHandle(set);
+ var filter = new crosstalk.FilterHandle(set);
+
+ var filterChange = function(e) {
+ removeBrush(el);
+ traceManager.updateFilter(set, e.value);
+ };
+ filter.on("change", filterChange);
+
+
+ var selectionChange = function(e) {
+
+ // Workaround for 'plotly_selected' now firing previously selected
+ // points (in addition to new ones) when holding shift key. In our case,
+ // we just want the new keys
+ if (x.highlight.on === "plotly_selected" && x.highlight.persistentShift) {
+ // https://stackoverflow.com/questions/1187518/how-to-get-the-difference-between-two-arrays-in-javascript
+ Array.prototype.diff = function(a) {
+ return this.filter(function(i) {return a.indexOf(i) < 0;});
+ };
+ e.value = e.value.diff(e.oldValue);
+ }
+
+ // array of "event objects" tracking the selection history
+ // this is used to avoid adding redundant selections
+ var selectionHistory = crosstalk.var("plotlySelectionHistory").get() || [];
+
+ // Construct an event object "defining" the current event.
+ var event = {
+ receiverID: traceManager.gd.id,
+ plotlySelectionColour: crosstalk.group(set).var("plotlySelectionColour").get()
+ };
+ event[set] = e.value;
+ // TODO: is there a smarter way to check object equality?
+ if (selectionHistory.length > 0) {
+ var ev = JSON.stringify(event);
+ for (var i = 0; i < selectionHistory.length; i++) {
+ var sel = JSON.stringify(selectionHistory[i]);
+ if (sel == ev) {
+ return;
+ }
+ }
+ }
+
+ // accumulate history for persistent selection
+ if (!x.highlight.persistent) {
+ selectionHistory = [event];
+ } else {
+ selectionHistory.push(event);
+ }
+ crosstalk.var("plotlySelectionHistory").set(selectionHistory);
+
+ // do the actual updating of traces, frames, and the selectize widget
+ traceManager.updateSelection(set, e.value);
+ // https://github.com/selectize/selectize.js/blob/master/docs/api.md#methods_items
+ if (x.selectize) {
+ if (!x.highlight.persistent || e.value === null) {
+ selectize.clear(true);
+ }
+ selectize.addItems(e.value, true);
+ selectize.close();
+ }
+ }
+ selection.on("change", selectionChange);
+
+ // Set a crosstalk variable selection value, triggering an update
+ var turnOn = function(e) {
+ if (e) {
+ var selectedKeys = pointsToKeys(e.points);
+ // Keys are group names, values are array of selected keys from group.
+ for (var set in selectedKeys) {
+ if (selectedKeys.hasOwnProperty(set)) {
+ selection.set(selectedKeys[set].value, {sender: el});
+ }
+ }
+ }
+ };
+ if (x.highlight.debounce > 0) {
+ turnOn = debounce(turnOn, x.highlight.debounce);
+ }
+ graphDiv.on(x.highlight.on, turnOn);
+
+ graphDiv.on(x.highlight.off, function turnOff(e) {
+ // remove any visual clues
+ removeBrush(el);
+ // remove any selection history
+ crosstalk.var("plotlySelectionHistory").set(null);
+ // trigger the actual removal of selection traces
+ selection.set(null, {sender: el});
+ });
+
+ // register a callback for selectize so that there is bi-directional
+ // communication between the widget and direct manipulation events
+ if (x.selectize) {
+ var selectizeID = Object.keys(x.selectize)[i];
+ var options = x.selectize[selectizeID];
+ var first = [{value: "", label: "(All)"}];
+ var opts = $.extend({
+ options: first.concat(options.items),
+ searchField: "label",
+ valueField: "value",
+ labelField: "label",
+ maxItems: 50
+ },
+ options
+ );
+ var select = $("#" + selectizeID).find("select")[0];
+ var selectize = $(select).selectize(opts)[0].selectize;
+ // NOTE: this callback is triggered when *directly* altering
+ // dropdown items
+ selectize.on("change", function() {
+ var currentItems = traceManager.groupSelections[set] || [];
+ if (!x.highlight.persistent) {
+ removeBrush(el);
+ for (var i = 0; i < currentItems.length; i++) {
+ selectize.removeItem(currentItems[i], true);
+ }
+ }
+ var newItems = selectize.items.filter(function(idx) {
+ return currentItems.indexOf(idx) < 0;
+ });
+ if (newItems.length > 0) {
+ traceManager.updateSelection(set, newItems);
+ } else {
+ // Item has been removed...
+ // TODO: this logic won't work for dynamically changing palette
+ traceManager.updateSelection(set, null);
+ traceManager.updateSelection(set, selectize.items);
+ }
+ });
+ }
+ } // end of selectionChange
+
+ } // end of renderValue
+}); // end of widget definition
+
+/**
+ * @param graphDiv The Plotly graph div
+ * @param highlight An object with options for updating selection(s)
+ */
+function TraceManager(graphDiv, highlight) {
+ // The Plotly graph div
+ this.gd = graphDiv;
+
+ // Preserve the original data.
+ // TODO: try using Lib.extendFlat() as done in
+ // https://github.com/plotly/plotly.js/pull/1136
+ this.origData = JSON.parse(JSON.stringify(graphDiv.data));
+
+ // avoid doing this over and over
+ this.origOpacity = [];
+ for (var i = 0; i < this.origData.length; i++) {
+ this.origOpacity[i] = this.origData[i].opacity === 0 ? 0 : (this.origData[i].opacity || 1);
+ }
+
+ // key: group name, value: null or array of keys representing the
+ // most recently received selection for that group.
+ this.groupSelections = {};
+
+ // selection parameters (e.g., transient versus persistent selection)
+ this.highlight = highlight;
+}
+
+TraceManager.prototype.close = function() {
+ // TODO: Unhook all event handlers
+};
+
+TraceManager.prototype.updateFilter = function(group, keys) {
+
+ if (typeof(keys) === "undefined" || keys === null) {
+
+ this.gd.data = JSON.parse(JSON.stringify(this.origData));
+
+ } else {
+
+ var traces = [];
+ for (var i = 0; i < this.origData.length; i++) {
+ var trace = this.origData[i];
+ if (!trace.key || trace.set !== group) {
+ continue;
+ }
+ var matchFunc = getMatchFunc(trace);
+ var matches = matchFunc(trace.key, keys);
+
+ if (matches.length > 0) {
+ if (!trace._isSimpleKey) {
+ // subsetArrayAttrs doesn't mutate trace (it makes a modified clone)
+ trace = subsetArrayAttrs(trace, matches);
+ }
+ traces.push(trace);
+ }
+ }
+ this.gd.data = traces;
+ }
+
+ Plotly.redraw(this.gd);
+
+ // NOTE: we purposely do _not_ restore selection(s), since on filter,
+ // axis likely will update, changing the pixel -> data mapping, leading
+ // to a likely mismatch in the brush outline and highlighted marks
+
+};
+
+TraceManager.prototype.updateSelection = function(group, keys) {
+
+ if (keys !== null && !Array.isArray(keys)) {
+ throw new Error("Invalid keys argument; null or array expected");
+ }
+
+ // if selection has been cleared, or if this is transient
+ // selection, delete the "selection traces"
+ var nNewTraces = this.gd.data.length - this.origData.length;
+ if (keys === null || !this.highlight.persistent && nNewTraces > 0) {
+ var tracesToRemove = [];
+ for (var i = 0; i < this.gd.data.length; i++) {
+ if (this.gd.data[i]._isCrosstalkTrace) tracesToRemove.push(i);
+ }
+ Plotly.deleteTraces(this.gd, tracesToRemove);
+ this.groupSelections[group] = keys;
+ } else {
+ // add to the groupSelection, rather than overwriting it
+ // TODO: can this be removed?
+ this.groupSelections[group] = this.groupSelections[group] || [];
+ for (var i = 0; i < keys.length; i++) {
+ var k = keys[i];
+ if (this.groupSelections[group].indexOf(k) < 0) {
+ this.groupSelections[group].push(k);
+ }
+ }
+ }
+
+ if (keys === null) {
+
+ Plotly.restyle(this.gd, {"opacity": this.origOpacity});
+
+ } else if (keys.length >= 1) {
+
+ // placeholder for new "selection traces"
+ var traces = [];
+ // this variable is set in R/highlight.R
+ var selectionColour = crosstalk.group(group).var("plotlySelectionColour").get() ||
+ this.highlight.color[0];
+
+ for (var i = 0; i < this.origData.length; i++) {
+ // TODO: try using Lib.extendFlat() as done in
+ // https://github.com/plotly/plotly.js/pull/1136
+ var trace = JSON.parse(JSON.stringify(this.gd.data[i]));
+ if (!trace.key || trace.set !== group) {
+ continue;
+ }
+ // Get sorted array of matching indices in trace.key
+ var matchFunc = getMatchFunc(trace);
+ var matches = matchFunc(trace.key, keys);
+
+ if (matches.length > 0) {
+ // If this is a "simple" key, that means select the entire trace
+ if (!trace._isSimpleKey) {
+ trace = subsetArrayAttrs(trace, matches);
+ }
+ // reach into the full trace object so we can properly reflect the
+ // selection attributes in every view
+ var d = this.gd._fullData[i];
+
+ /*
+ / Recursively inherit selection attributes from various sources,
+ / in order of preference:
+ / (1) official plotly.js selected attribute
+ / (2) highlight(selected = attrs_selected(...))
+ */
+ // TODO: it would be neat to have a dropdown to dynamically specify these!
+ $.extend(true, trace, this.highlight.selected);
+
+ // if it is defined, override color with the "dynamic brush color""
+ if (d.marker) {
+ trace.marker = trace.marker || {};
+ trace.marker.color = selectionColour || trace.marker.color || d.marker.color;
+ }
+ if (d.line) {
+ trace.line = trace.line || {};
+ trace.line.color = selectionColour || trace.line.color || d.line.color;
+ }
+ if (d.textfont) {
+ trace.textfont = trace.textfont || {};
+ trace.textfont.color = selectionColour || trace.textfont.color || d.textfont.color;
+ }
+ if (d.fillcolor) {
+ // TODO: should selectionColour inherit alpha from the existing fillcolor?
+ trace.fillcolor = selectionColour || trace.fillcolor || d.fillcolor;
+ }
+ // attach a sensible name/legendgroup
+ trace.name = trace.name || keys.join("
");
+ trace.legendgroup = trace.legendgroup || keys.join("
");
+
+ // keep track of mapping between this new trace and the trace it targets
+ // (necessary for updating frames to reflect the selection traces)
+ trace._originalIndex = i;
+ trace._newIndex = this.gd._fullData.length + traces.length;
+ trace._isCrosstalkTrace = true;
+ traces.push(trace);
+ }
+ }
+
+ if (traces.length > 0) {
+
+ Plotly.addTraces(this.gd, traces).then(function(gd) {
+ // incrementally add selection traces to frames
+ // (this is heavily inspired by Plotly.Plots.modifyFrames()
+ // in src/plots/plots.js)
+ var _hash = gd._transitionData._frameHash;
+ var _frames = gd._transitionData._frames || [];
+
+ for (var i = 0; i < _frames.length; i++) {
+
+ // add to _frames[i].traces *if* this frame references selected trace(s)
+ var newIndices = [];
+ for (var j = 0; j < traces.length; j++) {
+ var tr = traces[j];
+ if (_frames[i].traces.indexOf(tr._originalIndex) > -1) {
+ newIndices.push(tr._newIndex);
+ _frames[i].traces.push(tr._newIndex);
+ }
+ }
+
+ // nothing to do...
+ if (newIndices.length === 0) {
+ continue;
+ }
+
+ var ctr = 0;
+ var nFrameTraces = _frames[i].data.length;
+
+ for (var j = 0; j < nFrameTraces; j++) {
+ var frameTrace = _frames[i].data[j];
+ if (!frameTrace.key || frameTrace.set !== group) {
+ continue;
+ }
+
+ var matchFunc = getMatchFunc(frameTrace);
+ var matches = matchFunc(frameTrace.key, keys);
+
+ if (matches.length > 0) {
+ if (!trace._isSimpleKey) {
+ frameTrace = subsetArrayAttrs(frameTrace, matches);
+ }
+ var d = gd._fullData[newIndices[ctr]];
+ if (d.marker) {
+ frameTrace.marker = d.marker;
+ }
+ if (d.line) {
+ frameTrace.line = d.line;
+ }
+ if (d.textfont) {
+ frameTrace.textfont = d.textfont;
+ }
+ ctr = ctr + 1;
+ _frames[i].data.push(frameTrace);
+ }
+ }
+
+ // update gd._transitionData._frameHash
+ _hash[_frames[i].name] = _frames[i];
+ }
+
+ });
+
+ // dim traces that have a set matching the set of selection sets
+ var tracesToDim = [],
+ opacities = [],
+ sets = Object.keys(this.groupSelections),
+ n = this.origData.length;
+
+ for (var i = 0; i < n; i++) {
+ var opacity = this.origOpacity[i] || 1;
+ // have we already dimmed this trace? Or is this even worth doing?
+ if (opacity !== this.gd._fullData[i].opacity || this.highlight.opacityDim === 1) {
+ continue;
+ }
+ // is this set an element of the set of selection sets?
+ var matches = findMatches(sets, [this.gd.data[i].set]);
+ if (matches.length) {
+ tracesToDim.push(i);
+ opacities.push(opacity * this.highlight.opacityDim);
+ }
+ }
+
+ if (tracesToDim.length > 0) {
+ Plotly.restyle(this.gd, {"opacity": opacities}, tracesToDim);
+ // turn off the selected/unselected API
+ Plotly.restyle(this.gd, {"selectedpoints": null});
+ }
+
+ }
+
+ }
+};
+
+/*
+Note: in all of these match functions, we assume needleSet (i.e. the selected keys)
+is a 1D (or flat) array. The real difference is the meaning of haystack.
+findMatches() does the usual thing you'd expect for
+linked brushing on a scatterplot matrix. findSimpleMatches() returns a match iff
+haystack is a subset of the needleSet. findNestedMatches() returns
+*/
+
+function getMatchFunc(trace) {
+ return (trace._isNestedKey) ? findNestedMatches :
+ (trace._isSimpleKey) ? findSimpleMatches : findMatches;
+}
+
+// find matches for "flat" keys
+function findMatches(haystack, needleSet) {
+ var matches = [];
+ haystack.forEach(function(obj, i) {
+ if (obj === null || needleSet.indexOf(obj) >= 0) {
+ matches.push(i);
+ }
+ });
+ return matches;
+}
+
+// find matches for "simple" keys
+function findSimpleMatches(haystack, needleSet) {
+ var match = haystack.every(function(val) {
+ return val === null || needleSet.indexOf(val) >= 0;
+ });
+ // yes, this doesn't make much sense other than conforming
+ // to the output type of the other match functions
+ return (match) ? [0] : []
+}
+
+// find matches for a "nested" haystack (2D arrays)
+function findNestedMatches(haystack, needleSet) {
+ var matches = [];
+ for (var i = 0; i < haystack.length; i++) {
+ var hay = haystack[i];
+ var match = hay.every(function(val) {
+ return val === null || needleSet.indexOf(val) >= 0;
+ });
+ if (match) {
+ matches.push(i);
+ }
+ }
+ return matches;
+}
+
+function isPlainObject(obj) {
+ return (
+ Object.prototype.toString.call(obj) === '[object Object]' &&
+ Object.getPrototypeOf(obj) === Object.prototype
+ );
+}
+
+function subsetArrayAttrs(obj, indices) {
+ var newObj = {};
+ Object.keys(obj).forEach(function(k) {
+ var val = obj[k];
+
+ if (k.charAt(0) === "_") {
+ newObj[k] = val;
+ } else if (k === "transforms" && Array.isArray(val)) {
+ newObj[k] = val.map(function(transform) {
+ return subsetArrayAttrs(transform, indices);
+ });
+ } else if (k === "colorscale" && Array.isArray(val)) {
+ newObj[k] = val;
+ } else if (isPlainObject(val)) {
+ newObj[k] = subsetArrayAttrs(val, indices);
+ } else if (Array.isArray(val)) {
+ newObj[k] = subsetArray(val, indices);
+ } else {
+ newObj[k] = val;
+ }
+ });
+ return newObj;
+}
+
+function subsetArray(arr, indices) {
+ var result = [];
+ for (var i = 0; i < indices.length; i++) {
+ result.push(arr[indices[i]]);
+ }
+ return result;
+}
+
+// Convenience function for removing plotly's brush
+function removeBrush(el) {
+ var outlines = el.querySelectorAll(".select-outline");
+ for (var i = 0; i < outlines.length; i++) {
+ outlines[i].remove();
+ }
+}
+
+
+// https://davidwalsh.name/javascript-debounce-function
+
+// Returns a function, that, as long as it continues to be invoked, will not
+// be triggered. The function will be called after it stops being called for
+// N milliseconds. If `immediate` is passed, trigger the function on the
+// leading edge, instead of the trailing.
+function debounce(func, wait, immediate) {
+ var timeout;
+ return function() {
+ var context = this, args = arguments;
+ var later = function() {
+ timeout = null;
+ if (!immediate) func.apply(context, args);
+ };
+ var callNow = immediate && !timeout;
+ clearTimeout(timeout);
+ timeout = setTimeout(later, wait);
+ if (callNow) func.apply(context, args);
+ };
+};
diff --git a/docs/reference/libs/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css b/docs/reference/libs/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
new file mode 100644
index 00000000..f35906d5
--- /dev/null
+++ b/docs/reference/libs/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
@@ -0,0 +1,9 @@
+/*
+just here so that plotly works
+correctly with ioslides.
+see https://github.com/ropensci/plotly/issues/463
+*/
+
+slide:not(.current) .plotly.html-widget{
+ display: none;
+}
diff --git a/docs/reference/libs/plotly-main-2.11.1/plotly-latest.min.js b/docs/reference/libs/plotly-main-2.11.1/plotly-latest.min.js
new file mode 100644
index 00000000..27bfdaa9
--- /dev/null
+++ b/docs/reference/libs/plotly-main-2.11.1/plotly-latest.min.js
@@ -0,0 +1,69 @@
+/**
+* plotly.js v2.11.1
+* Copyright 2012-2022, Plotly, Inc.
+* All rights reserved.
+* Licensed under the MIT license
+*/
+!function(t){if("object"==typeof exports&&"undefined"!=typeof module)module.exports=t();else if("function"==typeof define&&define.amd)define([],t);else{("undefined"!=typeof window?window:"undefined"!=typeof global?global:"undefined"!=typeof self?self:this).Plotly=t()}}((function(){return function t(e,r,n){function i(o,s){if(!r[o]){if(!e[o]){var l="function"==typeof require&&require;if(!s&&l)return l(o,!0);if(a)return a(o,!0);var c=new Error("Cannot find module '"+o+"'");throw c.code="MODULE_NOT_FOUND",c}var u=r[o]={exports:{}};e[o][0].call(u.exports,(function(t){return i(e[o][1][t]||t)}),u,u.exports,t,e,r,n)}return r[o].exports}for(var a="function"==typeof require&&require,o=0;o
:not(.watermark)":"opacity:0;-webkit-transition:opacity .3s ease 0s;-moz-transition:opacity .3s ease 0s;-ms-transition:opacity .3s ease 0s;-o-transition:opacity .3s ease 0s;transition:opacity .3s ease 0s;","X:hover .modebar--hover .modebar-group":"opacity:1;","X .modebar-group":"float:left;display:inline-block;box-sizing:border-box;padding-left:8px;position:relative;vertical-align:middle;white-space:nowrap;","X .modebar-btn":"position:relative;font-size:16px;padding:3px 4px;height:22px;cursor:pointer;line-height:normal;box-sizing:border-box;","X .modebar-btn svg":"position:relative;top:2px;","X .modebar.vertical":"display:flex;flex-direction:column;flex-wrap:wrap;align-content:flex-end;max-height:100%;","X .modebar.vertical svg":"top:-1px;","X .modebar.vertical .modebar-group":"display:block;float:none;padding-left:0px;padding-bottom:8px;","X .modebar.vertical .modebar-group .modebar-btn":"display:block;text-align:center;","X [data-title]:before,X [data-title]:after":"position:absolute;-webkit-transform:translate3d(0, 0, 0);-moz-transform:translate3d(0, 0, 0);-ms-transform:translate3d(0, 0, 0);-o-transform:translate3d(0, 0, 0);transform:translate3d(0, 0, 0);display:none;opacity:0;z-index:1001;pointer-events:none;top:110%;right:50%;","X [data-title]:hover:before,X [data-title]:hover:after":"display:block;opacity:1;","X [data-title]:before":'content:"";position:absolute;background:transparent;border:6px solid transparent;z-index:1002;margin-top:-12px;border-bottom-color:#69738a;margin-right:-6px;',"X [data-title]:after":"content:attr(data-title);background:#69738a;color:#fff;padding:8px 10px;font-size:12px;line-height:12px;white-space:nowrap;margin-right:-18px;border-radius:2px;","X .vertical [data-title]:before,X .vertical [data-title]:after":"top:0%;right:200%;","X .vertical [data-title]:before":"border:6px solid transparent;border-left-color:#69738a;margin-top:8px;margin-right:-30px;","X .select-outline":"fill:none;stroke-width:1;shape-rendering:crispEdges;","X .select-outline-1":"stroke:#fff;","X .select-outline-2":"stroke:#000;stroke-dasharray:2px 2px;",Y:'font-family:"Open Sans",verdana,arial,sans-serif;position:fixed;top:50px;right:20px;z-index:10000;font-size:10pt;max-width:180px;',"Y p":"margin:0;","Y .notifier-note":"min-width:180px;max-width:250px;border:1px solid #fff;z-index:3000;margin:0;background-color:#8c97af;background-color:rgba(140,151,175,.9);color:#fff;padding:10px;overflow-wrap:break-word;word-wrap:break-word;-ms-hyphens:auto;-webkit-hyphens:auto;hyphens:auto;","Y .notifier-close":"color:#fff;opacity:.8;float:right;padding:0 5px;background:none;border:none;font-size:20px;font-weight:bold;line-height:20px;","Y .notifier-close:hover":"color:#444;text-decoration:none;cursor:pointer;"};for(var a in i){var o=a.replace(/^,/," ,").replace(/X/g,".js-plotly-plot .plotly").replace(/Y/g,".plotly-notifier");n.addStyleRule(o,i[a])}},{"../src/lib":498}],2:[function(t,e,r){"use strict";e.exports=t("../src/transforms/aggregate")},{"../src/transforms/aggregate":1113}],3:[function(t,e,r){"use strict";e.exports=t("../src/traces/bar")},{"../src/traces/bar":651}],4:[function(t,e,r){"use strict";e.exports=t("../src/traces/barpolar")},{"../src/traces/barpolar":664}],5:[function(t,e,r){"use strict";e.exports=t("../src/traces/box")},{"../src/traces/box":674}],6:[function(t,e,r){"use strict";e.exports=t("../src/components/calendars")},{"../src/components/calendars":359}],7:[function(t,e,r){"use strict";e.exports=t("../src/traces/candlestick")},{"../src/traces/candlestick":683}],8:[function(t,e,r){"use strict";e.exports=t("../src/traces/carpet")},{"../src/traces/carpet":702}],9:[function(t,e,r){"use strict";e.exports=t("../src/traces/choropleth")},{"../src/traces/choropleth":716}],10:[function(t,e,r){"use strict";e.exports=t("../src/traces/choroplethmapbox")},{"../src/traces/choroplethmapbox":723}],11:[function(t,e,r){"use strict";e.exports=t("../src/traces/cone")},{"../src/traces/cone":729}],12:[function(t,e,r){"use strict";e.exports=t("../src/traces/contour")},{"../src/traces/contour":744}],13:[function(t,e,r){"use strict";e.exports=t("../src/traces/contourcarpet")},{"../src/traces/contourcarpet":755}],14:[function(t,e,r){"use strict";e.exports=t("../src/core")},{"../src/core":476}],15:[function(t,e,r){"use strict";e.exports=t("../src/traces/densitymapbox")},{"../src/traces/densitymapbox":763}],16:[function(t,e,r){"use strict";e.exports=t("../src/transforms/filter")},{"../src/transforms/filter":1114}],17:[function(t,e,r){"use strict";e.exports=t("../src/traces/funnel")},{"../src/traces/funnel":773}],18:[function(t,e,r){"use strict";e.exports=t("../src/traces/funnelarea")},{"../src/traces/funnelarea":782}],19:[function(t,e,r){"use strict";e.exports=t("../src/transforms/groupby")},{"../src/transforms/groupby":1115}],20:[function(t,e,r){"use strict";e.exports=t("../src/traces/heatmap")},{"../src/traces/heatmap":795}],21:[function(t,e,r){"use strict";e.exports=t("../src/traces/heatmapgl")},{"../src/traces/heatmapgl":806}],22:[function(t,e,r){"use strict";e.exports=t("../src/traces/histogram")},{"../src/traces/histogram":818}],23:[function(t,e,r){"use strict";e.exports=t("../src/traces/histogram2d")},{"../src/traces/histogram2d":824}],24:[function(t,e,r){"use strict";e.exports=t("../src/traces/histogram2dcontour")},{"../src/traces/histogram2dcontour":828}],25:[function(t,e,r){"use strict";e.exports=t("../src/traces/icicle")},{"../src/traces/icicle":834}],26:[function(t,e,r){"use strict";e.exports=t("../src/traces/image")},{"../src/traces/image":847}],27:[function(t,e,r){"use strict";var n=t("./core");n.register([t("./bar"),t("./box"),t("./heatmap"),t("./histogram"),t("./histogram2d"),t("./histogram2dcontour"),t("./contour"),t("./scatterternary"),t("./violin"),t("./funnel"),t("./waterfall"),t("./image"),t("./pie"),t("./sunburst"),t("./treemap"),t("./icicle"),t("./funnelarea"),t("./scatter3d"),t("./surface"),t("./isosurface"),t("./volume"),t("./mesh3d"),t("./cone"),t("./streamtube"),t("./scattergeo"),t("./choropleth"),t("./scattergl"),t("./splom"),t("./pointcloud"),t("./heatmapgl"),t("./parcoords"),t("./parcats"),t("./scattermapbox"),t("./choroplethmapbox"),t("./densitymapbox"),t("./sankey"),t("./indicator"),t("./table"),t("./carpet"),t("./scattercarpet"),t("./contourcarpet"),t("./ohlc"),t("./candlestick"),t("./scatterpolar"),t("./scatterpolargl"),t("./barpolar"),t("./scattersmith"),t("./aggregate"),t("./filter"),t("./groupby"),t("./sort"),t("./calendars")]),e.exports=n},{"./aggregate":2,"./bar":3,"./barpolar":4,"./box":5,"./calendars":6,"./candlestick":7,"./carpet":8,"./choropleth":9,"./choroplethmapbox":10,"./cone":11,"./contour":12,"./contourcarpet":13,"./core":14,"./densitymapbox":15,"./filter":16,"./funnel":17,"./funnelarea":18,"./groupby":19,"./heatmap":20,"./heatmapgl":21,"./histogram":22,"./histogram2d":23,"./histogram2dcontour":24,"./icicle":25,"./image":26,"./indicator":28,"./isosurface":29,"./mesh3d":30,"./ohlc":31,"./parcats":32,"./parcoords":33,"./pie":34,"./pointcloud":35,"./sankey":36,"./scatter3d":37,"./scattercarpet":38,"./scattergeo":39,"./scattergl":40,"./scattermapbox":41,"./scatterpolar":42,"./scatterpolargl":43,"./scattersmith":44,"./scatterternary":45,"./sort":46,"./splom":47,"./streamtube":48,"./sunburst":49,"./surface":50,"./table":51,"./treemap":52,"./violin":53,"./volume":54,"./waterfall":55}],28:[function(t,e,r){"use 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-
-
-
-[](https://app.travis-ci.com/n8thangreen/BCEA)
-[](https://cran.r-project.org/package=BCEA) [](https://cran.r-project.org/package=BCEA)
-[](https://cran.r-project.org/package=BCEA)
-[](https://www.codefactor.io/repository/github/n8thangreen/bcea)
-
-
-## Contents
-
-- [Overview](#introduction)
-- [Features](#features)
-- [Installation](#installation)
-- [Further details](#further-details)
-
-## Overview
-
-Perform Bayesian Cost-Effectiveness Analysis in R.
-Given the results of a Bayesian model (possibly based on MCMC) in the form of simulations from the posterior distributions of suitable variables of costs and clinical benefits for two or more interventions, produces a health economic evaluation. Compares one of the interventions (the "reference") to the others ("comparators").
-
-## Features
-
-Main features of `BCEA` include:
-
-* Summary statistics and tables
-* Cost-effectiveness analysis plots, such as CE planes and CEAC
-* EVPPI calculations and plots
-
-This is the **development** version of BCEA (currently 2.4). It contains a major refactoring of the code to streamline the functions.
-
-## Installation
-The development version can be installed using this GitHub repository. On Windows machines, you need to install a few dependencies, including [Rtools](https://cran.r-project.org/bin/windows/Rtools/) first, e.g. by running
-
-```r
-pkgs <- c("MASS", "Rtools", "remotes")
-repos <- c("https://cran.rstudio.com", "https://inla.r-inla-download.org/R/stable/")
-install.packages(pkgs, repos=repos, dependencies = "Depends")
-```
-before installing the package using `remotes`:
-
-```r
-remotes::install_github("giabaio/BCEA", ref="dev")
-```
-Under Linux or MacOS, it is sufficient to install the package via `remotes`:
-
-```r
-install.packages("remotes")
-remotes::install_github("giabaio/BCEA", ref="dev")
-```
-
-## Further details
-The `pkgdown` site is [here](https://n8thangreen.github.io/BCEA/).
-More details on `BCEA` are available in our book [_Bayesian Cost-Effectiveness Analysis with the R Package BCEA_](https://gianluca.statistica.it/book/bcea/) (published in the UseR! Springer series). Also, details about the package, including some references and links to a pdf presentation and some posts on my own blog) are given [here](https://gianluca.statistica.it/software/bcea/).
-
-## Licence
-GPL-3 © [G Baio](https://github.com/giabaio/).
-
-Please note that this project is released with a [Contributor Code of Conduct](https://github.com/n8thangreen/BCEA/blob/dev/CONDUCT.md). By participating in this project you agree to abide by its terms.
diff --git a/_pkgdown.yml b/_pkgdown.yml
index e03de6e6..891e1399 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -9,6 +9,15 @@ template:
bslib:
font_scale: 1.0
+navbar:
+ structure:
+ left: [intro, reference, articles, tutorials, news, cheatsheet]
+ right: [search, github]
+ components:
+ cheatsheet:
+ text: "Cheatsheet"
+ href: "bcea_cheatsheet.pdf"
+
reference:
- title: "Main"
contents:
diff --git a/cran-comments.md b/cran-comments.md
index 01fa3693..1e88fbc5 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,19 +1,30 @@
-## Resubmission
-This is a resubmission. In this version I have:
-* Removed from the build large data files so that not more than 5 MB for a CRAN package.
+# Resubmission (2.4.4)
-* Reference about the method added in the Description with doi: prefix
+* Suggested package wasn't used conditionally in unit test causing CRAN check error. `MCMCvis` is now moved to Required packages.
+* Fixed R package CRAN webpage canonical form in README
## R CMD check results
-There were no ERRORs or WARNINGs.
+
+0 errors | 0 warnings | 1 note
* Any notes about using INLA has been condoned in previous versions, as they are only suggested.
+
+CHECK message:
+
+ Suggests or Enhances not in mainstream repositories:
+ INLA
+ Availability using Additional_repositories specification:
+ INLA yes https://inla.r-inla-download.org/R/stable/
+Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
+Check: package dependencies, Result: NOTE
+ Package suggested but not available for checking: 'INLA'
## Downstream dependencies
-We checked 2 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 2 reverse dependencies (missingHE, heesim), comparing R CMD check results across CRAN and dev versions of this package.
* We saw 0 new problems
* We failed to check 0 packages
+
diff --git a/data/Smoking.RData b/data/Smoking.RData
index c855d544..20dfc80f 100644
Binary files a/data/Smoking.RData and b/data/Smoking.RData differ
diff --git a/data/Vaccine.RData b/data/Vaccine.RData
index 86ce7677..c156a13b 100644
Binary files a/data/Vaccine.RData and b/data/Vaccine.RData differ
diff --git a/data/datalist b/data/datalist
index 31677fa0..c1af3b86 100644
--- a/data/datalist
+++ b/data/datalist
@@ -1,2 +1,2 @@
-Smoking: cost data eff life.years pi_post smoking treats
-Vaccine: cost cost.time.off cost.trt2 eff N.resources QALYs.inf vaccine_mat cost.GP cost.time.vac cost.vac e.pts QALYs.adv QALYs.pne cost.hosp cost.travel c.pts N QALYs.death treats cost.otc cost.trt1 N.outcomes QALYs.hosp
\ No newline at end of file
+Smoking: cost data eff life.years pi_post smoking smoking_output treats
+Vaccine: c.pts cost cost.GP cost.hosp cost.otc cost.time.off cost.time.vac cost.travel cost.trt1 cost.trt2 cost.vac e.pts eff N N.outcomes N.resources QALYs.adv QALYs.death QALYs.hosp QALYs.inf QALYs.pne treats vaccine_mat
diff --git a/docs/404.html b/docs/404.html
index f8bd2dba..77b316d0 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -6,33 +6,33 @@