").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/articles/heritability.html b/docs/articles/heritability.html
index 81849ca..e582bee 100644
--- a/docs/articles/heritability.html
+++ b/docs/articles/heritability.html
@@ -39,7 +39,7 @@
inti
-
0.6.0
+
0.6.1