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“).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 result = bindingDef.initialize(el, el.offsetWidth, el.offsetHeight); 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); if (hasClass(el, "html-widget-static-bound")) return; el.className = el.className + " html-widget-static-bound"; var initResult; if (binding.initialize) { initResult = binding.initialize(el, sizeObj ? sizeObj.getWidth() : el.offsetWidth, sizeObj ? sizeObj.getHeight() : el.offsetHeight ); elementData(el, "init_result", initResult); } if (binding.resize) { var lastSize = { w: sizeObj ? sizeObj.getWidth() : el.offsetWidth, h: sizeObj ? sizeObj.getHeight() : el.offsetHeight }; var resizeHandler = function(e) { var size = { w: sizeObj ? sizeObj.getWidth() : el.offsetWidth, h: sizeObj ? sizeObj.getHeight() : el.offsetHeight }; 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. 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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. 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HTMLWidgets.widget({ name: “forceNetwork”, type: “output”, initialize: function(el, width, height) { d3.select(el).append(“svg”) .attr(“width”, width) .attr(“height”, height); return d3.forceSimulation(); }, resize: function(el, width, height, force) { d3.select(el).select(“svg”) .attr(“width”, width) .attr(“height”, height); force.force(“center”, d3.forceCenter(width / 2, height / 2)) .restart(); }, renderValue: function(el, x, force) { // Compute the node radius using the javascript math expression specified function nodeSize(d) { if(options.nodesize){ return eval(options.radiusCalculation); }else{ return 6} } // alias options var options = x.options; // convert links and nodes data frames to d3 friendly format var links = HTMLWidgets.dataframeToD3(x.links); var nodes = HTMLWidgets.dataframeToD3(x.nodes); // create linkedByIndex to quickly search for node neighbors // adapted from: http://stackoverflow.com/a/8780277/4389763 var linkedByIndex = {}; links.forEach(function(d) { linkedByIndex[d.source + “,” + d.target] = 1; linkedByIndex[d.target + “,” + d.source] = 1; }); function neighboring(a, b) { return linkedByIndex[a.index + “,” + b.index]; } // get the width and height var width = el.offsetWidth; var height = el.offsetHeight; var color = eval(options.colourScale); // set this up even if zoom = F var zoom = d3.zoom(); // create d3 force layout force .nodes(d3.values(nodes)) .force(“link”, d3.forceLink(links).distance(options.linkDistance)) .force(“center”, d3.forceCenter(width / 2, height / 2)) .force(“charge”, d3.forceManyBody().strength(options.charge)) .on(“tick”, tick); force.alpha(1).restart(); var drag = d3.drag() .on(“start”, dragstart) .on(“drag”, dragged) .on(“end”, dragended) function dragstart(d) { if (!d3.event.active) force.alphaTarget(0.3).restart(); d.fx = d.x; d.fy = d.y; } function dragged(d) { d.fx = d3.event.x; d.fy = d3.event.y; } function dragended(d) { if (!d3.event.active) force.alphaTarget(0); d.fx = null; d.fy = null; } // select the svg element and remove existing children var svg = d3.select(el).select(“svg”); svg.selectAll(“*”).remove(); // add two g layers; the first will be zoom target if zoom = T // fine to have two g layers even if zoom = F svg = svg .append(“g”).attr(“class”,”zoom-layer”) .append(“g”) // add zooming if requested if (options.zoom) { function redraw() { d3.select(el).select(“.zoom-layer”) .attr(“transform”, d3.event.transform); } zoom.on(“zoom”, redraw) d3.select(el).select(“svg”) .attr(“pointer-events”, “all”) .call(zoom); } else { zoom.on(“zoom”, null); } // draw links var link = svg.selectAll(“.link”) .data(links) .enter().append(“line”) .attr(“class”, “link”) .style(“stroke”, function(d) { return d.colour ; }) //.style(“stroke”, options.linkColour) .style(“opacity”, options.opacity) .style(“stroke-width”, eval(“(” + options.linkWidth + “)”)) .on(“mouseover”, function(d) { d3.select(this) .style(“opacity”, 1); }) .on(“mouseout”, function(d) { d3.select(this) .style(“opacity”, options.opacity); }); if (options.arrows) { link.style(“marker-end”, function(d) { return “url(#arrow-” + d.colour + “)”; }); var linkColoursArr = d3.nest().key(function(d) { return d.colour; }).entries(links); svg.append(“defs”).selectAll(“marker”) .data(linkColoursArr) .enter().append(“marker”) .attr(“id”, function(d) { return “arrow-” + d.key; }) .attr(“viewBox”, “0, -5, 10, 10”) .attr(“refX”, 0) .attr(“markerWidth”, 4) .attr(“markerHeight”, 4) .attr(“orient”, “auto”) .style(“fill”, “context-fill”) .style(“fill”, function(d) { return d.key; }) .style(“opacity”, options.opacity) .append(“path”) .attr(“d”, “M0,-5 L10,0 L0,5”); } // draw nodes var node = svg.selectAll(“.node”) .data(force.nodes()) .enter().append(“g”) .attr(“class”, “node”) .style(“fill”, function(d) { return color(d.group); }) .style(“opacity”, options.opacity) .on(“mouseover”, mouseover) .on(“mouseout”, mouseout) .on(“click”, click) .call(drag); node.append(“circle”) .attr(“r”, function(d){return nodeSize(d);}) .style(“stroke”, “#fff”) .style(“opacity”, options.opacity) .style(“stroke-width”, “1.5px”); node.append(“svg:text”) .attr(“class”, “nodetext”) .attr(“dx”, 12) .attr(“dy”, “.35em”) .text(function(d) { return d.name }) .style(“font”, options.fontSize + “px ” + options.fontFamily) .style(“opacity”, options.opacityNoHover) .style(“pointer-events”, “none”); function tick() { node.attr(“transform”, function(d) { if(options.bounded){ // adds bounding box d.x = Math.max(nodeSize(d), Math.min(width – nodeSize(d), d.x)); d.y = Math.max(nodeSize(d), Math.min(height – nodeSize(d), d.y)); } return “translate(” + d.x + “,” + d.y + “)”}); function idx(d, type) { var linkWidthFunc = eval(“(” + options.linkWidth + “)”); var a = d.target.x – d.source.x; var b = d.target.y – d.source.y; var c = Math.sqrt(Math.pow(a, 2) + Math.pow(b, 2)); if (type == “x1”) return (d.source.x + ((nodeSize(d.source) * a) / c)); if (type == “y1”) return (d.source.y + ((nodeSize(d.source) * b) / c)); if (options.arrows) { if (type == “x2”) return (d.target.x – ((((5 * linkWidthFunc(d)) + nodeSize(d.target)) * a) / c)); if (type == “y2”) return (d.target.y – ((((5 * linkWidthFunc(d)) + nodeSize(d.target)) * b) / c)); } else { if (type == “x2”) return (d.target.x – ((nodeSize(d.target) * a) / c)); if (type == “y2”) return (d.target.y – ((nodeSize(d.target) * b) / c)); } } link .attr(“x1”, function(d) { return idx(d, “x1”); }) .attr(“y1”, function(d) { return idx(d, “y1”); }) .attr(“x2”, function(d) { return idx(d, “x2”); }) .attr(“y2”, function(d) { return idx(d, “y2”); }); } function mouseover(d) { // unfocus non-connected links and nodes //if (options.focusOnHover) { var unfocusDivisor = 4; link.transition().duration(200) .style(“opacity”, function(l) { return d != l.source && d != l.target ? +options.opacity / unfocusDivisor : +options.opacity }); node.transition().duration(200) .style(“opacity”, function(o) { return d.index == o.index || neighboring(d, o) ? +options.opacity : +options.opacity / unfocusDivisor; }); //} d3.select(this).select(“circle”).transition() .duration(750) .attr(“r”, function(d){return nodeSize(d)+5;}); d3.select(this).select(“text”).transition() .duration(750) .attr(“x”, 13) .style(“stroke-width”, “.5px”) .style(“font”, options.clickTextSize + “px “) .style(“opacity”, 1); } function mouseout() { node.style(“opacity”, +options.opacity); link.style(“opacity”, +options.opacity); d3.select(this).select(“circle”).transition() .duration(750) .attr(“r”, function(d){return nodeSize(d);}); d3.select(this).select(“text”).transition() .duration(1250) .attr(“x”, 0) .style(“font”, options.fontSize + “px “) .style(“opacity”, options.opacityNoHover); } function click(d) { return eval(options.clickAction) } // add legend option if(options.legend){ var legendRectSize = 18; var legendSpacing = 4; var legend = svg.selectAll(‘.legend’) .data(color.domain()) .enter() .append(‘g’) .attr(‘class’, ‘legend’) .attr(‘transform’, function(d, i) { var height = legendRectSize + legendSpacing; var offset = height * color.domain().length / 2; var horz = legendRectSize; var vert = i * height+4; return ‘translate(‘ + horz + ‘,’ + vert + ‘)’; }); legend.append(‘rect’) .attr(‘width’, legendRectSize) .attr(‘height’, legendRectSize) .style(‘fill’, color) .style(‘stroke’, color); legend.append(‘text’) .attr(‘x’, legendRectSize + legendSpacing) .attr(‘y’, legendRectSize – legendSpacing) .text(function(d) { return d; }); } // make font-family consistent across all elements d3.select(el).selectAll(‘text’).style(‘font-family’, options.fontFamily); }, });

{“x”:{“links”:{“source”:[1,4,3,0,1,3,5,4],”target”:[0,0,1,2,2,2,3,5],”value”:[1,1,1,1,1,1,1,1],”colour”:[“#666″,”#666″,”#666″,”#666″,”#666″,”#666″,”#666″,”#666″]},”nodes”:{“name”:[“Virginia Opossum”,”Eastern Rat Snake”,”Red-Shouldered Hawk”,”Northern Short-Tailed Shrew”,”Jewelweed”,”Pavement Ant”],”group”:[“Primary Consumer”,”Primary Consumer”,”Apex Predator”,”Primary Consumer”,”Producer”,”Primary Consumer”]},”options”:{“NodeID”:”species”,”Group”:”group”,”colourScale”:”d3.scaleOrdinal(d3.schemeCategory10);”,”fontSize”:7,”fontFamily”:”mono”,”clickTextSize”:17.5,”linkDistance”:50,”linkWidth”:”function(d) { return Math.sqrt(d.value); }”,”charge”:-30,”opacity”:0.8,”zoom”:false,”legend”:true,”arrows”:true,”nodesize”:false,”radiusCalculation”:” Math.sqrt(d.nodesize)+6″,”bounded”:false,”opacityNoHover”:0,”clickAction”:null}},”evals”:[],”jsHooks”:[]} {“viewer”:{“width”:450,”height”:350,”padding”:10,”fill”:true},”browser”:{“width”:960,”height”:500,”padding”:10,”fill”:true}}

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