d3.geom.min.js

(function(){function c(a){var b=0,c=0;for(;;){if(a(b,c))return[b,c];b===0?(b=c+1,c=0):(b-=1,c+=1)}}function d(a,b,c,d){var e,f,g,h,i,j,k;return e=d[a],f=e[0],g=e[1],e=d[b],h=e[0],i=e[1],e=d[c],j=e[0],k=e[1],(k-g)*(h-f)-(i-g)*(j-f)>0}function e(a,b,c){return(c[0]-b[0])*(a[1]-b[1])<(c[1]-b[1])*(a[0]-b[0])}function f(a,b,c,d){var e=a[0],f=b[0],g=c[0],h=d[0],i=a[1],j=b[1],k=c[1],l=d[1],m=e-g,n=f-e,o=h-g,p=i-k,q=j-i,r=l-k,s=(o*p-r*m)/(r*n-o*q);return[e+s*n,i+s*q]}function h(a,b){var c={list:a.map(function(a,b){return{index:b,x:a[0],y:a[1]}}).sort(function(a,b){return a.y<b.y?-1:a.y>b.y?1:a.x<b.x?-1:a.x>b.x?1:0}),bottomSite:null},d={list:[],leftEnd:null,rightEnd:null,init:function(){d.leftEnd=d.createHalfEdge(null,"l"),d.rightEnd=d.createHalfEdge(null,"l"),d.leftEnd.r=d.rightEnd,d.rightEnd.l=d.leftEnd,d.list.unshift(d.leftEnd,d.rightEnd)},createHalfEdge:function(a,b){return{edge:a,side:b,vertex:null,l:null,r:null}},insert:function(a,b){b.l=a,b.r=a.r,a.r.l=b,a.r=b},leftBound:function(a){var 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f.list.shift()}};d.init(),c.bottomSite=c.list.shift();var h=c.list.shift(),i,j,k,l,m,n,o,p,q,r,s,t,u;for(;;){f.empty()||(i=f.min());if(h&&(f.empty()||h.y<i.y||h.y==i.y&&h.x<i.x))j=d.leftBound(h),k=d.right(j),o=d.rightRegion(j),t=e.bisect(o,h),n=d.createHalfEdge(t,"l"),d.insert(j,n),r=e.intersect(j,n),r&&(f.del(j),f.insert(j,r,e.distance(r,h))),j=n,n=d.createHalfEdge(t,"r"),d.insert(j,n),r=e.intersect(n,k),r&&f.insert(n,r,e.distance(r,h)),h=c.list.shift();else if(!f.empty())j=f.extractMin(),l=d.left(j),k=d.right(j),m=d.right(k),o=d.leftRegion(j),p=d.rightRegion(k),s=j.vertex,e.endPoint(j.edge,j.side,s),e.endPoint(k.edge,k.side,s),d.del(j),f.del(k),d.del(k),u="l",o.y>p.y&&(q=o,o=p,p=q,u="r"),t=e.bisect(o,p),n=d.createHalfEdge(t,u),d.insert(l,n),e.endPoint(t,g[u],s),r=e.intersect(l,n),r&&(f.del(l),f.insert(l,r,e.distance(r,o))),r=e.intersect(n,m),r&&f.insert(n,r,e.distance(r,o));else break}for(j=d.right(d.leftEnd);j!=d.rightEnd;j=d.right(j))b(j.edge)}function 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d3.layout.min.js

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data.js

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index.html

<!DOCTYPE html>
<html>                                                                  
 <head>                                                                  
 <script type="text/javascript" src="jquery-1.7.1.min.js"></script>          
 <script type="text/javascript" src="jquery.flot.min.js"></script>
 <script type="text/javascript" src="d3.min.js"></script>
 <script type="text/javascript" src="d3.geom.min.js"></script>
 <script type="text/javascript" src="d3.layout.min.js"></script>
 <script type="text/javascript" src="data.js"></script>
 <link type="text/css" rel="stylesheet" href="sirtoy.css"/>
 <title>SIR toy</title>
 </head>

<body>

  <div id="container">

  <div id="epicurves"></div>

  <div id="counters">
    <span id="susceptible"><span id="count_S">0</span> susceptible</span><br />
    <span id="infectious"><span id="count_I">0</span> infectious</span><br />
    <span id="recovered"><span id="count_R">0</span> recovered</span>
 </div>

 <div id="controls">
   <span>p(<span style="color: #0ff">S</span> + <span style="color: #ff0">I</span> &rarr; <span style="color: #ff0">I</span> + <span style="color: #ff0">I</span>) = <input id="p_SI" type="text" name="p_SI" value="0.00" /></span><br />
   <span>p(<span style="color: #ff0">I</span> &rarr; <span style="color: #f0f">R</span>) = <input id="p_IR" type="text" name="p_IR" value="0.00" /></span>
 </div>

  <div id="graph-layout">
    <div id="graph-control">
      <span id="start-text">click a susceptible node to infect it</span>
      <button id="reset-button">reset</button>
    </div>
  </div>

  <div id="credits"><a href="https://github.com/ccattuto/SIRtoy">code</a> by <a href="http://isiosf.isi.it/~cattuto/">Ciro Cattuto</a>, using <a href="http://mbostock.github.com/d3/">d3.js</a>, <a href="http://jquery.com/">jQuery</a>, <a href="http://code.google.com/p/flot/">flot</a>, inspired by <a href="http://blockses.appspot.com/929623">this</a> and with help from <a href="http://knowledgecartography.org/">Marco Quaggiotto</a></div>
  </div>

  <script type="text/javascript" src="sirtoy.js"></script>
  
 </body>                                                                 
</html>

jquery-1.7.1.min.js

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jquery.flot.min.js

/* Javascript plotting library for jQuery, v. 0.7.
 *
 * Released under the MIT license by IOLA, December 2007.
 *
 */
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SIR_toy_README.md

SIRtoy

This is a Javascript toy implementation of an SIR epidemic model on a graph. It allows to explore the behavior of a simple dynamical process over a complex network. The hardcoded sample network is a small Barabási–Albert graph.

It is built on top of d3.js, jQuery and flot, and borrows code from http://blockses.appspot.com/929623.

sirtoy.css

body {
  font-family: Sans-Serif;
}

div#container {
   border-style: solid;
   border-width: 1px;
   border-color: #eee;
   margin: 10px;
}

div#counters {
   font-size: 36px;
   float: left;
   height: 180px;
   margin-top: 20px;
   margin-bottom: 20px;
}

div#controls {
   font-size: 36px;
   float: right;
   height: 180px;
   margin: 20px;
   text-align: right;
}

#p_SI, #p_IR {
 width: 75px;
 padding: 3px;
 font-size: 32px;
 border: 1px solid #aaa;
}

span#susceptible {
	color: #0ff;
    font-size: 14px;
}

span#infectious {
	color: #ff0;
    font-size: 14px;
}

span#recovered {
	color: #f0f;
    font-size: 14px;
}

span#count_S, span#count_I, span#count_R {
   font-size: 48px;
   font-weight: bold;
}

div#graph-layout {
   height: 500px;
   margin: 20px;
   background: #fafafa;
   border-style: solid;
   border-width: 1px;
   border-color: #eee;
   clear: both;
   position: relative;
}

div#epicurves {
   width: 320px;
   height: 180px;
   background: #fff;
   margin: 20px;
   float: left;
}

circle.node {
  stroke: #000;
  stroke-width: 1.5px;
  fill: #ff0;
}

line.link {
  stroke: #333;
  stroke-opacity: .75;
  stroke-width: 1.5px;
}

div#graph-control {
   position: absolute;
   top: 0px;
   width: 100%;
   pointer-events: none;
}

span#start-text {
  font-size: 28px;
  text-align: left;
  float: left;
  color: #666;
  padding: 10px;
}

button#reset-button {
  float: right;
  font-size: 28px;
  color: #666;
  pointer-events: all;
}

div#credits {
   text-align: right;
   font-size: 14px;
   padding: 5px;
}

sirtoy.js

// -----------------------------------------------------------

var valid_data = 1;
var running = 0;
var p_SI = 0.2;
var p_IR = 0.08;
var time_interval = 500;
var count = 0;
var timeseries;

var nodeArray = G.nodes;
var edgeArray = G.links;

var sir_color = {S: "#00ffff", I: "#ffff00", R: "#ff00ff" }

var epi_state = { S: nodeArray.length, I: 0, R: 0 };

function reset_history () {
  timeseries = {S: {label: "S", color: sir_color.S, data: []},
                I: {label: "I", color: sir_color.I, data: []},
                R: {label: "R", color: sir_color.R, data: []}};

  timeseries.S.data.push([count, epi_state.S]);
  timeseries.I.data.push([count, epi_state.I]);
  timeseries.R.data.push([count, epi_state.R]);
}

reset_history();

var plotOptions = {
     //   lines: { show: true },
	 //	points: { show: true },
        xaxis: {min: 0},
        series: { shadowSize: 0 }
    };

var plot = $.plot($("#epicurves"), [], plotOptions);

var kArray = [];

for (i in nodeArray) {
	kArray[nodeArray[i].name] = 0;
}

for (i in edgeArray) {
	kArray[edgeArray[i].source]++;
	kArray[edgeArray[i].target]++;
}

for (i in nodeArray) {
	nodeArray[i].k = kArray[i];
    nodeArray[i].state = "S";
}


var w = "100%";
var h = 500;

var vis = d3.select("#graph-layout")
    .append("svg:svg")
    .attr("width", w)
    .attr("height", h);

var force = d3.layout.force()
      .charge(-100)
      .friction(0.6)
      .gravity(0.02)
      .linkDistance(100)
      .nodes(nodeArray)
      .links(edgeArray)
      .size([900, h]);

  force.on("tick", function() {
	vis.selectAll("line.link")
        .attr("x1", function(d) { return d.source.x; })
        .attr("y1", function(d) { return d.source.y; })
        .attr("x2", function(d) { return d.target.x; })
        .attr("y2", function(d) { return d.target.y; });

	vis.selectAll("circle.node")
    	.attr("cx", function(d) { return d.x; })
        .attr("cy", function(d) { return d.y; })
        .style("fill", function(d) { return sir_color[d.state]; } );
  });

$("#p_SI").val(p_SI)
$("#p_SI").keyup(update_p_SI);

$("#p_IR").val(p_IR)
$("#p_IR").keyup(update_p_IR);

update_graph();
update_plot();
update_counters();

$("#reset-button").click(reset_all);

setInterval(run_SIR, time_interval);


function run_SIR() {

    if (running == 0)
       return;

    for (k in nodeArray)
        nodeArray[k].new_state = nodeArray[k].state;

    for (k in edgeArray) {
        i = edgeArray[k].source;
        j = edgeArray[k].target;

        if (i.state == "S" && j.state == "I") {
            tmp = i; i = j; j = tmp;
        }

        if (i.state == "I" && j.state == "S" && j.new_state == "S") {
          if (Math.random() < p_SI) {
             j.new_state = "I";
             epi_state.I ++;
             epi_state.S --;
          }
       }
    }

    for (k in nodeArray) {
        if (nodeArray[k].state == "I") {
          if (Math.random() < p_IR) {
             nodeArray[k].new_state = "R";
             epi_state.R ++;
             epi_state.I --;
          }
       }
    }

    for (k in nodeArray)
        nodeArray[k].state = nodeArray[k].new_state;

    update_graph();

    count++;

    timeseries.S.data.push([count, epi_state.S]);
    timeseries.I.data.push([count, epi_state.I]);
    timeseries.R.data.push([count, epi_state.R]);

    update_plot();

    update_counters();

    if (epi_state.I == 0)
       running = 0;
}

function update_graph () {

  x = vis.selectAll("line.link").data(edgeArray, function(d) { return d.source.name + "-" + d.target.name; });
  x.enter().insert("svg:line", "circle.node")
      .attr("class", "link")
      .attr("x1", function(d) { return d.source.x; })
      .attr("y1", function(d) { return d.source.y; })
      .attr("x2", function(d) { return d.target.x; })
      .attr("y2", function(d) { return d.target.y; });
  x.exit().remove();

  x = vis.selectAll("circle.node").data(nodeArray, function(d) { return d.name; });
  x.enter().insert("svg:circle")
      .attr("class", "node")
      .attr("cx", function(d) { return d.x; })
      .attr("cy", function(d) { return d.y; })
      .attr("r", function(d) { return 3*Math.sqrt(d.k); })
      .style("fill", function(d) { return sir_color[d.state]; } )
      .call(force.drag)
      .on("click", function(d,i) { if (running == 0 && valid_data == 1 && d.state == "S") {d.state = "I"; epi_state.S--; epi_state.I++; running = 1; $("#start-text").fadeOut(); }} );
  x.exit().remove();

  force.start();

}

function update_plot () {
 plot.setData([timeseries.S, timeseries.I, timeseries.R]);
 plot.setupGrid();
 plot.draw();
}


function update_counters () {
  $("#count_S").html(epi_state.S);
  $("#count_I").html(epi_state.I);
  $("#count_R").html(epi_state.R);
}

function update_p_SI () {
  p = Number($("#p_SI").val());
  if (isNaN(p) || p<0.0 || p>1.0) {
     valid_data = 0;
     $("#p_SI").css("background-color", "#f88");
  } else {
     p_SI = p;
     valid_data = 1;
     $("#p_SI").css("background-color", "#fff");
  }
}

function update_p_IR () {
  p = Number($("#p_IR").val());
  if (isNaN(p) || p<0.0 || p>1.0) {
     valid_data = 0;
     $("#p_IR").css("background-color", "#f88");
  } else {
     p_IR = p;
     valid_data = 1;
     $("#p_IR").css("background-color", "#fff");
  }
}

function reset_all () {
	running = 0;

    count = 0;
    epi_state = { S: nodeArray.length, I: 0, R: 0 };

    reset_history();
    update_plot();

    update_counters();

    for (k in nodeArray)
		nodeArray[k].state = "S";

    update_graph();

   $("#start-text").fadeIn();
}