D3 force directed graph direction

I'm new to D3, and am trying to make a graph similar to this example but a few things confuse me. I'm unsure when the example is referring to things built in to D3, or just the data set they are using.

Like here, I'm not sure about the id in d.id. as the example's data looks like this, which makes me think id is from the data. Or does it represent an index value?

"nodes": [
    {"id": "Myriel", "group": 1},
    {"id": "Napoleon", "group": 1}
         ],
            // etc
"links": [
    {"source": "Napoleon", "target": "Myriel", "value": 1},
    {"source": "Mlle.Baptistine", "target": "Myriel", "value": 8},
    {"source": "Mme.Magloire", "target": "Myriel", "value": 10},
          //etc

var simulation = d3.forceSimulation()
    .force("link", d3.forceLink().id(function(d) { return d.id; })) <-- where is this from?
    .force("charge", d3.forceManyBody())
    .force("center", d3.forceCenter(width / 2, height / 2));

SO! In my code I get an error repeating thousands of times, 'Uncaught Error: missing: X', where X is the value of the first source in my links array. I can console.log my data and it looks fine, and the elements are rendering to the DOM, but all bunched up to the top left of the SVG. I don't know what is wrong. I guess I have 2 questions.

1. Could someone clarify about the example id thing?

2. What does my error mean?

Any help would be appreciated.

My code;

var graph

var svg = d3.select("svg"),
    width = +svg.attr("width"),
    height = +svg.attr("height");


d3.json("./mock.json", function(json) {
  var graph = json
      console.log(graph);
      console.log(graph.nodes);

      var simulation = d3.forceSimulation()
      .force("link", d3.forceLink(graph.links))
      .force("charge", d3.forceManyBody())
      .force("center", d3.forceCenter(width/2, height/2));

  var link = svg.append("g")
    .attr("class", "links")
    .selectAll("line")
    .data(graph.links)
    .enter().append("line")
    //.attr("stroke-width", function(d) {return Math.sqrt(d.value); });

  var node = svg.append("g")
    .attr("class", "nodes")
    .selectAll("circle")
    .data(graph.nodes)
    .enter().append("circle")
      .attr("r", 5)
      //.attr("fill", function(d) { return color(d.id); })
      .call(d3.drag()
        .on("start", dragstarted)
        .on("drag", dragged)
        .on("end", dragended));

    node.append("title")
      .text(function(d) {return d.text });

    simulation
      .nodes(graph.nodes)
      .on("tick", ticked);

    simulation.force("link")
      .links(graph.links);

})

function ticked() {

  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; })

  node
      .attr("cx", function(d) {return d.x; })
      .attr("cy", function(d) {return d.y; });
}


function dragstarted(d) {
    if(!d3.event.active) simulation.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) simulation.alphaTarget(0);
    d.fx = null;
    d.fy = null;
}

});

Data:

{
 "nodes":[
         {"reference":5, "year": 0, "text":"The amount of time spent on video gaming is related negatively to academic achievement", "tags":["Academic disturbance"]},
         {"reference":5, "year": 0, "text":"Digital addiction ranges from <1% and 38%", "tags":["Addiction"]},
         {"reference":58, "year": 0, "text":"Patological video game play impacts negativelly academic achievement", "tags":["Addiction"]},
         {"reference":77, "year": 2009, "text":"74% of adults have Internet access at home", "tags":["Adults"]},
         {"reference":64, "year": 0, "text":"Apathetic users spend short times on web pages, follow no logical order, and make random selections", "tags":["Apathetic hypertext users3"]},
         {"reference":8, "year": 0, "text":"49.8% of sessions are shorter than 5 seconds", "tags":["App usage"]}
       ],
 "links": [
       {"source":0,"target":2},
       {"source":0,"target":6},
       {"source":1,"target":6},
       {"source":1,"target":3},
       {"source":1,"target":2}

 ]
 }