picky-statistics 4.0.0pre3 → 4.0.0pre5

data/lib/picky-statistics/application/javascripts/d3/src/layout/bundle.js

@@ -0,0 +1,57 @@
+// Implements hierarchical edge bundling using Holten's algorithm. For each
+// input link, a path is computed that travels through the tree, up the parent
+// hierarchy to the least common ancestor, and then back down to the destination
+// node. Each path is simply an array of nodes.
+d3.layout.bundle = function() {
+  return function(links) {
+    var paths = [],
+        i = -1,
+        n = links.length;
+    while (++i < n) paths.push(d3_layout_bundlePath(links[i]));
+    return paths;
+  };
+};
+
+function d3_layout_bundlePath(link) {
+  var start = link.source,
+      end = link.target,
+      lca = d3_layout_bundleLeastCommonAncestor(start, end),
+      points = [start];
+  while (start !== lca) {
+    start = start.parent;
+    points.push(start);
+  }
+  var k = points.length;
+  while (end !== lca) {
+    points.splice(k, 0, end);
+    end = end.parent;
+  }
+  return points;
+}
+
+function d3_layout_bundleAncestors(node) {
+  var ancestors = [],
+      parent = node.parent;
+  while (parent != null) {
+    ancestors.push(node);
+    node = parent;
+    parent = parent.parent;
+  }
+  ancestors.push(node);
+  return ancestors;
+}
+
+function d3_layout_bundleLeastCommonAncestor(a, b) {
+  if (a === b) return a;
+  var aNodes = d3_layout_bundleAncestors(a),
+      bNodes = d3_layout_bundleAncestors(b),
+      aNode = aNodes.pop(),
+      bNode = bNodes.pop(),
+      sharedNode = null;
+  while (aNode === bNode) {
+    sharedNode = aNode;
+    aNode = aNodes.pop();
+    bNode = bNodes.pop();
+  }
+  return sharedNode;
+}

data/lib/picky-statistics/application/javascripts/d3/src/layout/chord.js

@@ -0,0 +1,153 @@
+d3.layout.chord = function() {
+  var chord = {},
+      chords,
+      groups,
+      matrix,
+      n,
+      padding = 0,
+      sortGroups,
+      sortSubgroups,
+      sortChords;
+
+  function relayout() {
+    var subgroups = {},
+        groupSums = [],
+        groupIndex = d3.range(n),
+        subgroupIndex = [],
+        k,
+        x,
+        x0,
+        i,
+        j;
+
+    chords = [];
+    groups = [];
+
+    // Compute the sum.
+    k = 0, i = -1; while (++i < n) {
+      x = 0, j = -1; while (++j < n) {
+        x += matrix[i][j];
+      }
+      groupSums.push(x);
+      subgroupIndex.push(d3.range(n));
+      k += x;
+    }
+
+    // Sort groups…
+    if (sortGroups) {
+      groupIndex.sort(function(a, b) {
+        return sortGroups(groupSums[a], groupSums[b]);
+      });
+    }
+
+    // Sort subgroups…
+    if (sortSubgroups) {
+      subgroupIndex.forEach(function(d, i) {
+        d.sort(function(a, b) {
+          return sortSubgroups(matrix[i][a], matrix[i][b]);
+        });
+      });
+    }
+
+    // Convert the sum to scaling factor for [0, 2pi].
+    // TODO Allow start and end angle to be specified.
+    // TODO Allow padding to be specified as percentage?
+    k = (2 * Math.PI - padding * n) / k;
+
+    // Compute the start and end angle for each group and subgroup.
+    // Note: Opera has a bug reordering object literal properties!
+    x = 0, i = -1; while (++i < n) {
+      x0 = x, j = -1; while (++j < n) {
+        var di = groupIndex[i],
+            dj = subgroupIndex[di][j],
+            v = matrix[di][dj],
+            a0 = x,
+            a1 = x += v * k;
+        subgroups[di + "-" + dj] = {
+          index: di,
+          subindex: dj,
+          startAngle: a0,
+          endAngle: a1,
+          value: v
+        };
+      }
+      groups.push({
+        index: di,
+        startAngle: x0,
+        endAngle: x,
+        value: (x - x0) / k
+      });
+      x += padding;
+    }
+
+    // Generate chords for each (non-empty) subgroup-subgroup link.
+    i = -1; while (++i < n) {
+      j = i - 1; while (++j < n) {
+        var source = subgroups[i + "-" + j],
+            target = subgroups[j + "-" + i];
+        if (source.value || target.value) {
+          chords.push(source.value < target.value
+              ? {source: target, target: source}
+              : {source: source, target: target});
+        }
+      }
+    }
+
+    if (sortChords) resort();
+  }
+
+  function resort() {
+    chords.sort(function(a, b) {
+      return sortChords(
+          (a.source.value + a.target.value) / 2,
+          (b.source.value + b.target.value) / 2);
+    });
+  }
+
+  chord.matrix = function(x) {
+    if (!arguments.length) return matrix;
+    n = (matrix = x) && matrix.length;
+    chords = groups = null;
+    return chord;
+  };
+
+  chord.padding = function(x) {
+    if (!arguments.length) return padding;
+    padding = x;
+    chords = groups = null;
+    return chord;
+  };
+
+  chord.sortGroups = function(x) {
+    if (!arguments.length) return sortGroups;
+    sortGroups = x;
+    chords = groups = null;
+    return chord;
+  };
+
+  chord.sortSubgroups = function(x) {
+    if (!arguments.length) return sortSubgroups;
+    sortSubgroups = x;
+    chords = null;
+    return chord;
+  };
+
+  chord.sortChords = function(x) {
+    if (!arguments.length) return sortChords;
+    sortChords = x;
+    if (chords) resort();
+    return chord;
+  };
+
+  chord.chords = function() {
+    if (!chords) relayout();
+    return chords;
+  };
+
+  chord.groups = function() {
+    if (!groups) relayout();
+    return groups;
+  };
+
+  return chord;
+};

data/lib/picky-statistics/application/javascripts/d3/src/layout/cluster.js

@@ -0,0 +1,78 @@
+// Implements a hierarchical layout using the cluster (or dendogram) algorithm.
+d3.layout.cluster = function() {
+  var hierarchy = d3.layout.hierarchy().sort(null).value(null),
+      separation = d3_layout_treeSeparation,
+      size = [1, 1]; // width, height
+
+  function cluster(d, i) {
+    var nodes = hierarchy.call(this, d, i),
+        root = nodes[0],
+        previousNode,
+        x = 0,
+        kx,
+        ky;
+
+    // First walk, computing the initial x & y values.
+    d3_layout_treeVisitAfter(root, function(node) {
+      var children = node.children;
+      if (children && children.length) {
+        node.x = d3_layout_clusterX(children);
+        node.y = d3_layout_clusterY(children);
+      } else {
+        node.x = previousNode ? x += separation(node, previousNode) : 0;
+        node.y = 0;
+        previousNode = node;
+      }
+    });
+
+    // Compute the left-most, right-most, and depth-most nodes for extents.
+    var left = d3_layout_clusterLeft(root),
+        right = d3_layout_clusterRight(root),
+        x0 = left.x - separation(left, right) / 2,
+        x1 = right.x + separation(right, left) / 2;
+
+    // Second walk, normalizing x & y to the desired size.
+    d3_layout_treeVisitAfter(root, function(node) {
+      node.x = (node.x - x0) / (x1 - x0) * size[0];
+      node.y = (1 - node.y / root.y) * size[1];
+    });
+
+    return nodes;
+  }
+
+  cluster.separation = function(x) {
+    if (!arguments.length) return separation;
+    separation = x;
+    return cluster;
+  };
+
+  cluster.size = function(x) {
+    if (!arguments.length) return size;
+    size = x;
+    return cluster;
+  };
+
+  return d3_layout_hierarchyRebind(cluster, hierarchy);
+};
+
+function d3_layout_clusterY(children) {
+  return 1 + d3.max(children, function(child) {
+    return child.y;
+  });
+}
+
+function d3_layout_clusterX(children) {
+  return children.reduce(function(x, child) {
+    return x + child.x;
+  }, 0) / children.length;
+}
+
+function d3_layout_clusterLeft(node) {
+  var children = node.children;
+  return children && children.length ? d3_layout_clusterLeft(children[0]) : node;
+}
+
+function d3_layout_clusterRight(node) {
+  var children = node.children, n;
+  return children && (n = children.length) ? d3_layout_clusterRight(children[n - 1]) : node;
+}

data/lib/picky-statistics/application/javascripts/d3/src/layout/force.js

@@ -0,0 +1,342 @@
+// A rudimentary force layout using Gauss-Seidel.
+d3.layout.force = function() {
+  var force = {},
+      event = d3.dispatch("tick"),
+      size = [1, 1],
+      drag,
+      alpha,
+      friction = .9,
+      linkDistance = d3_layout_forceLinkDistance,
+      linkStrength = d3_layout_forceLinkStrength,
+      charge = -30,
+      gravity = .1,
+      theta = .8,
+      interval,
+      nodes = [],
+      links = [],
+      distances,
+      strengths,
+      charges;
+
+  function repulse(node) {
+    return function(quad, x1, y1, x2, y2) {
+      if (quad.point !== node) {
+        var dx = quad.cx - node.x,
+            dy = quad.cy - node.y,
+            dn = 1 / Math.sqrt(dx * dx + dy * dy);
+
+        /* Barnes-Hut criterion. */
+        if ((x2 - x1) * dn < theta) {
+          var k = quad.charge * dn * dn;
+          node.px -= dx * k;
+          node.py -= dy * k;
+          return true;
+        }
+
+        if (quad.point && isFinite(dn)) {
+          var k = quad.pointCharge * dn * dn;
+          node.px -= dx * k;
+          node.py -= dy * k;
+        }
+      }
+      return !quad.charge;
+    };
+  }
+
+  function tick() {
+    var n = nodes.length,
+        m = links.length,
+        q,
+        i, // current index
+        o, // current object
+        s, // current source
+        t, // current target
+        l, // current distance
+        k, // current force
+        x, // x-distance
+        y; // y-distance
+
+    // gauss-seidel relaxation for links
+    for (i = 0; i < m; ++i) {
+      o = links[i];
+      s = o.source;
+      t = o.target;
+      x = t.x - s.x;
+      y = t.y - s.y;
+      if (l = (x * x + y * y)) {
+        l = alpha * strengths[i] * ((l = Math.sqrt(l)) - distances[i]) / l;
+        x *= l;
+        y *= l;
+        t.x -= x * (k = s.weight / (t.weight + s.weight));
+        t.y -= y * k;
+        s.x += x * (k = 1 - k);
+        s.y += y * k;
+      }
+    }
+
+    // apply gravity forces
+    if (k = alpha * gravity) {
+      x = size[0] / 2;
+      y = size[1] / 2;
+      i = -1; if (k) while (++i < n) {
+        o = nodes[i];
+        o.x += (x - o.x) * k;
+        o.y += (y - o.y) * k;
+      }
+    }
+
+    // compute quadtree center of mass and apply charge forces
+    if (charge) {
+      d3_layout_forceAccumulate(q = d3.geom.quadtree(nodes), alpha, charges);
+      i = -1; while (++i < n) {
+        if (!(o = nodes[i]).fixed) {
+          q.visit(repulse(o));
+        }
+      }
+    }
+
+    // position verlet integration
+    i = -1; while (++i < n) {
+      o = nodes[i];
+      if (o.fixed) {
+        o.x = o.px;
+        o.y = o.py;
+      } else {
+        o.x -= (o.px - (o.px = o.x)) * friction;
+        o.y -= (o.py - (o.py = o.y)) * friction;
+      }
+    }
+
+    event.tick({type: "tick", alpha: alpha});
+
+    // simulated annealing, basically
+    return (alpha *= .99) < .005;
+  }
+
+  force.nodes = function(x) {
+    if (!arguments.length) return nodes;
+    nodes = x;
+    return force;
+  };
+
+  force.links = function(x) {
+    if (!arguments.length) return links;
+    links = x;
+    return force;
+  };
+
+  force.size = function(x) {
+    if (!arguments.length) return size;
+    size = x;
+    return force;
+  };
+
+  force.linkDistance = function(x) {
+    if (!arguments.length) return linkDistance;
+    linkDistance = d3.functor(x);
+    return force;
+  };
+
+  // For backwards-compatibility.
+  force.distance = force.linkDistance;
+
+  force.linkStrength = function(x) {
+    if (!arguments.length) return linkStrength;
+    linkStrength = d3.functor(x);
+    return force;
+  };
+
+  force.friction = function(x) {
+    if (!arguments.length) return friction;
+    friction = x;
+    return force;
+  };
+
+  force.charge = function(x) {
+    if (!arguments.length) return charge;
+    charge = typeof x === "function" ? x : +x;
+    return force;
+  };
+
+  force.gravity = function(x) {
+    if (!arguments.length) return gravity;
+    gravity = x;
+    return force;
+  };
+
+  force.theta = function(x) {
+    if (!arguments.length) return theta;
+    theta = x;
+    return force;
+  };
+
+  force.start = function() {
+    var i,
+        j,
+        n = nodes.length,
+        m = links.length,
+        w = size[0],
+        h = size[1],
+        neighbors,
+        o;
+
+    for (i = 0; i < n; ++i) {
+      (o = nodes[i]).index = i;
+      o.weight = 0;
+    }
+
+    distances = [];
+    strengths = [];
+    for (i = 0; i < m; ++i) {
+      o = links[i];
+      if (typeof o.source == "number") o.source = nodes[o.source];
+      if (typeof o.target == "number") o.target = nodes[o.target];
+      distances[i] = linkDistance.call(this, o, i);
+      strengths[i] = linkStrength.call(this, o, i);
+      ++o.source.weight;
+      ++o.target.weight;
+    }
+
+    for (i = 0; i < n; ++i) {
+      o = nodes[i];
+      if (isNaN(o.x)) o.x = position("x", w);
+      if (isNaN(o.y)) o.y = position("y", h);
+      if (isNaN(o.px)) o.px = o.x;
+      if (isNaN(o.py)) o.py = o.y;
+    }
+
+    charges = [];
+    if (typeof charge === "function") {
+      for (i = 0; i < n; ++i) {
+        charges[i] = +charge.call(this, nodes[i], i);
+      }
+    } else {
+      for (i = 0; i < n; ++i) {
+        charges[i] = charge;
+      }
+    }
+
+    // initialize node position based on first neighbor
+    function position(dimension, size) {
+      var neighbors = neighbor(i),
+          j = -1,
+          m = neighbors.length,
+          x;
+      while (++j < m) if (!isNaN(x = neighbors[j][dimension])) return x;
+      return Math.random() * size;
+    }
+
+    // initialize neighbors lazily
+    function neighbor() {
+      if (!neighbors) {
+        neighbors = [];
+        for (j = 0; j < n; ++j) {
+          neighbors[j] = [];
+        }
+        for (j = 0; j < m; ++j) {
+          var o = links[j];
+          neighbors[o.source.index].push(o.target);
+          neighbors[o.target.index].push(o.source);
+        }
+      }
+      return neighbors[i];
+    }
+
+    return force.resume();
+  };
+
+  force.resume = function() {
+    alpha = .1;
+    d3.timer(tick);
+    return force;
+  };
+
+  force.stop = function() {
+    alpha = 0;
+    return force;
+  };
+
+  // use `node.call(force.drag)` to make nodes draggable
+  force.drag = function() {
+    if (!drag) drag = d3.behavior.drag()
+        .origin(Object)
+        .on("dragstart", dragstart)
+        .on("drag", d3_layout_forceDrag)
+        .on("dragend", d3_layout_forceDragEnd);
+
+    this.on("mouseover.force", d3_layout_forceDragOver)
+        .on("mouseout.force", d3_layout_forceDragOut)
+        .call(drag);
+  };
+
+  function dragstart(d) {
+    d3_layout_forceDragOver(d3_layout_forceDragNode = d);
+    d3_layout_forceDragForce = force;
+  }
+
+  return d3.rebind(force, event, "on");
+};
+
+var d3_layout_forceDragForce,
+    d3_layout_forceDragNode;
+
+function d3_layout_forceDragOver(d) {
+  d.fixed |= 2;
+}
+
+function d3_layout_forceDragOut(d) {
+  if (d !== d3_layout_forceDragNode) d.fixed &= 1;
+}
+
+function d3_layout_forceDragEnd() {
+  d3_layout_forceDrag();
+  d3_layout_forceDragNode.fixed &= 1;
+  d3_layout_forceDragForce = d3_layout_forceDragNode = null;
+}
+
+function d3_layout_forceDrag() {
+  d3_layout_forceDragNode.px = d3.event.x;
+  d3_layout_forceDragNode.py = d3.event.y;
+  d3_layout_forceDragForce.resume(); // restart annealing
+}
+
+function d3_layout_forceAccumulate(quad, alpha, charges) {
+  var cx = 0,
+      cy = 0;
+  quad.charge = 0;
+  if (!quad.leaf) {
+    var nodes = quad.nodes,
+        n = nodes.length,
+        i = -1,
+        c;
+    while (++i < n) {
+      c = nodes[i];
+      if (c == null) continue;
+      d3_layout_forceAccumulate(c, alpha, charges);
+      quad.charge += c.charge;
+      cx += c.charge * c.cx;
+      cy += c.charge * c.cy;
+    }
+  }
+  if (quad.point) {
+    // jitter internal nodes that are coincident
+    if (!quad.leaf) {
+      quad.point.x += Math.random() - .5;
+      quad.point.y += Math.random() - .5;
+    }
+    var k = alpha * charges[quad.point.index];
+    quad.charge += quad.pointCharge = k;
+    cx += k * quad.point.x;
+    cy += k * quad.point.y;
+  }
+  quad.cx = cx / quad.charge;
+  quad.cy = cy / quad.charge;
+}
+
+function d3_layout_forceLinkDistance(link) {
+  return 20;
+}
+
+function d3_layout_forceLinkStrength(link) {
+  return 1;
+}