コード例 #1
0
ファイル: IBDReporter.java プロジェクト: benb/beast-mcmc
  public void forwardIBD() {
    int numNodes = treeModel.getNodeCount();
    int stateCount = substitutionModel.getStateCount();
    getDiagonalRates(diag);
    for (int nodeId = 0; nodeId < numNodes; ++nodeId) {
      NodeRef node = treeModel.getNode(nodeId);
      NodeRef parent = treeModel.getParent(node);
      if (parent == null) { // handle the root

      } else if (treeModel.isExternal(node)) { // Handle the tip
        double branchTime =
            branchRateModel.getBranchRate(treeModel, node)
                * (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));

        for (int state = 0; state < stateCount; ++state) {
          ibdForward[nodeId][state] = Math.exp(-diag[state] * branchTime);
        }
      } else { // Handle internal node
        double branchTime =
            branchRateModel.getBranchRate(treeModel, node)
                * (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));

        int childCount = treeModel.getChildCount(node);
        for (int state = 0; state < stateCount; ++state) {
          ibdForward[nodeId][state] = 0;
          for (int child = 0; child < childCount; ++child) {
            int childNodeId = treeModel.getChild(node, child).getNumber();
            ibdForward[nodeId][state] += ibdForward[childNodeId][state];
          }
          ibdForward[nodeId][state] *= Math.exp(-diag[state] * branchTime);
        }
      }
    }
  }
コード例 #2
0
ファイル: IBDReporter.java プロジェクト: benb/beast-mcmc
 public void backwardIBD(NodeRef node) {
   int stateCount = substitutionModel.getStateCount();
   if (node == null) {
     node = treeModel.getRoot();
     int nodeId = node.getNumber();
     for (int state = 0; state < stateCount; ++state) {
       ibdBackward[nodeId][state] = 0;
     }
   }
   getDiagonalRates(diag);
   int childCount = treeModel.getChildCount(node);
   int nodeId = node.getNumber();
   for (int child = 0; child < childCount; ++child) {
     NodeRef childNode = treeModel.getChild(node, child);
     int childNodeId = childNode.getNumber();
     double branchTime =
         branchRateModel.getBranchRate(treeModel, childNode)
             * (treeModel.getNodeHeight(node) - treeModel.getNodeHeight(childNode));
     for (int state = 0; state < stateCount; ++state) {
       ibdBackward[childNodeId][state] = ibdBackward[nodeId][state];
       for (int sibling = 0; sibling < childCount; ++sibling) {
         if (sibling != child) {
           int siblingId = treeModel.getChild(node, sibling).getNumber();
           ibdBackward[childNodeId][state] += ibdForward[siblingId][state];
         }
       }
       ibdBackward[childNodeId][state] *= Math.exp(-diag[state] * branchTime);
     }
   }
   for (int child = 0; child < childCount; ++child) {
     NodeRef childNode = treeModel.getChild(node, child);
     backwardIBD(childNode);
   }
 }
コード例 #3
0
  /** Calculates the actual rates corresponding to the category indices. */
  protected void setupRates() {

    // System.out.println("BRRRTTZZZ " + distributionIndexParameter.getValue(0));
    for (int i = 0; i < tree.getNodeCount(); i++) {
      // rates[i] = distributionModel.quantile(rateCategoryQuantiles.getNodeValue(
      // rateCategoryQuantiles.getTreeModel(), rateCategoryQuantiles.getTreeModel().getNode(i) ));
      if (!tree.isRoot(tree.getNode(i))) {

        if (useQuantilesForRates) {
            /* Using quantiles to represent rates */
          rates[tree.getNode(i).getNumber()] =
              distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].quantile(
                  rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i)));
        } else {
            /* Not using quantiles to represent rates. This is practically useless for anything else other than simulation */
          rates[tree.getNode(i).getNumber()] =
              rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i));
        }
      }
    }
    /*System.out.print(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName() + "\t" + (int) Math.round(distributionIndexParameter.getValue(0)) + "\t" + rates[1] + "\t" + rateCategoryQuantiles.getNodeValue(tree, tree.getNode(1)));// + "\t" + distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].);
    if(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.LogNormalDistributionModel")) {
        LogNormalDistributionModel lndm = (LogNormalDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
        System.out.println("\t" + lndm.getS());
    }
    else if (distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.InverseGaussianDistributionModel")) {
        InverseGaussianDistributionModel lndm = (InverseGaussianDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
        System.out.println("\t" + lndm.getS());
    }*/
    if (normalize) computeFactor();
  }
コード例 #4
0
  /** provide information to the categoriesParameter about the number of sites */
  public void setCategoriesParameter(int siteCount) {
    categoriesParameter.setDimension(siteCount);
    categoriesParameter.addBounds(new Parameter.DefaultBounds(categoryCount, 0.0, siteCount));
    for (int i = 0; i < siteCount; i++) {

      int r = (int) (Math.random() * categoryCount);
      categoriesParameter.setParameterValue(i, r);
    }

    for (int j = 0; j < categoryCount; j++) {
      sitesInCategory[j] = 0;
    }

    for (int i = 0; i < siteCount; i++) {
      int value = (int) categoriesParameter.getParameterValue(i);
      sitesInCategory[value] = sitesInCategory[value] + 1;
    }
  }
コード例 #5
0
  public static Transform[] parseListOfTransforms(XMLObject xo, int maxDim)
      throws XMLParseException {
    Transform[] transforms = null;

    boolean anyTransforms = false;
    for (int i = 0; i < xo.getChildCount(); ++i) {
      if (xo.getChild(i) instanceof Transform.ParsedTransform) {
        Transform.ParsedTransform t = (Transform.ParsedTransform) xo.getChild(i);
        if (transforms == null) {
          transforms = Transform.Util.getListOfNoTransforms(maxDim);
        }

        t.end = Math.max(t.end, maxDim);
        if (t.start < 0 || t.end < 0 || t.start > t.end) {
          throw new XMLParseException("Invalid bounds for transform in " + xo.getId());
        }
        for (int j = t.start; j < t.end; j += t.every) {
          transforms[j] = t.transform;
          anyTransforms = true;
        }
      }
    }
    if (anyTransforms) {
      StringBuilder sb =
          new StringBuilder("Using distributional transforms in " + xo.getId() + "\n");
      for (int i = 0; i < transforms.length; ++i) {
        if (transforms[i] != Transform.NONE) {
          sb.append("\t")
              .append(transforms[i].getTransformName())
              .append(" on index ")
              .append(i + 1)
              .append("\n");
        }
      }
      sb.append("Please cite:\n").append(Citable.Utils.getCitationString(Transform.LOG));
      Logger.getLogger("dr.utils.Transform").info(sb.toString());
    }
    return transforms;
  }