Constructor Detail

• LikelihoodSummary

  public LikelihoodSummary(DataType dt,
                           double overallLogLikelihood,
                           double[] categoryProbabilities,
                           double[][] individualLikelihoods,
                           int[] sitePatternMatchup)

  Parameters:

  dt - The data type used (for reference)

  overallLogLikelihood - (the overall log likelihood found)

  categoryProbabilities - (the probabilities of each category ([1] if not separate categories)

  individualLikelihoods - The individual likelihoods of each pattern/category (organised [site][category])

  sitePatternMatchup - for each site indicates which is the related pattern (it is assumed categoryProbabilities given with regard to patterns, if not sitePatternMatchup should contain {0,1,2, ... numberOfSites-1)

Method Detail

• getOverallLogLikelihood

  public final double getOverallLogLikelihood()

• generateCategoryRankings

  public final int[][] generateCategoryRankings()

• generateSiteLikelihoods

  public final double[] generateSiteLikelihoods(int site)

• generateSitePosteriors

  public final double[] generateSitePosteriors(int site)

• generateCategoryRanking

  public final int[] generateCategoryRanking(int site)

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object