Package pal.statistics
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
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Interface Summary Interface Description LikelihoodEvaluator LikelihoodEvaluator.MLResult ReplicateLikelihoodEvaluator TopologyTestEngine.StatisticsHandler TopologyTestEngine.TestResult TopologyTestEngine.TopologyPool -
Class Summary Class Description BootstrapStatistics computation of bootstrap estimators (BIAS, SD, VAR, CI) given a statistic theta and corresponding bootstrap replicates.ChiSquareDistribution chi-square distribution (distribution of sum of squares of n uniform random variables) (Parameter: n; mean: n; variance: 2*n) The chi-square distribution is a special case of the Gamma distribution (shape parameter = n/2.0, scale = 2.0).ChiSquareTest chi-square testContigencyTable Class for permuting contigency tables and determining the likelihood of the table.DiscreteStatistics simple discrete statistics (mean, variance, cumulative probability, quantiles etc.)ExponentialDistribution exponential distribution.FisherExact This does a one tail fisher exact test.GammaDistribution gamma distribution.GeneralTopologyPool KishinoHasegawaTest Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypothesesLikelihoodEvaluator.SimpleMLResult LikelihoodEvaluator.Utils LikelihoodRatioTest Likelihood ratio test based on chi-square statisticsModelSupport Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence setsNormalDistribution normal distribution (pdf, cdf, quantile)ParetoDistribution Pareto distribution (scale-free distribution without characteristic length scale).PenalizedLikelihood Penalized likelihood criteriaRELLTopologyPool ReplicateLikelihoodEvaluator.Utils ShimodairaHasegawaStatistics Title: ShimodairaHasegawaStatisticsShimodairaHasegawaTest Shimodaira-Hasegawa-Test (1999) to compare a set of evolutionary hypothesesTopologyTestEngine