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.)

See:
          Description

Interface Summary
LikelihoodEvaluator  
LikelihoodEvaluator.MLResult  
ReplicateLikelihoodEvaluator  
TopologyTestEngine.StatisticsHandler  
TopologyTestEngine.TestResult  
TopologyTestEngine.TopologyPool  
 

Class Summary
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 test
ContigencyTable 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 hypotheses
LikelihoodEvaluator.SimpleMLResult  
LikelihoodEvaluator.Utils  
LikelihoodRatioTest Likelihood ratio test based on chi-square statistics
ModelSupport Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence sets
NormalDistribution normal distribution (pdf, cdf, quantile)
ParetoDistribution Pareto distribution (scale-free distribution without characteristic length scale).
PenalizedLikelihood Penalized likelihood criteria
RELLTopologyPool  
ReplicateLikelihoodEvaluator.Utils  
ShimodairaHasegawaStatistics Title: ShimodairaHasegawaStatistics
ShimodairaHasegawaTest Shimodaira-Hasegawa-Test (1999) to compare a set of evolutionary hypotheses
TopologyTestEngine  
 

Package pal.statistics Description

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.)