pal.eval
Class LikelihoodValue

java.lang.Object
  pal.eval.LikelihoodValue

Direct Known Subclasses:

DemographicLikelihoodValue

public class LikelihoodValue

extends java.lang.Object

Computes the likelihood for a tree given a model of sequence evolution and a sequence alignment; also optimises tree parameters such as branch lengths by maximising the likelihood (for optimal performance special optimisation procedures are employed for UnconstrainedTree, ClockTree and DatedTipsClockTree; a general optimisation precedure is used for another ParameterizedTree).

Field Summary

double	logL Log-Likelihood
int[]	rateAtSite map estimation of rate at site pattern
double[]	siteLogL log-likelihood for each site pattern

Constructor Summary

LikelihoodValue(SitePattern sp)
initialization

Method Summary

double	compute() compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
SubstitutionModel	getModel() Returns the model of this likelihood value.
SitePattern	getSitePattern() Returns the site pattern of this likelihood value
Tree	getTree() Returns the (potentially parameterized) tree of this likelihood value.
double	optimiseParameters() optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
double	optimiseParameters(MultivariateMinimum mm) optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
void	renewSitePattern(SitePattern sp) Set new site pattern (while keeping tree and model)
void	setModel(SubstitutionModel m) define model (a site pattern must have been set before calling this method)
void	setTree(Tree t) define (parameterized) tree ,(must only be called only after a site pattern has been defined).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logL

public double logL

Log-Likelihood

siteLogL

public double[] siteLogL

log-likelihood for each site pattern

rateAtSite

public int[] rateAtSite

map estimation of rate at site pattern

Constructor Detail

LikelihoodValue

public LikelihoodValue(SitePattern sp)

initialization

Parameters:

sp - site pattern

Method Detail

getSitePattern

public SitePattern getSitePattern()

Returns the site pattern of this likelihood value

renewSitePattern

public void renewSitePattern(SitePattern sp)

Set new site pattern (while keeping tree and model)

setModel

public void setModel(SubstitutionModel m)

define model (a site pattern must have been set before calling this method)

Parameters:

m - model of substitution (rate matrix + rate distribution)

getModel

public SubstitutionModel getModel()

Returns the model of this likelihood value.

setTree

public void setTree(Tree t)

define (parameterized) tree ,(must only be called only after a site pattern has been defined).

Parameters:

t - tree

getTree

public Tree getTree()

Returns the (potentially parameterized) tree of this likelihood value.

compute

public double compute()

compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood

optimiseParameters

public double optimiseParameters()

optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)

Returns:

minimimum log-likelihood value

optimiseParameters

public double optimiseParameters(MultivariateMinimum mm)

optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)

Parameters:

mm - optimiser for generic ParameterisedTree

Returns:

minimimum log-likelihood value