Package pal.eval
Class LikelihoodValue
- java.lang.Object
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- pal.eval.LikelihoodValue
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- 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).- Version:
- $Id: LikelihoodValue.java,v 1.40 2003/09/04 03:22:34 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
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Field Summary
Fields Modifier and Type Field Description double
logL
Log-Likelihoodint[]
rateAtSite
map estimation of rate at site patterndouble[]
siteLogL
log-likelihood for each site pattern
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Constructor Summary
Constructors Constructor Description LikelihoodValue(SitePattern sp)
initialization
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
compute()
compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihoodSubstitutionModel
getModel()
Returns the model of this likelihood value.SitePattern
getSitePattern()
Returns the site pattern of this likelihood valueTree
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).
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Constructor Detail
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LikelihoodValue
public LikelihoodValue(SitePattern sp)
initialization- Parameters:
sp
- site pattern
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Method Detail
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getSitePattern
public SitePattern getSitePattern()
Returns the site pattern of this likelihood value
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renewSitePattern
public void renewSitePattern(SitePattern sp)
Set new site pattern (while keeping tree and model)
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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)
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getModel
public SubstitutionModel getModel()
Returns the model of this likelihood value.
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setTree
public void setTree(Tree t)
define (parameterized) tree ,(must only be called only after a site pattern has been defined).- Parameters:
t
- tree
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getTree
public Tree getTree()
Returns the (potentially parameterized) tree of this likelihood value.
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compute
public double compute()
compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
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optimiseParameters
public double optimiseParameters()
optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)- Returns:
- minimimum log-likelihood value
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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
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