Package pal.eval
Class LikelihoodValue
java.lang.Object
pal.eval.LikelihoodValue
- Direct Known Subclasses:
DemographicLikelihoodValue
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
FieldsModifier and TypeFieldDescriptiondouble
Log-Likelihoodint[]
map estimation of rate at site patterndouble[]
log-likelihood for each site pattern -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
compute()
compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihoodgetModel()
Returns the model of this likelihood value.Returns the site pattern of this likelihood valuegetTree()
Returns the (potentially parameterized) tree of this likelihood value.double
optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)double
optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)void
Set new site pattern (while keeping tree and model)void
define model (a site pattern must have been set before calling this method)void
define (parameterized) tree ,(must only be called only after a site pattern has been defined).
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Field Details
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logL
public double logLLog-Likelihood -
siteLogL
public double[] siteLogLlog-likelihood for each site pattern -
rateAtSite
public int[] rateAtSitemap estimation of rate at site pattern
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Constructor Details
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LikelihoodValue
initialization- Parameters:
sp
- site pattern
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Method Details
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getSitePattern
Returns the site pattern of this likelihood value -
renewSitePattern
Set new site pattern (while keeping tree and model) -
setModel
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
Returns the model of this likelihood value. -
setTree
define (parameterized) tree ,(must only be called only after a site pattern has been defined).- Parameters:
t
- tree
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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
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optimiseParameters
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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