pal.eval
public class LikelihoodValue extends java.lang.Object
Modifier and Type | Field and Description |
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double |
logL
Log-Likelihood
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int[] |
rateAtSite
map estimation of rate at site pattern
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double[] |
siteLogL
log-likelihood for each site pattern
|
Constructor and Description |
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LikelihoodValue(SitePattern sp)
initialization
|
Modifier and Type | Method and Description |
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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)
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double |
optimiseParameters(MultivariateMinimum mm)
optimise parameters of tree by maximising its likelihood
(this assumes that tree is a ParameterizedTree)
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void |
renewSitePattern(SitePattern sp)
Set new site pattern (while keeping tree and model)
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void |
setModel(SubstitutionModel m)
define model
(a site pattern must have been set before calling this method)
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void |
setTree(Tree t)
define (parameterized) tree
,(must only be called only after a site pattern has been defined).
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public double logL
public double[] siteLogL
public int[] rateAtSite
public LikelihoodValue(SitePattern sp)
sp
- site patternpublic SitePattern getSitePattern()
public void renewSitePattern(SitePattern sp)
public void setModel(SubstitutionModel m)
m
- model of substitution (rate matrix + rate distribution)public SubstitutionModel getModel()
public void setTree(Tree t)
t
- treepublic Tree getTree()
public double compute()
public double optimiseParameters()
public double optimiseParameters(MultivariateMinimum mm)
mm
- optimiser for generic ParameterisedTree