DemographicLikelihoodValue
public class LikelihoodValue
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
double |
logL |
Log-Likelihood
|
int[] |
rateAtSite |
map estimation of rate at site pattern
|
double[] |
siteLogL |
log-likelihood for each site pattern
|
Constructor | Description |
---|---|
LikelihoodValue(SitePattern sp) |
initialization
|
Modifier and Type | Method | Description |
---|---|---|
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).
|
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