DemographicLikelihoodValue

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java.lang.Object
- pal.eval.LikelihoodValue
- - pal.eval.DemographicLikelihoodValue

```
public class DemographicLikelihoodValue
extends LikelihoodValue
```
Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals. Must be used in conjunction with DemographicClockTree!

Version:

$Id: DemographicLikelihoodValue.java,v 1.2 2001/07/13 14:39:13 korbinian Exp $

Author:

Alexei Drummond

Field Summary
- Fields inherited from class pal.eval.LikelihoodValue
  logL, rateAtSite, siteLogL

Constructor Summary

Constructors
Constructor Description

DemographicLikelihoodValue(SitePattern sp)
Parameter taking a site pattern.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`compute()`	compute log-likelihood for current branch lengths and model return negative log-likelihood

Methods inherited from class pal.eval.LikelihoodValue
getModel, getSitePattern, getTree, optimiseParameters, optimiseParameters, renewSitePattern, setModel, setTree

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - DemographicLikelihoodValue
```
public DemographicLikelihoodValue(SitePattern sp)
```
    Parameter taking a site pattern.
- Method Detail
  - compute
```
public double compute()
```
    compute log-likelihood for current branch lengths and model return negative log-likelihood
    
    Overrides:
    
    compute in class LikelihoodValue

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