Package pal.eval
Class DemographicValue
java.lang.Object
pal.eval.DemographicValue
- All Implemented Interfaces:
MultivariateFunction
estimates demographic parameters by maximising the coalescent
prior for a tree with given branch lengths.
- Version:
- $Id: DemographicValue.java,v 1.6 2002/04/16 05:37:05 matt Exp $
- Author:
- Alexei Drummond
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected CoalescentIntervals
double
Log-Likelihoodprotected DemographicModel
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
compute()
compute log-likelihood for current model return negative log-likelihoodprotected void
double
evaluate
(double[] params) compute function valueReturns the coalescent tree of this likelihood value.Returns the demographic model of this likelihood valuedouble
getLowerBound
(int n) get lower bound of argument nint
get number of argumentsdouble
getUpperBound
(int n) get upper bound of argument ndouble
optimize()
optimize log-likelihood using default optimizer return minimum negative log-likelihooddouble
optimize
(MultivariateMinimum givenMvm) optimize log-likelihood value and compute corresponding SEs given an optimizervoid
define coalescent tree.void
define model
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Field Details
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logL
public double logLLog-Likelihood -
intervals
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model
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Constructor Details
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DemographicValue
public DemographicValue()
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Method Details
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setDemographicModel
define model- Parameters:
m
- model of demographic
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getDemographicModel
Returns the demographic model of this likelihood value -
getCoalescentIntervals
Returns the coalescent tree of this likelihood value. -
setCoalescentIntervals
define coalescent tree.- Parameters:
t
- tree
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compute
public double compute()compute log-likelihood for current model return negative log-likelihood -
optimize
public double optimize()optimize log-likelihood using default optimizer return minimum negative log-likelihood -
optimize
optimize log-likelihood value and compute corresponding SEs given an optimizer- Returns:
- minimimum negative log-likelihood value
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evaluate
public double evaluate(double[] params) Description copied from interface:MultivariateFunction
compute function value- Specified by:
evaluate
in interfaceMultivariateFunction
- Parameters:
params
- function argument (vector)- Returns:
- function value
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getNumArguments
public int getNumArguments()Description copied from interface:MultivariateFunction
get number of arguments- Specified by:
getNumArguments
in interfaceMultivariateFunction
- Returns:
- number of arguments
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getLowerBound
public double getLowerBound(int n) Description copied from interface:MultivariateFunction
get lower bound of argument n- Specified by:
getLowerBound
in interfaceMultivariateFunction
- Parameters:
n
- argument number- Returns:
- lower bound
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getUpperBound
public double getUpperBound(int n) Description copied from interface:MultivariateFunction
get upper bound of argument n- Specified by:
getUpperBound
in interfaceMultivariateFunction
- Parameters:
n
- argument number- Returns:
- upper bound
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computeLogLikelihood
protected void computeLogLikelihood() -
getOrthogonalHints
- Specified by:
getOrthogonalHints
in interfaceMultivariateFunction
- Returns:
- null
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