pal.eval
public class DemographicValue extends java.lang.Object implements MultivariateFunction
Modifier and Type | Field and Description |
---|---|
protected CoalescentIntervals |
intervals |
double |
logL
Log-Likelihood
|
protected DemographicModel |
model |
Constructor and Description |
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DemographicValue() |
Modifier and Type | Method and Description |
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double |
compute()
compute log-likelihood
for current model
return negative log-likelihood
|
protected void |
computeLogLikelihood() |
double |
evaluate(double[] params)
compute function value
|
CoalescentIntervals |
getCoalescentIntervals()
Returns the coalescent tree of this likelihood value.
|
DemographicModel |
getDemographicModel()
Returns the demographic model of this likelihood value
|
double |
getLowerBound(int n)
get lower bound of argument n
|
int |
getNumArguments()
get number of arguments
|
OrthogonalHints |
getOrthogonalHints() |
double |
getUpperBound(int n)
get upper bound of argument n
|
double |
optimize()
optimize log-likelihood
using default optimizer
return minimum negative log-likelihood
|
double |
optimize(MultivariateMinimum givenMvm)
optimize log-likelihood value and compute corresponding SEs
given an optimizer
|
void |
setCoalescentIntervals(CoalescentIntervals ci)
define coalescent tree.
|
void |
setDemographicModel(DemographicModel m)
define model
|
public double logL
protected CoalescentIntervals intervals
protected DemographicModel model
public void setDemographicModel(DemographicModel m)
m
- model of demographicpublic DemographicModel getDemographicModel()
public CoalescentIntervals getCoalescentIntervals()
public void setCoalescentIntervals(CoalescentIntervals ci)
t
- treepublic double compute()
public double optimize()
public double optimize(MultivariateMinimum givenMvm)
public double evaluate(double[] params)
MultivariateFunction
evaluate
in interface MultivariateFunction
params
- function argument (vector)public int getNumArguments()
MultivariateFunction
getNumArguments
in interface MultivariateFunction
public double getLowerBound(int n)
MultivariateFunction
getLowerBound
in interface MultivariateFunction
n
- argument numberpublic double getUpperBound(int n)
MultivariateFunction
getUpperBound
in interface MultivariateFunction
n
- argument numberprotected void computeLogLikelihood()
public OrthogonalHints getOrthogonalHints()
getOrthogonalHints
in interface MultivariateFunction