Package pal.coalescent
Class SkylinePlot
java.lang.Object
pal.coalescent.SkylinePlot
- All Implemented Interfaces:
Serializable
,Report
,Units
Skyline plot derived from a strictly bifurcating tree
or a coalescent interval.
This class provides the "classic" skyline plot method by
Pybus, Rambaut and Harvey .2000. Genetics 155:1429-1437, as well
as the "generalized" skyline plot method described in
Strimmer and Pybus. 2001. MBE submitted.
- Version:
- $Id: SkylinePlot.java,v 1.16 2001/07/11 13:51:16 korbinian Exp $
- Author:
- Korbinian Strimmer
- See Also:
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Field Summary
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Constructor Summary
ConstructorsConstructorDescriptionSkylinePlot
(CoalescentIntervals ci, double epsilon) Construct skyline plot from given coalescent intervalsSkylinePlot
(Tree tree, double epsilon) Construct skyline plot from tree -
Method Summary
Modifier and TypeMethodDescriptionvoid
Compute classic skyline plotvoid
computeGeneralized
(double epsilon) Compute generalized skyline plotdouble
findInterval
(double time) Find interval corresponding to a specific timedouble
getAICC()
Compute AICC-corrected log-likelihooddouble
Returns epsilonReturns the coalescent intervals in this skyline plot.double
Compute log-likelihooddouble
Returns the largest estimate of population size.double
Returns the largest value of time defined in this plot (= maximum value for epsilon)int
Returns the number of composite intervals (=number of parameters).double
getPopulationSize
(int i) Returns the population size in interval i.int
getSize()
Returns the number of intervals in this skyline plot.int
getUnits()
Returns unit of time.void
optimize()
Optimize generalized skyline plotvoid
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)toString()
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Constructor Details
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SkylinePlot
Construct skyline plot from tree- Parameters:
epsilon
- smoothing parameter (if set < 0 then epsilon will be optimized)
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SkylinePlot
Construct skyline plot from given coalescent intervals- Parameters:
epsilon
- smoothing parameter (if set < 0 then epsilon will be optimized)
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Method Details
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toString
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model) -
computeClassic
public void computeClassic()Compute classic skyline plot -
computeGeneralized
public void computeGeneralized(double epsilon) Compute generalized skyline plot -
optimize
public void optimize()Optimize generalized skyline plot -
getLogLikelihood
public double getLogLikelihood()Compute log-likelihood -
getAICC
public double getAICC()Compute AICC-corrected log-likelihood -
findInterval
public double findInterval(double time) Find interval corresponding to a specific time -
getMaxTime
public double getMaxTime()Returns the largest value of time defined in this plot (= maximum value for epsilon) -
getMaxPopulationSize
public double getMaxPopulationSize()Returns the largest estimate of population size. -
getIntervals
Returns the coalescent intervals in this skyline plot. -
getSize
public int getSize()Returns the number of intervals in this skyline plot. -
getParameterCount
public int getParameterCount()Returns the number of composite intervals (=number of parameters). -
getEpsilon
public double getEpsilon()Returns epsilon -
getPopulationSize
public double getPopulationSize(int i) Returns the population size in interval i. -
getUnits
public int getUnits()Returns unit of time.
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