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java.lang.Objectpal.coalescent.SkylinePlot
public class SkylinePlot
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.
Field Summary |
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Fields inherited from interface pal.misc.Units |
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DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS |
Constructor Summary | |
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SkylinePlot(CoalescentIntervals ci,
double epsilon)
Construct skyline plot from given coalescent intervals |
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SkylinePlot(Tree tree,
double epsilon)
Construct skyline plot from tree |
Method Summary | |
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void |
computeClassic()
Compute classic skyline plot |
void |
computeGeneralized(double epsilon)
Compute generalized skyline plot |
double |
findInterval(double time)
Find interval corresponding to a specific time |
double |
getAICC()
Compute AICC-corrected log-likelihood |
double |
getEpsilon()
Returns epsilon |
CoalescentIntervals |
getIntervals()
Returns the coalescent intervals in this skyline plot. |
double |
getLogLikelihood()
Compute log-likelihood |
double |
getMaxPopulationSize()
Returns the largest estimate of population size. |
double |
getMaxTime()
Returns the largest value of time defined in this plot (= maximum value for epsilon) |
int |
getParameterCount()
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 plot |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
java.lang.String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public SkylinePlot(Tree tree, double epsilon)
epsilon
- smoothing parameter (if set < 0 then epsilon will be optimized)public SkylinePlot(CoalescentIntervals ci, double epsilon)
epsilon
- smoothing parameter (if set < 0 then epsilon will be optimized)Method Detail |
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public java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output streampublic void computeClassic()
public void computeGeneralized(double epsilon)
public void optimize()
public double getLogLikelihood()
public double getAICC()
public double findInterval(double time)
public double getMaxTime()
public double getMaxPopulationSize()
public CoalescentIntervals getIntervals()
public int getSize()
public int getParameterCount()
public double getEpsilon()
public double getPopulationSize(int i)
public int getUnits()
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