public class SkylinePlot extends java.lang.Object implements Report, Units, java.io.Serializable
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Constructor | Description |
---|---|
SkylinePlot(CoalescentIntervals ci,
double epsilon) |
Construct skyline plot from given coalescent intervals
|
SkylinePlot(Tree tree,
double epsilon) |
Construct skyline plot from tree
|
Modifier and Type | Method | Description |
---|---|---|
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() |
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)public java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter out)
Report
public 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()