Package | Description |
---|---|
jebl.evolution.coalescent | |
jebl.evolution.treesimulation |
Modifier and Type | Class and Description |
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class |
CataclysmicDemographic
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
|
class |
ConstantPopulation
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
|
class |
ConstExponential
This class models exponential growth from an initial population size.
|
class |
ConstLogistic
This class models logistic growth from an initial population size.
|
class |
EmpiricalDemographicFunction |
class |
Expansion
This class models exponential growth from an initial ancestral population size.
|
class |
ExponentialGrowth
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
|
class |
ExponentialLogistic
This class models logistic growth from an initial exponential phase.
|
class |
LogisticGrowth
This class models logistic growth.
|
Modifier and Type | Method and Description |
---|---|
static double |
Coalescent.calculateLogLikelihood(IntervalList intervals,
DemographicFunction demographicFunction)
Calculates the log likelihood of this set of coalescent intervals,
given a demographic model.
|
static void |
DemographicFunction.Utils.testConsistency(DemographicFunction demographicFunction,
int steps,
double maxTime)
This function tests the consistency of the
getIntensity and getInverseIntensity methods
of this demographic model.
|
Constructor and Description |
---|
Coalescent(IntervalList intervals,
DemographicFunction demographicFunction) |
Coalescent(RootedTree tree,
DemographicFunction demographicFunction) |
Constructor and Description |
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CoalescentIntervalGenerator(DemographicFunction demographicFunction) |
http://code.google.com/p/jebl2/