Package | Description |
---|---|
jebl.evolution.coalescent | |
jebl.evolution.treesimulation |
Modifier and Type | Class | Description |
---|---|---|
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 | 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 | Description |
---|---|
Coalescent(IntervalList intervals,
DemographicFunction demographicFunction) |
|
Coalescent(RootedTree tree,
DemographicFunction demographicFunction) |
Constructor | Description |
---|---|
CoalescentIntervalGenerator(DemographicFunction demographicFunction) |
http://code.google.com/p/jebl2/