Package | Description |
---|---|
Ancestors |
Provides classed to calculate ancestral reconstruction.
|
Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
Models |
Provides classes for defing a phylogenetic model.
|
Optimizers |
Provides classes for optimising a likelihood.
|
Simulations |
Provides a class to create simulate data.
|
Modifier and Type | Method and Description |
---|---|
abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction
|
Alignment |
AncestralJointBB.calculate(Parameters p) |
Alignment |
AncestralJointDP.calculate(Parameters params) |
AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction
|
Modifier and Type | Method and Description |
---|---|
Likelihood |
Calculator.calculate(Parameters p)
Calculates the likelihood for a given set of parameters
|
Range |
ConfidenceInterval.getCI(Parameter param,
double conf)
Calculates the confidence interval for a single parameter
|
Constructor and Description |
---|
Probabilities(Model m,
Tree t,
Parameters p)
Constructor
|
Modifier and Type | Method and Description |
---|---|
static Model |
Model.fromFile(java.io.File f)
Creates a new model from a file.
|
void |
Model.setParameters(Parameters p)
Sets the parameters of a model to the values contained in the
Parameters data structure. |
Constructor and Description |
---|
Model(java.util.Map<RateCategory,java.lang.String> freq)
Creates a new model with multiple rate classes
|
Modifier and Type | Method and Description |
---|---|
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params) |
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params) |
Likelihood |
Optimizer.maximise(Calculator l,
Parameters p)
Maximises the likelihood, logging to screen.
|
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params,
java.io.File log) |
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params,
java.io.File log) |
Likelihood |
Optimizer.maximise(Calculator l,
Parameters params,
java.io.File log)
Maximises the likelihood, logging to a file.
|
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint) |
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint) |
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint)
Maximises the likelihood starting from a checkpoint file (see
Optimizer.setCheckPointFile(java.io.File) ,
logging to the screen. |
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint,
java.io.File log) |
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint,
java.io.File log) |
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
Maximises the likelihood starting from a checkpoint file (see
Optimizer.setCheckPointFile(java.io.File) ,
logging to a file. |
Constructor and Description |
---|
Simulate(Model m,
Tree t,
Parameters p)
Creates an object to simulate data for a given model, tree and parameters.
|
Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given model, tree, parameters
and unobserved states.
|
Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved,
Constrainer con)
Creates an object to simulate data for a given model, tree, parameters,
unobserved states and constraints.
|