Package | Description |
---|---|
Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
Optimizers |
Provides classes for optimising a likelihood.
|
Modifier and Type | Method and Description |
---|---|
Likelihood |
Calculator.calculate(Parameters p)
Calculates the likelihood for a given set of parameters
|
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. |