Package | Description |
---|---|
Ancestors |
Provides classed to calculate ancestral reconstruction.
|
Constraints |
Provides classes to constrain the state of internal nodes.
|
Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
Optimizers |
Provides classes for optimising a likelihood.
|
Simulations |
Provides a class to create simulate data.
|
Trees |
Provides classes to define a tree and any constraints on that tree.
|
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 |
---|---|
SiteConstraints |
Constrainer.getConstraints(Tree t,
Site s)
Gets the consraints on an the external nodes of a site given the tree
and the state of the leafs.
|
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 |
---|---|
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. |
Modifier and Type | Method and Description |
---|---|
Alignment |
Simulate.getAlignment(int length)
Gets a simulated alignment, not returing the state of internal nodes
|
Alignment |
Simulate.getAlignment(int length,
boolean internal)
Gets a simulated alignment
|
Alignment |
Simulate.getAlignment(int length,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment.
|
Alignment |
Simulate.getAlignment(int length,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returing the state of internal nodes.
|
Site |
Simulate.getSite()
Gets a simulated site without returning the state of the internal nodes
|
Site |
Simulate.getSite(boolean internal)
Gets a simulated site
|
Site |
Simulate.getSite(boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated site.
|
Site |
Simulate.getSite(java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated site without returning the state of the internal nodes.
|
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.
|
Modifier and Type | Method and Description |
---|---|
static Tree |
Tree.fromNewickString(java.lang.String newick)
Creates a tree from a newick string
|
Branch |
Tree.getBranchByChild(java.lang.String child)
Gets the branch which has the given node as the child node
|
java.util.Set<Branch> |
Tree.getBranchesByParent(java.lang.String parent)
Gets the set of branches which have the passed node as a parent
|
double |
Branch.getLength()
Get the length of the branch
|
double |
Tree.getLength()
Gets the length of the tree
|
Parameters |
Tree.getParameters()
Returns a Parameters object containing a parameter for each branch length.
|
java.lang.String |
Tree.getParent(java.lang.String child)
Gets the parent node of the given node
|
Tree |
Tree.midPointRoot(java.lang.String newRootName)
Mid point roots the tree and returns a new tree
|
java.lang.String |
Tree.MRCA(java.util.List<java.lang.String> leaves)
Returns the most recent common ancestor of a set of leaves
|
Tree |
Tree.scaledTo(double length)
Returns a new tree where the lengths are scales so the total length is
different
|
Constructor and Description |
---|
Tree(java.util.List<Branch> branches)
Creates a tree from a list of branches
|