Uses of Class pal.mep.MutationRateModel

Packages that use MutationRateModel
Package	Description
pal.coalescent	Classes to model population genetic processes using the coalescent.
pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.supgma
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
pal.xml	Utility classes for converting PAL objects to and from XML documents.

Uses of MutationRateModel in pal.coalescent

Methods in pal.coalescent with parameters of type MutationRateModel
Modifier and Type	Method	Description
`static CoalescentIntervals`	IntervalsExtractor.`extractFromTree(Tree tree, MutationRateModel muModel)`	extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model.

Uses of MutationRateModel in pal.mep

Subclasses of MutationRateModel in pal.mep
Modifier and Type	Class	Description
`class`	`ConstantMutationRate`	This class models a constant mutation rate (parameter: mu = mutation rate).
`class`	`SteppedMutationRate`	This class models a step-wise mutation rate.
`class`	`WindowedMutationRate`	This class models a windowed mutation rate (parameter: mu = mutation rate).

Methods in pal.mep that return MutationRateModel
Modifier and Type	Method	Description
`MutationRateModel`	MutationRateModel.Factory.`generateNewModel()`	Request a new MutationRateModel instance
`MutationRateModel`	ConstantMutationRate.`getCopy()`
`abstract MutationRateModel`	MutationRateModel.`getCopy()`
`MutationRateModel`	SteppedMutationRate.`getCopy()`
`MutationRateModel`	WindowedMutationRate.`getCopy()`

Constructors in pal.mep with parameters of type MutationRateModel
Constructor	Description
`MutationRateModel(MutationRateModel toCopy)`

Uses of MutationRateModel in pal.supgma

Methods in pal.supgma with parameters of type MutationRateModel
Modifier and Type Method Description

static RateHandler RateHandler.Utils.getSetRateHandler(MutationRateModel model)

Uses of MutationRateModel in pal.tree

Methods in pal.tree that return MutationRateModel
Modifier and Type	Method	Description
`MutationRateModel`	MutationRateModelTree.`getMutationRateModel()`	returns mu

Methods in pal.tree with parameters of type MutationRateModel
Modifier and Type	Method	Description
`static Tree`	TreeUtils.`generationsToMutations(Tree generationTree, MutationRateModel muModel)`	Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
`static Tree`	TreeUtils.`generationsToMutations(Tree generationTree, MutationRateModel muModel, double generationTime)`	Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
`static Tree`	TreeUtils.`getScaled(Tree mutationRateTree, MutationRateModel muModel)`	Takes a tree and returns a scaled version of it.
`static Tree`	TreeUtils.`getScaled(Tree mutationRateTree, MutationRateModel muModel, int newUnits)`	Takes a tree and returns a scaled version of it.
`static Tree`	TreeUtils.`mutationsToGenerations(Tree mutationTree, MutationRateModel muModel)`	Takes a tree (in mutation units) and returns a scaled version of it (in generation units).
`static Tree`	TreeUtils.`scale(Tree mutationRateTree, MutationRateModel muModel)`	Deprecated. use getScaled()
`static Tree`	TreeUtils.`scale(Tree mutationRateTree, MutationRateModel muModel, int newUnits)`	Deprecated. use getScaled()

Constructors in pal.tree with parameters of type MutationRateModel
Constructor	Description
`MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model)`	take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
`MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model, boolean includeModelParameters)`	take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

Uses of MutationRateModel in pal.xml

Methods in pal.xml that return MutationRateModel
Modifier and Type	Method	Description
`static MutationRateModel`	ElementParser.`parseMutationRateModel(org.w3c.dom.Element e)`	Reads a mutation rate model from a DOM Document element.

Methods in pal.xml with parameters of type MutationRateModel
Modifier and Type	Method	Description
`static org.w3c.dom.Element`	ElementFactory.`createMutationRateModelElement(MutationRateModel muModel, org.w3c.dom.Document document)`	Creates an XML element representing a mutation rate model.