A B C D E F G H I J K L M N O P Q R S T U V W

R

randomTree(List<String>, boolean) - Static method in class Trees.Tree

Creates a random rooted or unrooted tree from a list of taxa

Range - Class in Utils

Used to represent a range (using doubles)

Range(double, double) - Constructor for class Utils.Range

Constructor.

rank(double[]) - Static method in class Utils.Array1D

Returns the rank of each element in an array.

RateCategory - Class in Models

Represents a rate category of a phylogenetic model.

RateCategory(String[][], RateCategory.FrequencyType, HashMap<String, Integer>) - Constructor for class Models.RateCategory

Constructor for when the root distribution is defined as the stationary or quasi-stationary distribution.

RateCategory(String[][], String[], Map<String, Integer>) - Constructor for class Models.RateCategory

Constructor for when the root distribution is defined.

RateCategory.FrequencyType - Enum in Models

Enumeration of the different ways of defining the root frequency

RateCategory.RateException - Exception in Models

Exception thrown if there is a problem within a RateClass

RateCategory.RateException(String, String, String, Throwable) - Constructor for exception Models.RateCategory.RateException

Constructor when there is a problem at a specific point in the rate matrix or frequency array

RateCategory.RateException(String) - Constructor for exception Models.RateCategory.RateException

Constructor for other exception when there isn't an underlying cause

RateCategory.RateException(String, Throwable) - Constructor for exception Models.RateCategory.RateException

Constructor for other exception when there is an underlying cause

rates(double, int) - Static method in class Maths.Gamma

Returns the rates that should be used for a set number of rate categories and a set value of alpha as per the methodology of Yang 1993

readLine() - Method in class Utils.CommentedFileReader

Reads a line from the file

Real - Interface in Maths

Represents a Real number.

RealFactory - Class in Maths

A factory for creating reals

RealFactory() - Constructor for class Maths.RealFactory

RealFactory.RealType - Enum in Maths

An enumeration of the different Real types

realType(RealFactory.RealType) - Static method in class Ancestors.AncestralJointDP

Sets the real type to be used during calculations, either SmallDouble or StandardDouble

realType(RealFactory.RealType) - Static method in class Likelihood.SiteLikelihood

Sets the real type to be used during calculations, either SmallDouble or StandardDouble.

recode(Map<String, String>) - Method in class Alignments.Alignment

Recodes the alignment and returns it

recode(Map<String, String>, Ambiguous) - Method in class Alignments.Alignment

Recodes the alignment and returns it and also allows the definition of new ambiguous states

recode(Map<String, String>) - Method in class Alignments.Site

Recodes the site and returns it

recode(Map<String, String>, Ambiguous) - Method in class Alignments.Site

Recodes the alignment and returns it and also allows the definition of new ambiguous states

reset() - Method in class Utils.TimePassed

Reset the timer.

restart(Optimizable<R>, File) - Method in class Optimizers.ConjugateGradient

restart(Optimizable<R>, File, File) - Method in class Optimizers.ConjugateGradient

restart(Optimizable<R>, File) - Method in class Optimizers.GoldenSection

restart(Optimizable<R>, File, File) - Method in class Optimizers.GoldenSection

restart(Optimizable<R>, File) - Method in class Optimizers.NelderMead

restart(Optimizable<R>, File, File) - Method in class Optimizers.NelderMead

restart(Optimizable<R>, File) - Method in interface Optimizers.Optimizer

Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to the screen.

restart(Optimizable<R>, File, File) - Method in interface Optimizers.Optimizer

Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to a file.

RF(Tree) - Method in class Trees.Tree

Calculates the RF distance between this tree and another tree

Root - Interface in Likelihood

Provides information on what to do once the root of the tree is reached.

RY(Parameters) - Static method in class Models.RYModelFactory

Creates an instance of a RY model

RY() - Static method in class Models.RYModelFactory

Creates an instance of a RY model

RY_Gamma(Parameters, int) - Static method in class Models.RYModelFactory

Creates an instance of a RY model with gamma-distributed rate across sites

RY_Gamma(int) - Static method in class Models.RYModelFactory

Creates an instance of a RY model with gamma-distributed rate across sites

RYModelFactory - Class in Models

A factory for easing the creation of the standard RY model

RYModelFactory() - Constructor for class Models.RYModelFactory

A B C D E F G H I J K L M N O P Q R S T U V W