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R

Range - Class in Utils
Used to represent a range (using doubkes)
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
Constrcutor for when the root distribution is defined as the stationary or quasi-staionary distribution.
RateCategory(String[][], String[], HashMap<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
recalculateMatrix() - Method in class Parameters.Parameters
Tests whether any parameters that would require recalculation of the probability matrices have been changed since the last call to Parameters.calculated()
recode(Map<String, String>) - Method in class Alignments.Alignment
Recodes the alignment and returns it
recode(Map<String, String>) - Method in class Alignments.Site
Recodes the site and returns it
reset() - Method in class Utils.TimePassed
Reset the timer.
restart(Calculator, File) - Method in class Optimizers.GoldenSection
 
restart(Calculator, File, File) - Method in class Optimizers.GoldenSection
 
restart(Calculator, File) - Method in class Optimizers.NelderMead
 
restart(Calculator, File, File) - Method in class Optimizers.NelderMead
 
restart(Calculator, 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(Calculator, 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.
reverseLookup(Map<K, V>, V) - Static method in class Utils.MapUtils
Reverse lookup in the map.
reverseLookupMulti(Map<K, V>, V) - Static method in class Utils.MapUtils
Reverse lookup in the map.
run() - Method in class Likelihood.Calculator.SiteCalculator
 
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