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R
 radius  Variable in class HAL.GridsAndAgents.SphericalAgent2D
 radius  Variable in class HAL.GridsAndAgents.SphericalAgent3D
 Rand  Class in HAL

contains functions for random value generation and distribution sampling.
 Rand()  Constructor for class HAL.Rand
 Rand(long)  Constructor for class HAL.Rand
 Rand(RNG)  Constructor for class HAL.Rand

creates a Rand object using the RNG argument as its internal generator
 RandomAgent(int, int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates
 RandomAgent(int, int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true
 RandomAgent(int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates
 RandomAgent(int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true
 RandomAgent(int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the provided coordinates
 RandomAgent(int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates
 RandomAgent(int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates
 RandomAgent(int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true
 RandomAgent(int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true
 RandomAgent(int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true
 RandomAgent(Rand)  Method in class HAL.GridsAndAgents.AgentGrid0D

gets a random agent from the grid, be careful not to use this during iteration over the grid
 RandomAgent(Rand)  Method in class HAL.GridsAndAgents.AgentGrid1D

gets a random agent from the grid, be careful not to use this during iteration over the grid
 RandomAgent(Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

gets a random agent from the grid, be careful not to use this during iteration over the grid
 RandomAgent(Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

gets a random agent from the grid, be careful not to use this during iteration over the grid
 RandomAgent(Rand)  Method in class HAL.GridsAndAgents.AgentList

returns a random agent from the AgentList
 RandomAgentHood(int[], int, int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood
 RandomAgentHood(int[], int, int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true
 RandomAgentHood(int[], int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood
 RandomAgentHood(int[], int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true
 RandomAgentHood(int[], int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood
 RandomAgentHood(int[], int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true
 RandomAgentHoodMapped(int[], int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood, assumes the neighborhood has already been mapped
 RandomAgentHoodMapped(int[], int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood, assumes the neighborhood has already been mapped
 RandomAgentHoodMapped(int[], int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood, assumes the neighborhood has already been mapped
 RandomAgentHoodMapped(int[], int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true, assumes the neighborhood has already been mapped
 RandomAgentHoodMapped(int[], int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true, assumes the neighborhood has already been mapped
 RandomAgentHoodMapped(int[], int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true, assumes the neighborhood has already been mapped
 RandomAgentRad(double, double, double, double, Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified radius
 RandomAgentRad(double, double, double, double, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified radius
 RandomAgentRad(double, double, double, Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified radius
 RandomAgentRad(double, double, double, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified radius forwhich EvalAgent returns true
 RandomAgentRad(double, double, Rand)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified radius
 RandomAgentRad(double, double, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified radius forwhich EvalAgent returns true
 RandomAgentRect(int, int, int, int, int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified rectangle
 RandomAgentRect(int, int, int, int, int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified rectangle forwhich EvalAgent returns true
 RandomAgentRect(int, int, int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified rectangle
 RandomAgentRect(int, int, int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified rectangle forwhich EvalAgent returns true
 RandomAgentRect(int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified rectangle
 RandomAgentRect(int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified rectangle forwhich EvalAgent returns true
 RandomAgentSafe(int, int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent, will apply wraparound if the coordiantes are outside of the grid
 RandomAgentSafe(int, int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent that satisfies EvalAgent, will apply wraparound if the coordiantes are outside of the grid
 RandomAgentSafe(int, int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent, will apply wraparound if the coordiantes are outside of the grid
 RandomAgentSafe(int, int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent that satisfies EvalAgent, will apply wraparound if the coordiantes are outside of the grid
 RandomAgentSafe(int, Rand)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent, will apply wraparound if the coordiantes are outside of the grid
 RandomAgentSafe(int, Rand, AgentToBool<T>)  Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent that satisfies EvalAgent, will apply wraparound if the coordiantes are outside of the grid
 RandomDS(double[], double, double)  Method in class HAL.Rand

Fills out with random doubles between min and max inclusive
 RandomHoodI(int[], int, int, int, Rand)  Method in interface HAL.Interfaces.Grid3D

gets a random index from the full neighborhood, if the index does not map, returns 1
 RandomHoodI(int[], int, int, Rand)  Method in interface HAL.Interfaces.Grid2D

gets a random index from the full neighborhood, if the index does not map, returns 1
 RandomHoodI(int[], int, Rand)  Method in interface HAL.Interfaces.Grid1D

gets a random index from the full neighborhood, if the index does not map, returns 1
 RandomIS(int[], int, int)  Method in class HAL.Rand

Fills out with random integers between min (inclusive) and max (exclusive)
 RandomPointInCircle(double, double[])  Method in class HAL.Rand
 RandomPointInSphere(double, double[])  Method in class HAL.Rand
 RandomPointOnCircleEdge(double, double[])  Method in class HAL.Rand

gets a random point on the surface of a circle centered at 0,0, with the provided radius.
 RandomPointOnSphereEdge(double, double[])  Method in class HAL.Rand

gets a random point on the surface of a sphere centered at 0,0,0, with the provided radius.
 RandomVariable(double[])  Method in class HAL.Rand

Samples a discrete random variable from the probabilities provided
 RandomVariable(double[], double, int, int)  Method in class HAL.Rand
 RandomVariable(double[], int, int)  Method in class HAL.Rand
 Read()  Method in class HAL.Tools.FileIO

requires read mode ("r") returns an array list of all lines from the file as strings
 ReadBinBool()  Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a boolean from the binary file
 ReadBinBools(boolean[])  Method in class HAL.Tools.FileIO
 ReadBinDouble()  Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single double from the binary file
 ReadBinDoubles(double[])  Method in class HAL.Tools.FileIO
 ReadBinFloat()  Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single float from the binary file
 ReadBinFloats(float[])  Method in class HAL.Tools.FileIO
 ReadBinInt()  Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single int from the binary file
 ReadBinInts(int[])  Method in class HAL.Tools.FileIO
 ReadBinLong()  Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single long from the binary file
 ReadBinLongs(long[])  Method in class HAL.Tools.FileIO
 ReadBinString()  Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a string from the binary file
 ReadDelimit(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of line segments from that line
 ReadDoubles(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of doubles from that line
 reader  Variable in class HAL.Tools.FileIO
 readerBin  Variable in class HAL.Tools.FileIO
 ReadInts(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of ints from that line
 ReadLine()  Method in class HAL.Tools.FileIO

requires read mode ("r") returns one line from the file as a string
 ReadLineDelimit(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimiter, and returns an array of line segments
 ReadLineDoubles(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of doubles from that line
 ReadLineFloats(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of floats from that line
 ReadLineInts(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of integers from that line
 ReadLineLongs(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of longs from that line
 ReadLongs(String)  Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of longs from that line
 ReadObject()  Method in class HAL.Tools.FileIO
 ReadWriteAppend  Variable in class HAL.Tools.FileIO
 RecordClones(double)  Method in class HAL.Tools.PhylogenyTracker.Genome
 RecordClones(String)  Method in class HAL.Tools.PhylogenyTracker.Genome
 Rectangle(double, double, double, double, int)  Method in class HAL.Gui.OpenGL2DWindow

draws a rectangle between (x1,y1) and (x2,y2) coded by Jill Gallaher
 RectangleAtPoint(double, double, double, double, int)  Method in class HAL.Gui.OpenGL2DWindow

draws a rectangle centered at position x,y
 RectangleHood(boolean, int, int)  Static method in class HAL.Util

Returns the coordinates of all squares whose centers lie within a rectangle of the provided radius, centered on (0,0)
 RectangleXY(double, double, double, double, double, int)  Method in class HAL.Gui.OpenGL3DWindow

draws a rectangle between (x1,y1,z) and (x2,y2,z)
 RectangleXZ(double, double, double, double, double, int)  Method in class HAL.Gui.OpenGL3DWindow
 RectangleYZ(double, double, double, double, double, int)  Method in class HAL.Gui.OpenGL3DWindow
 RED  Static variable in class HAL.Util
 RemoveAgent(T)  Method in class HAL.GridsAndAgents.AgentList

removes all instances of the agent from the AgentList, returns the number of instances removed
 Rescale(double, double, double, double, double)  Static method in class HAL.Util

rescales the value from being between oldMin and oldMax to being between newMin and newMax
 Reset()  Method in class HAL.GridsAndAgents.AgentGrid0D

calls dispose on all agents in the typeGrid
 Reset()  Method in class HAL.GridsAndAgents.AgentGrid1D

calls dispose on all agents, resets the tick timer to 0.
 Reset()  Method in class HAL.GridsAndAgents.AgentGrid2D

calls dispose on all agents in the typeGrid, resets the tick timer to 0.
 Reset()  Method in class HAL.GridsAndAgents.AgentGrid3D

calls dispose on all agents in the typeGrid, resets the tick timer to 0.
 ResetCloneRecord()  Method in class HAL.Tools.PhylogenyTracker.Genome
 ResetHard()  Method in class HAL.GridsAndAgents.AgentGrid1D

calls dispose on all agents and completely resets the internal agentlist, also resets the tick timer to 0.
 ResetHard()  Method in class HAL.GridsAndAgents.AgentGrid2D

calls dispose on all agents and completely resets the internal agentlist, also resets the tick timer to 0.
 ResetHard()  Method in class HAL.GridsAndAgents.AgentGrid3D

calls dispose on all agents and completely resets the internal agentlist, also resets the tick timer to 0.
 ResetTick()  Method in class HAL.GridsAndAgents.AgentGrid0D
 ResetTick()  Method in class HAL.GridsAndAgents.AgentGrid1D

sets the tick to 0.
 ResetTick()  Method in class HAL.GridsAndAgents.AgentGrid2D

sets the tick to 0.
 ResetTick()  Method in class HAL.GridsAndAgents.AgentGrid3D

sets the tick to 0.
 Response(char, int)  Method in interface HAL.Interfaces.KeyResponse
 RGB(double, double, double)  Static method in class HAL.Util

returns a color integer based on the RGB components passed in.
 RGB256(int, int, int)  Static method in class HAL.Util

returns a color integer based on the RGB components passed in.
 RGBA(double, double, double, double)  Static method in class HAL.Util

returns a color integer based on the RGBA components passed in.
 RGBA256(int, int, int, int)  Static method in class HAL.Util

returns a color integer based on the RGB components passed in.
 rk_binomial_inversion(int, double, Rand)  Method in class HAL.Tools.Internal.Binomial
 rk_binomial_inversion(long, double, Rand)  Method in class HAL.Tools.Internal.Binomial
 rn  Variable in class HAL.Rand
 RNG  Interface in HAL.Interfaces
 run()  Method in class HAL.Tools.Internal.SweepRun
 Run(int)  Method in interface HAL.Interfaces.ParallelFunction
 Run(int, boolean, int)  Method in class HAL.Tools.MultiWellExperiment.MultiWellExperiment

runs a multiwell experiment for a numTicks duration.
 Runge4(Derivative, double[], double[], double, double)  Method in class HAL.Tools.ODESolver.ODESolver

runs 1 round of RungeKutta 4 integration, putting the result in the out array
 Runge4(Derivative, double[], double, double)  Method in class HAL.Tools.ODESolver.ODESolver

runs 1 round of RungeKutta 4 integration, putting the result in the state array
 Runge4(Derivative, double[], double, double, double)  Method in class HAL.Tools.ODESolver.ODESolver

runs RungeKutta 4 integration from t0 to tf in increments of dt
 Runge4(Derivative, ArrayList<double[]>, ArrayList<Double>, double, double, int)  Method in class HAL.Tools.ODESolver.ODESolver

runs RungeKutta 4,5 integration from t0 to tf in increments of dt, puts the resulting states in the states array, and the resulting ts in the ts array
 Runge45(Derivative, double[], double[], double, double, double, double)  Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, updating the state array until tf.
 Runge45(Derivative, double[], double[], double, double, double, double, double, double)  Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, updating the state array until tf.
 Runge45(Derivative, double[], double, double, double, double)  Method in class HAL.Tools.ODESolver.ODESolver
 Runge45(Derivative, double[], double, double, double, double, double, double)  Method in class HAL.Tools.ODESolver.ODESolver
 Runge45(Derivative, ArrayList<double[]>, ArrayList<Double>, double, double, double, int)  Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, putting new states and the times for which those states were computed into the states and ts arraylists.
 Runge45(Derivative, ArrayList<double[]>, ArrayList<Double>, double, double, double, int, double, double)  Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, putting new states and the times for which those states were computed into the states and ts arraylists.
 RunGIF(int, String, int, boolean)  Method in class HAL.Tools.MultiWellExperiment.MultiWellExperiment

runs a multiwell experiment for a numTicks duration.
 RunGui()  Method in class HAL.Gui.UIWindow

starts the gui thread and reveals the gui to the user
 RunGui()  Method in class HAL.Tools.InteractiveModel.InteractiveModel
 RunNextStep()  Method in class HAL.Tools.InteractiveModel.InteractiveModel
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