Simulate Codons with Darwinian Selection Modelled as an OU Process

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Documentation for package ‘scoup’ version 1.1.4

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A B C D E F H L N O P R S T V W

scoup-package

Simulate Codons with Darwinian Selection Imposed as an OU Process

-- A --

aaGamma	Obtain Gamma Distributed Amino Acid Selection Coefficients
aaGauss	Obtain Gaussian Distributed Amino Acid Selection Coefficients
aaSCupdate	Simulate Codon Sequence Alignment
aaSCupdate-method	(Deterministic) Episodic Simulation Model Input
aaSCupdate-method	Ornstein-Uhlenbeck Stochastic Simulation Model Object
aaSCupdate.discrete	Simulate Codon Sequence Alignment
aaSCupdate.ou	Simulate Codon Sequence Alignment
aInfo	Output from the 'scoup::alignsim' Genetic Sequence Simulator
aInfo-method	Output from the 'scoup::alignsim' Genetic Sequence Simulator
alignsim	Simulate Codon Sequence Alignment
alignsim-method	(Deterministic) Episodic Simulation Model Input
alignsim-method	Frequency-Dependent Evolutionary Model Object
alignsim-method	Ornstein-Uhlenbeck Stochastic Simulation Model Object
alignsim.discrete	Simulate Codon Sequence Alignment
alignsim.omega	Simulate Codon Sequence Alignment
alignsim.ou	Simulate Codon Sequence Alignment
aminoSC-class	Amino Acid Selection Coefficients
asymMean	Ornstein-Uhlenbeck Stochastic Simulation Model Object
asymMean-method	Ornstein-Uhlenbeck Stochastic Simulation Model Object
asymVar	Ornstein-Uhlenbeck Stochastic Simulation Model Object
asymVar-method	Ornstein-Uhlenbeck Stochastic Simulation Model Object

-- B --

biTree	Generate a Balanced Bifurcating Evolutionary Tree
branchL	Codon Sequence Structure
branchL-method	Codon Sequence Structure

-- C --

codonCoeffs	Transform Amino Acid to Codon Selection Coefficients
codonFreq	Generate Codon Frequencies From Selection Coefficients
codonvalues-class	Codon Frequencies and Selection Coefficients
coeffs	Amino Acid Selection Coefficients
coeffs-method	Amino Acid Selection Coefficients
coeffs-method	Codon Frequencies and Selection Coefficients
cseq	Output from the 'scoup::alignsim' Genetic Sequence Simulator
cseq-method	Output from the 'scoup::alignsim' Genetic Sequence Simulator

-- D --

details	Codon Sequence Structure
details-method	Codon Sequence Structure
discrete-class	(Deterministic) Episodic Simulation Model Input
discreteInput	Populate (Deterministic) Episodic Seascape Model Parameters
dNdS	Output from the 'scoup::alignsim' Genetic Sequence Simulator
dNdS-method	Output from the 'scoup::alignsim' Genetic Sequence Simulator
dndsCalculator	Estimate dN/dS Value Analytically

-- E --

effpop	Simulate Codon Sequence Alignment
effpop-method	(Deterministic) Episodic Simulation Model Input
effpop-method	Halpern-Bruno Mutation-Selection Evolutionary Model Input
effpop-method	Frequency-Dependent Evolutionary Model Object

-- F --

fixMatrix	Construct Fixation Rate Matrix
freqs	Codon Frequencies and Selection Coefficients
freqs-method	Codon Frequencies and Selection Coefficients

-- H --

hbInput	Generate Halpern-Bruno Substitution Model Parameters
hbParameters-class	Halpern-Bruno Mutation-Selection Evolutionary Model Input

-- L --

lscape	Simulate Codon Sequence Alignment
lscape-method	(Deterministic) Episodic Simulation Model Input
lscape-method	Frequency-Dependent Evolutionary Model Object

-- N --

nodes	Codon Sequence Structure
nodes-method	Codon Sequence Structure
nsynVar	Simulate Codon Sequence Alignment
nsynVar-method	Amino Acid Selection Coefficients
nsynVar-method	Halpern-Bruno Mutation-Selection Evolutionary Model Input
nsynVar-method	Frequency-Dependent Evolutionary Model Object

-- O --

omega-class	Frequency-Dependent Evolutionary Model Object
ou-class	Ornstein-Uhlenbeck Stochastic Simulation Model Object
ouEvolve	Simulate the Trend of an Ornstein-Uhlenbeck Process
ouInput	Populate Parameters of the Ornstein-Uhlenbeck Algorithm

-- P --

phylogeny	Codon Sequence Structure
phylogeny-method	Codon Sequence Structure

-- R --

reversion	Ornstein-Uhlenbeck Stochastic Simulation Model Object
reversion-method	Ornstein-Uhlenbeck Stochastic Simulation Model Object

-- S --

sampler	Simulate Codon Sequence Alignment
sampler-method	(Deterministic) Episodic Simulation Model Input
sampler-method	Halpern-Bruno Mutation-Selection Evolutionary Model Input
sampler-method	Frequency-Dependent Evolutionary Model Object
scoup	Simulate Codons with Darwinian Selection Imposed as an OU Process
scoup-class	Output from the 'scoup::alignsim' Genetic Sequence Simulator
seqCOL	Output from the 'scoup::alignsim' Genetic Sequence Simulator
seqCOL-method	Output from the 'scoup::alignsim' Genetic Sequence Simulator
seqDetails	Populate Sequence Alignment Information
seqParameters-class	Codon Sequence Structure
seqs	Output from the 'scoup::alignsim' Genetic Sequence Simulator
seqs-method	Output from the 'scoup::alignsim' Genetic Sequence Simulator
seqWriter	Write Numeric Codon Alignment to a NEXUS File
show-method	Amino Acid Selection Coefficients
show-method	Codon Frequencies and Selection Coefficients
show-method	(Deterministic) Episodic Simulation Model Input
show-method	Halpern-Bruno Mutation-Selection Evolutionary Model Input
show-method	Frequency-Dependent Evolutionary Model Object
show-method	Ornstein-Uhlenbeck Stochastic Simulation Model Object
show-method	Output from the 'scoup::alignsim' Genetic Sequence Simulator
show-method	Codon Sequence Structure
sites	Codon Sequence Structure
sites-method	Codon Sequence Structure
sitesim	Simulate Codon Sequence Alignment
sitesim-method	(Deterministic) Episodic Simulation Model Input
sitesim-method	Frequency-Dependent Evolutionary Model Object
sitesim-method	Ornstein-Uhlenbeck Stochastic Simulation Model Object
sitesim.discrete	Simulate Codon Sequence Alignment
sitesim.omega	Simulate Codon Sequence Alignment
sitesim.ou	Simulate Codon Sequence Alignment
subsMatrix	Build Mutation-Selection Codon Substitution Matrix
synVar	Amino Acid Selection Coefficients
synVar-method	Amino Acid Selection Coefficients

-- T --

taxa	Codon Sequence Structure
taxa-method	Codon Sequence Structure
tree	Generate a Balanced Bifurcating Evolutionary Tree

-- V --

vNvS	Simulate Codon Sequence Alignment
vNvS-method	Halpern-Bruno Mutation-Selection Evolutionary Model Input
vNvS-method	Frequency-Dependent Evolutionary Model Object

-- W --

wInput

Populate Frequency-Dependent Simulation Model Parameters