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