R: Simulate Codons with Darwinian Selection Modelled as an OU Process

# Simulate Codons with Darwinian Selection Modelled as an OU Process

## Documentation for package ‘scoup’ version 1.6.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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