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 |
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 |
biTree | Generate a Balanced Bifurcating Evolutionary Tree |
branchL | Codon Sequence Structure |
branchL-method | Codon Sequence Structure |
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 |
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 |
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 |
fixMatrix | Construct Fixation Rate Matrix |
freqs | Codon Frequencies and Selection Coefficients |
freqs-method | Codon Frequencies and Selection Coefficients |
hbInput | Generate Halpern-Bruno Substitution Model Parameters |
hbParameters-class | Halpern-Bruno Mutation-Selection Evolutionary Model Input |
lscape | Simulate Codon Sequence Alignment |
lscape-method | (Deterministic) Episodic Simulation Model Input |
lscape-method | Frequency-Dependent Evolutionary Model Object |
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 |
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 |
phylogeny | Codon Sequence Structure |
phylogeny-method | Codon Sequence Structure |
reversion | Ornstein-Uhlenbeck Stochastic Simulation Model Object |
reversion-method | Ornstein-Uhlenbeck Stochastic Simulation Model Object |
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 |
taxa | Codon Sequence Structure |
taxa-method | Codon Sequence Structure |
tree | Generate a Balanced Bifurcating Evolutionary Tree |
vNvS | Simulate Codon Sequence Alignment |
vNvS-method | Halpern-Bruno Mutation-Selection Evolutionary Model Input |
vNvS-method | Frequency-Dependent Evolutionary Model Object |
wInput | Populate Frequency-Dependent Simulation Model Parameters |