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 |