Rev Language Reference
dnPhyloCTMCDASequence
Usage
dnPhyloCTMCDASequence(Tree tree, RateGeneratorSequence Q, CladogeneticProbabilityMatrix cladoProbs, Simplex rootFrequencies, RealPos branchRates, RealPos[] siteRates, Probability pInv, Natural nSites, String type, Bool storeInternalNodes, Bool treatAmbiguousAsGap, String coding)
Arguments
| tree : | Tree (pass by const reference) |
| The tree along which the process evolves. | |
| Q : | RateGeneratorSequence (pass by const reference) |
| The global or branch-specific rate matrices. | |
| cladoProbs : | CladogeneticProbabilityMatrix (pass by const reference) |
| Default : NULL | |
| rootFrequencies : | Simplex (pass by const reference) |
| The root specific frequencies of the characters, if applicable. | |
| Default : NULL | |
| branchRates : | RealPos (pass by const reference) |
| The global or branch-specific rate multipliers. | |
| Default : 1 | |
| siteRates : | RealPos[] (pass by const reference) |
| The rate categories for the sites. | |
| Default : [ ] | |
| pInv : | Probability (pass by const reference) |
| The probability of a site being invariant. | |
| Default : 0 | |
| nSites : | Natural (pass by value) |
| The number of sites, used for simulation. | |
| Default : 10 | |
| type : | String (pass by value) |
| The data type, used for simulation and initialization. | |
| Default : DNA | |
| Options : DNA|RNA|AA|PoMo|Protein|Standard|NaturalNumbers|Restriction | |
| storeInternalNodes : | Bool (pass by value) |
| Should we store internal node states in the character matrix? | |
| Default : FALSE | |
| treatAmbiguousAsGap : | Bool (pass by value) |
| Should we treat ambiguous characters as gaps/missing? | |
| Default : FALSE | |
| coding : | String (pass by value) |
| Default : all |
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