Rev Language Reference
dnPhyloCTMCClado
Usage
dnPhyloCTMCClado(Tree tree, RateGenerator Q, CladogeneticProbabilityMatrix cladoProbs, Simplex rootFrequencies, RealPos branchRates, RealPos[] siteRates, Probability pInv, Natural nSites, String type, Bool treatAmbiguousAsGap, Bool storeInternalNodes, Bool gapMatchClamped)
Arguments
| tree : | Tree (pass by const reference) |
| Q : | RateGenerator (pass by const reference) |
| cladoProbs : | CladogeneticProbabilityMatrix (<deterministic> pass by const reference) |
| rootFrequencies : | Simplex (pass by const reference) |
| Default : NULL | |
| branchRates : | RealPos (pass by const reference) |
| Default : 1 | |
| siteRates : | RealPos[] (pass by const reference) |
| Default : [ ] | |
| pInv : | Probability (pass by const reference) |
| Default : 0 | |
| nSites : | Natural (pass by value) |
| Default : 10 | |
| type : | String (pass by value) |
| Default : NaturalNumbers | |
| Options : DNA|RNA|AA|PoMo|Protein|Standard|NaturalNumbers|Taxa | |
| treatAmbiguousAsGap : | Bool (pass by value) |
| Default : FALSE | |
| storeInternalNodes : | Bool (pass by value) |
| Should we store internal node states in the character matrix? | |
| Default : FALSE | |
| gapMatchClamped : | Bool (pass by value) |
| Should we set the simulated character to gap or missing if the corresponding character in the clamped matrix is gap or missing? | |
| Default : TRUE |
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