Rev Language Reference
dnPhyloCTMC
Usage
dnPhyloCTMC(Tree tree, RateGenerator Q, Simplex rootFrequencies, RealPos branchRates, Simplex siteMatrices, RealPos[] siteRates, Simplex siteRatesProbs, Probability pInv, Natural nSites, String type, Bool treatAmbiguousAsGap, String coding, Bool storeInternalNodes, Bool gapMatchClamped)
Arguments
| tree : | Tree (pass by const reference) |
| The tree along which the process evolves. | |
| Q : | RateGenerator (pass by const reference) |
| The global, branch-specific or site-mixture rate matrices. | |
| 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 | |
| siteMatrices : | Simplex (pass by const reference) |
| Simplex of site matrix mixture probabilities. Treats Q as vector of site mixture categories instead of branch-specific matrices. | |
| Default : NULL | |
| siteRates : | RealPos[] (pass by const reference) |
| The rate categories for the sites. | |
| Default : [ ] | |
| siteRatesProbs : | Simplex (pass by const reference) |
| The probability weights of rate categories for the sites. | |
| Default : NULL | |
| 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 : 0 | |
| type : | String (pass by value) |
| The data type, used for simulation and initialization. | |
| Default : DNA | |
| Options : DNA|RNA|AA|Codon|Doublet|PoMo|Protein|Standard|NaturalNumbers|Binary|Restriction | |
| treatAmbiguousAsGap : | Bool (pass by value) |
| Should we treat ambiguous characters as gaps/missing? | |
| Default : FALSE | |
| coding : | String (pass by value) |
| Default : all | |
| 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 be gap or missing if the corresponding character in the clamped matrix is gap or missing? | |
| Default : TRUE |
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