Rev Language Reference



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)


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

Domain Type