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|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

Domain Type