Rev Language Reference



dnPhyloCTMCDollo(Tree tree, RateGenerator Q, RealPos deathRate, Simplex rootFrequencies, RealPos branchRates, RealPos[] siteRates, Natural nSites, String type, Bool normalize, String coding)


tree : Tree (pass by const reference)
The tree along which the process evolves.
Q : RateGenerator (pass by const reference)
The global or branch-specific rate matrices.
Default : NULL
deathRate : RealPos (pass by const reference)
The Dollo character death rate
Default : 1
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 : [ ]
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 : Standard
Options : Standard|Binary|Restriction
normalize : Bool (pass by value)
Should we normalize the Dollo substitution matrices?
Default : TRUE
coding : String (pass by value)
Default : noabsencesites

Domain Type