Usage
pml.fit(tree, data, bf=rep(1/length(levels), length(levels)), shape=1, k=1, Q=rep(1, length(levels)*(length(levels)-1)/2), levels=attr(data, "levels"), inv=0, rate=1, g=NULL, w=NULL, eig=NULL, INV=NULL, ll.0=NULL, llMix=NULL, wMix=0, ..., site=FALSE)
pml.init(data, k)
pml.free()
edQt(Q = c(1, 1, 1, 1, 1, 1), bf = c(0.25, 0.25, 0.25, 0.25))
lli(data, tree, ...)
discrete.gamma(alpha, k)
Arguments
tree
A phylogenetic tree, object of class phylo.
data
An alignment, object of class phyDat.
shape
Shape parameter of the gamma distribution.
alpha
Shape parameter of the gamma distribution.
k
Number of intervals of the discrete gamma distribution.
Q
A vector containing the lower triangular part of the rate matrix.
levels
The alphabet used e.g. c("a", "c", "g", "t") for DNA
inv
Proportion of invariable sites.
g
vector of quantiles (default is NULL)
w
vector of probabilities (default is NULL)
eig
Eigenvalue decomposition of Q
INV
Sparse representation of invariant sites
...
Further arguments passed to or from other methods.
site
return the log-likelihood or vector of sitewise likelihood values