pmlPart {phangorn} | R Documentation |
Model to estimate phylogenies for partitioned data.
pmlPart(formula, object, ...)
formula |
a formula object (see details). |
object |
an object of class pml or a list of objects of class pml . |
... |
Further arguments passed to or from other methods. |
The formula
object allows to specify which parameter get
optimised. The formula is generally of the form edge + bf + Q
~ rate + shape + ...
, on the left side are the parameters which
get optimised over all partitions, on the right the parameter which
are optimised specific to each partition. The parameters available
are "nni", "bf", "Q", "inv", "shape", "edge", "rate"
.
Each parameters can be used only once in the formula.
"rate"
and "nni"
are only available for the right side
of the formula.
For partitions with different edge weights, but same topology, pmlPen
can try to find more parsimonious models (see example).
kcluster
returns a list with elements
logLik |
log-likelihood of the fit |
trees |
a list of all trees during the optimisation. |
object |
an object of class "pml" or "pmlPart" |
Klaus Schliep K.P.Schliep@massey.ac.nz
data(yeast) dm <- dist.logDet(yeast) tree <- NJ(dm) fit <- pml(tree,yeast) fits <- optim.pml(fit) weight=xtabs(~ index+genes,attr(yeast, "index"))[,1:10] set.seed(1) sp <- pmlPart(edge ~ rate + inv, fits, weight=weight) sp sp2 <- pmlPart(~ edge + inv, fits, weight=weight) sp2 AIC(sp2) sp3 <- pmlPen(sp2, lambda = 2) AIC(sp3)