bootstrap.pml {phangorn} | R Documentation |
bootstrap.pml
performs (non-parametric) bootstrap analysis and bootstrap.phyDat
produces a list of bootstrapped datasets. Under Linux the bootstrap is performed in parallel, if the multicore package is loaded. plotBS
plots a phylogenetic tree with the with the bootstrap values assigned to the (internal) edges.
bootstrap.pml(x, bs = 100, trees = TRUE, ...) bootstrap.phyDat(x, FUN, bs = 100, ...) plotBS(tree, BStrees, type="unrooted", bs.col="black", bs.adj=c(0.5, 0.5), ...)
x |
an object of class pml or phyDat. |
bs |
number of bootstrap samples. |
trees |
return trees only (default) or whole pml objects. |
... |
further parameters used by optim.pml or plot.phylo. |
FUN |
the function to estimate the trees. |
tree |
The tree on which edges the bootstrap values are plotted. |
BStrees |
a list of trees (object of class "multiPhylo"). |
type |
the type of tree. |
bs.col |
color of bootstrap support labels. |
bs.adj |
one or two numeric values specifying the horizontal and vertical justification of the bootstrap labels. |
returns an object of class multi.phylo or a list where each element is an object of class pml.
Klaus Schliep klaus.schliep@gmail.com
## Not run: data(Laurasiatherian) dm <- dist.logDet(Laurasiatherian) tree <- NJ(dm) fit=pml(tree,Laurasiatherian) fit = optim.pml(fit,TRUE) set.seed(1) bs <- bootstrap.pml(fit, bs=100, optNni=TRUE) plotBS(fit$tree,bs) ## End(Not run)