The argument FUN
in boot.phylo
must be the function used
to estimate the tree from the original data matrix. Thus, if the tree
was estimated with neighbor-joining (see nj
), one maybe wants
something like FUN = function(xx) nj(dist.dna(xx))
. block
in boot.phylo
specifies the number of columns to
be resampled altogether. For instance, if one wants to resample at the
codon-level, then block = 3
must be used.
Using check.labels = FALSE
in prop.part
decreases
computing times. This requires that (i) all trees have the same tip
labels, and (ii) these labels are ordered similarly in all
trees (in other words, the element tip.label
are identical in
all trees).
The plot function represents a contingency table of the different
partitions (on the x-axis) in the lower panel, and their observed
numbers in the upper panel. Any further arguments (...) are used to
change the aspects of the points in the lower panel: these may be
pch
, col
, bg
, cex
, etc. This function
works only if there is an attribute labels
in the object.
The print method displays the partitions and their numbers. The
summary method extracts the numbers only.