boot.phylo {ape} | R Documentation |
These functions analyse bipartitions found in a series of trees.
prop.part
counts the number of bipartitions found in a series
of trees given as ...
.
prop.clades
counts the number of times the bipartitions present
in phy
are present in a series of trees given as ...
or
in the list previously computed and given with part
.
boot.phylo
performs a bootstrap analysis.
boot.phylo(phy, x, FUN, B = 100, block = 1) prop.part(...) prop.clades(phy, ..., part = NULL)
phy |
an object of class "phylo" . |
x |
a taxa (rows) by characters (columns) matrix; this may be presented as a list. |
FUN |
the function used to estimate phy (see details). |
B |
the number of bootstrap replicates. |
block |
the number of columns in x that will be resampled
together (see details). |
... |
either (i) a single object of class "phylo" , (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects. |
part |
a list of partitions as returned by prop.part ; if
this is used then ... is ignored. |
The argument FUN
in boot.phylo
must be the function used
to estimate the tree from the original (resampled) data matrix. Thus,
if the tree is 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.
prop.part
returns a list with an attribute "number"
. The
elements of this list are the observed clades, and the attribute their
respective numbers.
prop.clades
and boot.phylo
returns a numeric vector
which ith element is the number associated to the ith
node of phy
.
Emmanuel Paradis paradis@isem.univ-montp2.fr
Efron, B., Halloran, E. and Holmes, S. (1996) Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences USA, 93, 13429–13434.
Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–791.