partitionsNumber computes the number of different models with a given
number of shifts K. It is also the number of colorings of the tips to the
tree in npart = K + 1 colors.
Arguments
- phylo
a phylogenetic tree of class
phylo.- npart
the numbers of partitions (colors) allowed at the tips. This is the number of shifts plus one (npart = K + 1).
Value
an object of class partitionsNumber. This is made of a matrix
with (Nnode + ntaxa) rows and (2*npart) columns. Each column contains two vectors:
for k=1:npart it contains the number of partitions with k groups compatible
with the tree and the shift process; and for k=(npart+1):2*npart, it contains
the number of "marked" partitions with (k-npart) groups compatible with the
tree and the shift process. The actual number can be extracted with function
extract.partitionsNumber (see examples below).
Examples
if (requireNamespace("combinat", quietly = TRUE)) {
npart <- 8 # number of colors at the tips allowed
tree <- read.tree(text="(A,(A,(A,A,A),A,A));") # a tree with polytomies
plot(tree)
parts_num <- partitionsNumber(tree, npart)
parts_num
## Number of possible colorings of the tips in npart colors
extract(parts_num)
## Get all the solutions for colorings with 1 to nparts colors
extract(parts_num, npart = 1:npart)
## Number of possible colorings of the tips in npart colors
## For the sub-tree starting at node 17
extract(parts_num, node = 10)
## Number of possible colorings of the tips in npart colors
## with one marked color
extract(parts_num, marked = TRUE)
}
#> [1] 0