View source: R/partitionsNumber.R
partitionsNumber | R Documentation |
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.
partitionsNumber(phylo, npart)
phylo |
a phylogenetic tree of class |
npart |
the numbers of partitions (colors) allowed at the tips. This is the number of shifts plus one (npart = K + 1). |
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).
extract.partitionsNumber
, parsimonyNumber
,
equivalent_shifts
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) }
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