R: Check whether an allocation of the shifts is parsimonious, in...

check_parsimony_clusters {PhylogeneticEM} | R Documentation

## Check whether an allocation of the shifts is parsimonious, in the "infinite site model".

### Description

`check_parsimony_clusters` takes a vector clusters of the tips, and checks whether the number of groups of the tips induced by this allocation is exactly the number of shifts plus one.

### Usage

    check_parsimony_clusters(tree, edges, clusters)

### Arguments

`tree` | phylogenetic tree.
`clusters` | a vector of clusters of the tips of the tree (result of function `clusters_from_shifts`).

### Details

This function computes explicitly the clustering of the tips, using function `check_parsimony`. By default, this function uses `enumerate_tips_under_edges` to compute the list of tips under each edge, but a list can be provided (if many tests are done).

### Value

boolean : TRUE if the allocation is parsimonious.

[Package PhylogeneticEM version 1.1.0 Index]