R: Check Parsimony, assuming no homoplasy

check_parsimony {PhylogeneticEM} | R Documentation

## Check Parsimony, assuming no homoplasy

### Description

`check_parsimony` take a vector of shifts edges, and check whether the number of groups of the tips induced by this allocation is exactly the number of shifts plus one. This is equivalent to parsimony when there is no homoplasy (i.e. no convergent regimes).

### Usage

    check_parsimony(tree, edges, ...)

### Arguments

`tree` | phylogenetic tree
`edges` | a vector of edges of the tree, where the shifts are
`...` | possibly, a list giving the descendant tips of each edge

### Details

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

### Value

boolean : TRUE if the allocation is parsimonious.

[Package PhylogeneticEM version 1.1.0 Index]