R: Calculate the distance matrix

calcDstMtrx {treeman} | R Documentation

## Calculate the distance matrix

### Description

Returns a distance matrix for specified ids of a tree.

### Usage

    calcDstMtrx(tree, ids, parallel = FALSE, progress = "none")

### Arguments

`tree` | `TreeMan` object
`ids` | IDs of nodes/tips
`parallel` | logical, make parallel?
`progress` | name of the progress bar to use, see `create_progress_bar`

### Details

The distance between every id in the tree is calculated by summing the lengths of the branches that connect them. This can be useful for testing the distances between trees, checking for evoltuionary isolated tips etc. Parallelizable.

### See Also

`calcDstBLD`, `calcDstRF`, `calcDstTrp` https://github.com/DomBennett/treeman/wiki/calc-methods

### Examples

    # checking the distance between two trees
    library(treeman)
    tree_1 <- randTree(10)
    tree_2 <- randTree(10)
    dmat1 <- calcDstMtrx(tree_1, tree_1['tips'])
    dmat2 <- calcDstMtrx(tree_2, tree_2['tips'])
    mdl <- cor.test(x=dmat1, y=dmat2)
    as.numeric(1 - mdl$estimate)  # 1 - Pearson's r

[Package treeman version 1.1.4 Index]