Description Usage Arguments Details See Also Examples
Returns a distance matrix for specified ids of a tree.
1 | calcDstMtrx(tree, ids, parallel = FALSE, progress = "none")
|
tree |
|
ids |
IDs of nodes/tips |
parallel |
logical, make parallel? |
progress |
name of the progress bar to use, see |
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.
calcDstBLD
, calcDstRF
, calcDstTrp
https://github.com/DomBennett/treeman/wiki/calc-methods
1 2 3 4 5 6 7 8 | # 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
|
[1] 0.4014857
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