Function for phylogeny resolution
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I couldn’t find any functions to calculate number of polytomies, and related metrics.
Here’s a simple function that gives four metrics on a phylo tree object:
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| # calculate tree resolution stats | |
| treeresstats <- function(x) { | |
| require(phangorn) # load the phangorn package | |
| todo <- ( 1+Ntip(x)) : (Ntip(x) + Nnode(x) ) | |
| trsize_tips <- Ntip(x) | |
| trsize_nodes <- Nnode(x) | |
| polytomyvec <- sapply(todo, function(y) length(Children(x, y))) | |
| numpolys <- length(polytomyvec[polytomyvec > 2]) | |
| numpolysbytrsize_tips <- numpolys/trsize_tips | |
| numpolysbytrsize_nodes <- numpolys/trsize_nodes | |
| proptipsdescpoly <- sum(polytomyvec[polytomyvec > 2])/trsize_tips | |
| propnodesdich <- length(polytomyvec[polytomyvec == 2])/trsize_nodes | |
| list(trsize_tips = trsize_tips, trsize_nodes = trsize_nodes, | |
| numpolys = numpolys, numpolysbytrsize_tips = numpolysbytrsize_tips, | |
| numpolysbytrsize_nodes = numpolysbytrsize_nodes, | |
| proptipsdescpoly = proptipsdescpoly, propnodesdich = propnodesdich) | |
| } | |
| # Single tree example | |
| tree <- read.tree(text="((((((artemisia_species:44,lactuca_species:44,senecio_species:44)6:46,campanula_species:90)5:17.75,((asclepias_species:71,galium_species:71)8:18.375,plantago_species:89.375)7:18.375)4:17.75,((cerastium_species:41.833332,silene_species:41.833332)10:41.833332,chenopodium_species:83.666664)9:41.833336)3:17.75,((geum_species:47,potentilla_species:47)12:48.125,lepidium_species:95.125)11:48.125)2:17.75,(bromus_species:12,elymus_species:12)13:149)1;") | |
| dat <- treeresstats(tree) | |
| dat | |
| # Many trees example | |
| maketrees <- function(numtrees) { | |
| require(ape); require(plyr) | |
| trees <- rmtree(numtrees, 20) | |
| llply(trees, di2multi, tol = 0.5) | |
| } | |
| trees <- maketrees(30) | |
| dat <- ldply(trees, function(x) data.frame(treeresstats(x))) | |
| dat |
Here’s output from the gist above:
`
dat $trsize [1] 15
$numpolys [1] 1
$numpolysbytrsize [1] 0.06666667
$proptipsdescpoly [1] 0.2
$propnodesdich [1] 12 `
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