Computation of species tip length using a phylogeny.
Arguments
- tree
phylo. A dated tree.
- edge.info
Object returned by
tip.root.pathconsisting of a list containing the edge matrix (H1) with the path from tip to root and and a numeric vector (edge.length) giving the length of each branch of the tree.- ...
additional arguments to be passed passed down from a calling function.
Examples
library(phyloraster)
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
species.tip.length(tree)
#> Litoria_revelata Litoria_rothii Litoria_longirostris
#> 0.589016 0.589015 0.395144
#> Litoria_dorsalis Litoria_rubella Litoria_nigrofrenata
#> 0.395144 0.589015 0.490836
#> Litoria_nasuta Litoria_tornieri Litoria_inermis
#> 0.288907 0.196139 0.129514
#> Litoria_pallida Litoria_latopalmata Litoria_bicolor
#> 0.129514 0.196139 0.511002
#> Litoria_fallax Litoria_genimaculata Litoria_andiirrmalin
#> 0.511002 0.466543 0.423350
#> Litoria_wilcoxii Litoria_jungguy Litoria_caerulea
#> 0.100568 0.100568 0.390538
#> Litoria_gracilenta Litoria_chloris Litoria_xanthomera
#> 0.122460 0.054075 0.054075
#> Cyclorana_brevipes Cyclorana_novaehollandiae Cyclorana_manya
#> 0.253980 0.253980 0.210977
#> Cyclorana_cultripes Litoria_alboguttata Cyclorana_longipes
#> 0.210978 0.178724 0.178724
#> Nyctimystes_dayi Litoria_nannotis Litoria_lorica
#> 0.749621 0.348570 0.348570
#> Litoria_rheocola Litoria_nyakalensis Litoria_infrafrenata
#> 0.267000 0.267000 0.998948
library(ape)
#>
#> Attaching package: ‘ape’
#> The following objects are masked from ‘package:terra’:
#>
#> rotate, trans, zoom
set.seed(1)
tree <- rtree(n=40)
plot(tree)
species.tip.length(tree)
#> t25 t15 t33 t20 t35 t6 t10
#> 0.05893438 0.87626921 0.77891468 0.79730883 0.35319727 0.27026015 0.21320814
#> t37 t28 t38 t26 t12 t40 t23
#> 0.47811803 0.92407447 0.97617069 0.35672691 0.14821156 0.10318424 0.44628435
#> t36 t32 t8 t29 t30 t7 t19
#> 0.64010105 0.17344233 0.75482094 0.20754511 0.59571200 0.57487220 0.07706438
#> t34 t22 t14 t2 t13 t16 t18
#> 0.92861520 0.56090075 0.98509522 0.68278808 0.60154122 0.23886868 0.45257083
#> t39 t1 t3 t31 t24 t27 t4
#> 0.10498764 0.86454495 0.55715954 0.32877732 0.18086636 0.52963060 0.21269952
#> t9 t11 t21 t17 t5
#> 0.28479048 0.44623532 0.77998489 0.41312421 0.06380848
edge.info <- tip.root.path(tree)
species.tip.length(edge.info = edge.info)
#> t25 t15 t33 t20 t35 t6 t10
#> 0.05893438 0.87626921 0.77891468 0.79730883 0.35319727 0.27026015 0.21320814
#> t37 t28 t38 t26 t12 t40 t23
#> 0.47811803 0.92407447 0.97617069 0.35672691 0.14821156 0.10318424 0.44628435
#> t36 t32 t8 t29 t30 t7 t19
#> 0.64010105 0.17344233 0.75482094 0.20754511 0.59571200 0.57487220 0.07706438
#> t34 t22 t14 t2 t13 t16 t18
#> 0.92861520 0.56090075 0.98509522 0.68278808 0.60154122 0.23886868 0.45257083
#> t39 t1 t3 t31 t24 t27 t4
#> 0.10498764 0.86454495 0.55715954 0.32877732 0.18086636 0.52963060 0.21269952
#> t9 t11 t21 t17 t5
#> 0.28479048 0.44623532 0.77998489 0.41312421 0.06380848