phyBranchAL_Inc: R code for phylo to Chaophyabu function, speed up performance

In chaolab2019/chaoUtility: chao lab utility

Description

R code for phylo to Chaophyabu function, speed up performance

Usage

phyBranchAL_Inc(phylo, data, datatype = "incidence_raw", refT = 0,
  rootExtend = T, remove0 = T)

Arguments

phylo	a phylo object
data	a vector with names

Value

a Chaophyabu objects

Examples

data(phybird.new)
bird.inc <- phybird.new$inci
bird.lab <- rownames(phybird.new$abun)
bird.phy <- phybird.new$chaophytree
tree<-tidytree::as.phylo(bird.phy$phytree)
Idata<-bird.inc$North.site
refTs<-c(80,90,100)
result<-phyBranchAL_Inc(tree,Idata,datatype="incidence_raw",refTs)
result$treeNabu
result$treeH
result$BLbyT

chaolab2019/chaoUtility documentation built on Feb. 26, 2020, 2:48 p.m.