taxa2phylo: Convert taxon data into Phylogeny

Description

Convert temporal and ancestor-descendant relationships of taxa into a time-scaled phylogeny

Usage

taxa2phylo(taxad, obs_time = NULL, plot = F)

Arguments

taxad

A five-column matrix of taxonomic data, as output by simFossilTaxa

obs_time

Per-taxon times of observation; if NULL, the LADs (column 4) in taxad2 are used

plot

Plot the resulting phylogeny?

Value

The resulting phylogeny with branch lengths is output as an object of class phylo

Details

This function will output trees with the element $root.time, which is the time of the root divergence in absolute time. As with many functions in the paleotree library, absolute time is always decreasing, i.e. the present day is zero. Please, DON'T use this function to time-scale a real tree. It assumes you know the use timePaleoPhy or srcTimePaleoPhy instead. Please, DO use this function when doing simulations and you want to make a tree of the 'true' history, such as for simulating trait evolution along phylogenetic branches.

Examples

Run this code

set.seed(444)
taxa<-simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,nExtant=0)
#let's use taxa2cladogram() to get the 'ideal' cladogram of the taxa
tree<-taxa2phylo(taxa)
phyloDiv(tree)
#now a phylogeny with tips placed at the apparent time of extinction
rangesCont<-sampleRanges(taxa,r=0.5)
tree<-taxa2phylo(taxa,obs_time=rangesCont[,2])
phyloDiv(tree)