R/utilities.R

In sevragorgia/chronotools: Visualize and Plot Chronograms with R and phytools

#
# Sergio Vargas
#
#



#extract node ages from a collection of trees
get_phylobayes_dates<-function(tree_set){


  phylo_dates<-data.frame(Node=c(1:tree_set[[1]]$Nnode))

  for(tree in 1:length(tree_set)){

    phylo_dates<-cbind(phylo_dates, tree_set[[tree]]$node.label)

  }

  phylo_dates<-apply(t(phylo_dates[,-1]), 2, function(x)as.numeric(as.character(x)))

}




#get histogram breaks that respect min and max ages.
get.age.histogram.breaks<-function(age.vector){

  min.age<-min(age.vector)
  max.age<-max(age.vector)
  age.range<-max.age - min.age

  bin.size<-age.range/nclass.FD(age.vector)

  seq(min.age, max.age, by=bin.size)

}