resampleTree: Altering phylogenetic trees

In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

Altering phylogenetic trees

Description

The function alters the topology and randomly removes a user-specified proportion of species from a phylogenetic tree.

Usage

resampleTree(tree,s=0.25,sdata=NULL,nodes=NULL,categories=NULL,
             swap.si=0.1,swap.si2=0.1,swap.node=NULL,nsim=1)

Arguments

tree	a phylogenetic tree. The tree needs not to be ultrametric or fully dichotomous.
s	the percentage of tips to be cut off. It is set at 25% by default.
sdata	to be supplied to condition the species sampling. It can be either a named vector or a data.frame/matrix having the species names as first column. In case of stratified random sampling, sdata should contain the strata. Otherwise, the user can provide a sampling probability (meant as the probability to be removed from the tree) for each species.
nodes	the clades to be preserved. In this case the function maintains no less than 5 species at least in each of them.
categories	the categories to be preserved. In this case the function maintains no less than 5 species at least in each of them.
swap.si, swap.si2, swap.node	arguments si, si2, node as passed to swapONE. The default for both si and si2 is 0.1.
nsim	number of phylogenies to return. It is set at 1 by default.

Value

The function returns phylo or multiPhylo object. The output always has an attribute "Call" which returns an unevaluated call to the function.

Author(s)

Silvia Castiglione, Giorgia Girardi

See Also

search.conv vignette; overfitRR vignette; Alternative-trees vignette

Examples

## Not run: 
DataCetaceans$treecet->treecet
plot(treecet,show.tip.label = FALSE,no.margin = TRUE)
nodelabels(frame="n",col="red")

# Select two clades for stratified random sampling
clanods=c("crown_Odo"=150,"crown_Mysti"=131)
sdata1<-do.call(rbind,lapply(1:length(clanods),function(w)
  data.frame(species=tips(treecet,clanods[w]),group=names(clanods)[w])))

# generate a vector of probabilities based on body mass
prdata<-max(DataCetaceans$masscet)-DataCetaceans$masscet

# select two nodes to be preserved
nn=c(180,159)

# generate two fictional categorical vectors to be preserved
cat1<-sample(rep(c("a","b","c"),each=39),Ntip(treecet))
names(cat1)<-treecet$tip.label
cat2<-rep(c("d","e"),each=100)
names(cat2)<-sample(treecet$tip.label,100)

# 1. Random sampling
resampleTree(treecet,s=0.25,swap.si=0.3)->treecet1

# 1.1 Random sampling preserving clades
resampleTree(treecet,s=0.25,nodes=nn)->treecet2

# 2. Stratified random sampling
resampleTree(treecet,sdata = sdata1,s=0.25)->treecet3

# 2.1 Stratified random sampling preserving clades and categories
resampleTree(treecet,sdata = sdata1,s=0.25,nodes=nn,categories = list(cat1,cat2))->treecet4

# 3. Sampling conditioned on probability
resampleTree(treecet,sdata = prdata,s=0.25,nsim=5)->treecet5

## End(Not run)

RRphylo documentation built on April 3, 2025, 9:43 p.m.