resampleTree function

Altering phylogenetic trees

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

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.

Returns

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

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)

See Also

c("list("search.conv")", " vignette"); c("list("overfitRR")", " vignette"); c("list("Alternative-trees")", " vignette")

Author(s)

Silvia Castiglione, Giorgia Girardi