convnum {convevol}

Quantify convergence by the number of convergent events

Description

This program takes in a set of taxa that are already suspected to be convergent in a particular area of morphospace. It then counts the number of times that a lineage has invaded that region of morphospace.

Usage

convnum(
  phy,
  phendata,
  convtips,
  plot = TRUE,
  ellipse = NULL,
  plotellipse = NULL
)

Arguments

phy

The phylogeny of interest in phylo format

phendata

Phenotypic data for all tips

convtips

A list consisting of the names of all convergent taxa

plot

Whether or not to plot a phylomorphospace with lineages that cross into the region of interest highlighted as red arrows. Default=TRUE

ellipse

Optional. An ellipse defining the region of interest, into which groups may or may not converge.

plotellipse

Optional. The ellipse defining the region of interest in the first two dimensions.

Details

This function will construct an ellipse around all convergent taxa. Then it will reconstruct ancestral states throughout the phylogeny, and use those to determine how many lineages have crossed into this ellipse from the outside.

Value

The number of lineages that have crossed into the region of trait space occupied by the convergent taxa.

References

Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K.(2013). cluster: Cluster Analysis Basics and Extensions. R package version 1.14.4.

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R langauge. Bioinformatics, 20, 289-290.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3 217-223.

Examples

phy<-rtree(10)
phendata<-fastBM(phy,nsim=2)
convtips<-c("t1","t2","t3")
answer<-convnum(phy,phendata,convtips,plot=TRUE,ellipse=NULL,plotellipse=NULL)