Description Usage Arguments Details Value References Examples

Simulates evolution along a given phylogeny, using parameters derived from observed data, and calculates the convnum metric for each simulation for a set of user-defined taxa. Then compares the observed convnum value to the simulated values to assess the significance of the observed levels of convergent evolution.

1 2 | ```
convnumsig(phyl, phendata, convtips, nsim, ellipse = NULL,
plot = FALSE, plotellipse = NULL)
``` |

`phyl` |
The phylogeny of interest in phylo format |

`phendata` |
Phenotypic data for all tips |

`convtips` |
A list consisting of the names of all convergent taxa |

`nsim` |
The number of simulatons to conduct |

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

`plot` |
Optional. Describes whether or not to show phylomorphospaces for all of the simulations. |

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

None

A list, consisting first of the p-value for the observed convnum, and second of a vector containing all of the simulated convnum values. Also displays a histogram of all of the simulated convnum values.

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.

1 2 3 4 | ```
phyl<-rtree(10)
phendata<-fastBM(phyl,nsim=2)
convtips<-c("t1","t2","t3")
answer<-convnumsig(phyl,phendata,convtips,10,plot=FALSE,ellipse=NULL,plotellipse=NULL)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.