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Dr. Natalie Cusimano

Use R!

In 2006, thanks to my colleague Christoph Heibl, I started to work with R, using the first edition of Emanuel Paradis's “Analysis of Phylogenetics and Evolution in R”, which provides a basic introduction to R and of course to the R package “ape”. This was one of the first packages for R offering a large set of tools to conduct phylogenetic analyses. Since then, the community using phylogenetic tools in R has grown continuously, and many new packages contributing to this field have been developed. In 2012, the second edition of Paradis's book came out, now nearly double the original, which reflects the growth of ape.
The ape package was, and still is, the most important tool for my work in R. I have written several functions to address diverse kinds of tasks, and most of them use or extend functions of ape. Even though they are still raw and without full documentation, I would like to make them available because of an increasing number of requests. I have also created an R package ChromEvol (see below) that I would like to share. Feel free to download, use and improve them. For questions and suggestions please contact me (cusimano@bio.lmu.de).

chromEvol – ChromEvol

chromEvol is a program developed by Mayrose et al. (2010) for reconstructing the evolution of chromosome numbers along a phylogeny. I wrote the R package ChromEvol, which contains functions to facilitate the use of the program chromEvol: It allows easy preparing of the input files and a fast reading of the results from the different output files back into R. It offers several functions for visualizing and summarizing the results of the analyses and preparation of publication-quality figures. For how to construct chromosome number evolution with chromEvol please see the chromEvol webpage.

Download the chromEvol package version 0.9-1 (13 Nov 2013, dependencies: ape)
Install with R CMD INSTALL ChromEvol

Functions and Scripts (raw)

All my functions and scripts require the package ape, if other packages are required they are specified within the files. Please see inside the files for instructions how to use the functions and feel free to contact me for questions about their handling.

  • Script to simulate missing species of a tree with corsim (TreeSim: Stadler 2009, Hartmann et al. 2010, Cusimano et al. 2012) and conduct diversification analyses in batch mode (corsimApplied.R)
  • Plotting lineage-through-time plots with some extras (LTT.R)
  • Function that compares two vectors and gives you elements that are present only in one of the vectors (which.isNOTin.R)
  • Script and function to transform the tip branches of a tree , i.e the thickness or to triangles, with the width of both correlating with certain parameters (e.g., species number of the clade) (tip.branches.R)
  • Some functions that add information to a plotted tree, i.e. adding bootstrap/other support values at the nodes, mapping characters/symbols at the tip of a tree, preparing and handling of the necessary input objects or reducing large clades into triangles (mapping.R)
  • Function to perform and visualize PCA analyses of a given character between all sister clade pairs present in a phylogeny (PCA_batch.R)

Links

The R Project for Statistical Computing
ape: Analyses of Phylogenetics and Evolution by Emmanuel Paradis
laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies by Dan Rabosky
LAGOPUS, PHYLOCLIM, PHYLOCH packages by Christoph Heibl
ChromEvol webpage by Itay Mayrose

References

N. Cusimano, T. Stadler, S. Renner: A new method for handling missing species in diversification analysis applicable to randomly or non-randomly sampled phylogenies. Syst. Biol. (2012) 61: 785 – 792.

Emanuel Paradis (2012): Analysis of Phylogenetics and Evolution in R. Second edition. Springer. New York, Dordrecht, Heidelberg, London.

Mayrose I, Barker MS, Otto S.P. (2010): Probabilistic models of chromosome number evolution and the inference of polyploidy. Systematic Biology. 59(2): 132 – 144

K. Hartmann, D. Wong, T. Stadler: Sampling trees from evolutionary models. Syst. Biol. (2010) 59: 465 – 476.

T. Stadler: On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theo. Biol. (2009) 261: 58 – 66.


Last update: 2014-02-12