Abstract
The objectives of this chapter are to quickly cover how to use R to interface with analytical software that is written in other programming languages. The chapter will focus primarily on integrating R commands with the software Phylocom written in C [14]. I have chosen to focus on this program because it carries out many of the types of analyses covered in this book. Although I have focused on this particular program, the general principles of how to call other programs from R and integrate them into your R-based analyses remain the same.
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References
Webb, C.O., D.D. Ackerly, and S.W. Kembel. 2008. Phylocom: Software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24: 2098–2100.
Webb, C.O. 2000. Exploring the phylogenetic structure of ecological communities: An example for rainforest trees. The American Naturalist 156: 145–155.
Webb, C.O., and M.J. Donoghue. 2005. Phylomatic: Tree assembly for applied phylogenetics. Molecular Ecology Notes 5: 181–183.
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Swenson, N.G. (2014). Integrating R with Other Phylogenetic and Functional Trait Analytical Software. In: Functional and Phylogenetic Ecology in R. Use R!. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9542-0_9
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DOI: https://doi.org/10.1007/978-1-4614-9542-0_9
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