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phylopath: Easy phylogenetic path analysis in R
Stockholm University, Faculty of Science, Department of Zoology.
Number of Authors: 12018 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4718Article in journal (Refereed) Published
Abstract [en]

Confirmatory path analysis allows researchers to evaluate and compare causal models using observational data. This tool has great value for comparative biologists since they are often unable to gather experimental data on macro-evolutionary hypotheses, but is cumbersome and error-prone to perform. I introduce phylopath, an R package that implements phylogenetic path analysis (PPA) as described by von Hardenberg Gonzalez-Vayer (2113). In addition to the published method, I provide support for the inclusion of binary variables. I illustrate PPA and phylopath by recreating part of a study on the relationship between brain size and vulnerability to extinction. The package aims to make the analysis straight-forward, providing convenience functions, and several plotting methods, which I hope will encourage the spread of the method.

Place, publisher, year, edition, pages
2018. Vol. 6, article id e4718
Keywords [en]
Phylogenetic path analysis, Evolution, Path analysis, Comparative methods, R package
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-156664DOI: 10.7717/peerj.4718ISI: 000430890200003PubMedID: 29713568OAI: oai:DiVA.org:su-156664DiVA, id: diva2:1213167
Available from: 2018-06-04 Created: 2018-06-04 Last updated: 2018-06-04Bibliographically approved

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