phylopath: Easy phylogenetic path analysis in R
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...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2018-04-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/4718.pdf |
| _version_ | 1797421750081814528 |
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| author | Wouter van der Bijl |
| author_facet | Wouter van der Bijl |
| author_sort | Wouter van der Bijl |
| collection | DOAJ |
| description | 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-Voyer (2013). 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. |
| first_indexed | 2024-03-09T07:21:56Z |
| format | Article |
| id | doaj.art-6e1ae93355be464984f366dafb7576f2 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:21:56Z |
| publishDate | 2018-04-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-6e1ae93355be464984f366dafb7576f22023-12-03T07:15:06ZengPeerJ Inc.PeerJ2167-83592018-04-016e471810.7717/peerj.4718phylopath: Easy phylogenetic path analysis in RWouter van der BijlConfirmatory 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-Voyer (2013). 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.https://peerj.com/articles/4718.pdfPhylogenetic path analysisEvolutionPath analysisComparative methodsR package |
| spellingShingle | Wouter van der Bijl phylopath: Easy phylogenetic path analysis in R PeerJ Phylogenetic path analysis Evolution Path analysis Comparative methods R package |
| title | phylopath: Easy phylogenetic path analysis in R |
| title_full | phylopath: Easy phylogenetic path analysis in R |
| title_fullStr | phylopath: Easy phylogenetic path analysis in R |
| title_full_unstemmed | phylopath: Easy phylogenetic path analysis in R |
| title_short | phylopath: Easy phylogenetic path analysis in R |
| title_sort | phylopath easy phylogenetic path analysis in r |
| topic | Phylogenetic path analysis Evolution Path analysis Comparative methods R package |
| url | https://peerj.com/articles/4718.pdf |
| work_keys_str_mv | AT woutervanderbijl phylopatheasyphylogeneticpathanalysisinr |