sensiPhy: An r-package for sensitivity analysis in phylogenetic comparative methods

Paterno, Gustavo B.; Penone, Caterina; Werner, Gijsbert D. A. (2018). sensiPhy: An r-package for sensitivity analysis in phylogenetic comparative methods. Methods in Ecology and Evolution, 9(6), pp. 1461-1467. Wiley-Blackwell 10.1111/2041-210X.12990

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Biological conclusions drawn from phylogenetic comparative methods can be sensitive to uncertainty in species sampling, phylogeny and data. To be confident about our conclusions, we need to quantify their robustness to such uncertainty. We present sensiPhy, an r-package, to easily and rapidly perform sensitivity analysis for phylogenetic comparative methods. sensiPhy allows researchers to evaluate the sampling effort, detect influential species and clades, assess phylogenetic uncertainty and quantify the effects of intraspecific variation, for phylogenetic regression and for metrics of phylogenetic signal, diversification and trait evolution. Uniquely, sensiPhy allows users to simultaneously quantify the effects of different types of uncertainty and potential interactions among them. Using real data, we show how conclusions from comparative methods can be affected by uncertainty and how sensiPhy can help determine if a conclusion is robust. By providing a single, intuitive and user-friendly resource that can evaluate various sources of uncertainty, sensiPhy aims to encourage researchers, and particularly less-experienced users, to incorporate sensitivity analyses in their phylogenetic comparative analyses. © 2018 The Authors. Methods in Ecology and Evolution © 2018 British Ecological Society

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Plant Ecology
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)

UniBE Contributor:

Penone, Caterina

Subjects:

500 Science > 580 Plants (Botany)

ISSN:

2041-210X

Publisher:

Wiley-Blackwell

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

26 Jun 2018 15:26

Last Modified:

23 Oct 2019 20:31

Publisher DOI:

10.1111/2041-210X.12990

Uncontrolled Keywords:

bias; diversification; PGLS; phylogenetic regression; robustness; trait evolution

BORIS DOI:

10.7892/boris.117428

URI:

https://boris.unibe.ch/id/eprint/117428

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