Guillerme, T. orcid.org/0000-0003-4325-1275 (2024) treats: a modular R package for simulating trees and traits. Methods in Ecology and Evolution, 15 (4). pp. 647-656. ISSN 2041-210X
Abstract
Simulating biological realistic data is an important step to understand and investigate biodiversity. Simulated data can be used to generate null, base line or neutral models. These can be used either in comparison to observed data to estimate the mechanisms that generated the data. Or they can be used to explore, understand and develop theoretical advances by proposing toy models. In evolutionary biology, simulations often involve the need of an evolutionary process where descent with modification is at the core of how the simulated data are generated. These evolutionary processes can then be nearly infinitely modified to include complex processes that affect the simulations such as traits co-evolution, competition mechanisms or mass extinction events. Here I present the treats package, a modular R package for trees and traits simulations. This package is based on a simple birth death algorithm from which all steps can easily be modified by users. treats also provides a tidy interface through the treats object, allowing users to easily run reproducible simulations. It also comes with an extend manual regularly updated following users' questions or suggestions.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2024 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes: https://creativecommons.org/licenses/by/4.0/ |
Keywords: | birth-death; disparity; ecology; evolution; null-models; simulations; traits; trees |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 12 Mar 2024 16:27 |
Last Modified: | 15 Nov 2024 11:47 |
Status: | Published |
Publisher: | Wiley |
Refereed: | Yes |
Identification Number: | 10.1111/2041-210x.14306 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:210154 |
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Licence: CC-BY-NC 4.0