Levin, S.C., Childs, D.Z. orcid.org/0000-0002-0675-4933, Compagnoni, A. et al. (3 more authors) (2021) ipmr: flexible implementation of integral projection models in R. Methods in Ecology and Evolution, 12 (10). pp. 1826-1834. ISSN 2041-210X
Abstract
1. Integral projection models (IPMs) are an important tool for studying the dynamics of populations structured by one or more continuous traits (e.g. size, height, body mass). Researchers use IPMs to investigate questions ranging from linking drivers to population dynamics, planning conservation and management strategies, and quantifying selective pressures in natural populations. The popularity of stage-structured population models has been supported by R scripts and packages (e.g. IPMpack, popbio, popdemo, lefko3) aimed at ecologists, which have introduced a broad repertoire of functionality and outputs. However, pressing ecological, evolutionary and conservation biology topics require developing more complex IPMs, and considerably more expertise to implement them. Here, we introduce ipmr, a flexible R package for building, analysing and interpreting IPMs.
2. The ipmr framework relies on the mathematical notation of the models to express them in code format. Additionally, this package decouples the model parameterization step from the model implementation step. The latter point substantially increases ipmr's flexibility to model complex life cycles and demographic processes.
3. ipmr can handle a wide variety of models, including those that incorporate density dependence, discretely and continuously varying stochastic environments, and multiple continuous and/or discrete traits. ipmr can accommodate models with individuals cross-classified by age and size. Furthermore, the package provides methods for demographic analyses (e.g. asymptotic and stochastic growth rates) and visualization (e.g. kernel plotting).
4. ipmr is a flexible R package for integral projection models. The package substantially reduces the amount of time required to implement general IPMs. We also provide extensive documentation with six vignettes and help files, accessible from an R session and online.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2021 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, (http://creativecommons.org/licenses/by-nc/4.0/) which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. |
Keywords: | elasticity; integral projection model; life history; population dynamics; population growth rate; sensitivity; structured populations |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) |
Funding Information: | Funder Grant number NATURAL ENVIRONMENT RESEARCH COUNCIL NE/M018458/1 |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 06 Apr 2022 12:45 |
Last Modified: | 10 Feb 2023 14:12 |
Status: | Published |
Publisher: | Wiley |
Refereed: | Yes |
Identification Number: | 10.1111/2041-210x.13683 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:185480 |
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Licence: CC-BY-NC 4.0