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Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie
Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for exampl...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley & Sons, Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9286827/ https://www.ncbi.nlm.nih.gov/pubmed/35060624 http://dx.doi.org/10.1002/ecy.3637 |
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author | Thorson, James T. Arimitsu, Mayumi L. Levi, Taal Roffler, Gretchen H. |
author_facet | Thorson, James T. Arimitsu, Mayumi L. Levi, Taal Roffler, Gretchen H. |
author_sort | Thorson, James T. |
collection | PubMed |
description | Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R (mgcv and ggplot2) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins (Fratercula cirrhata) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves (Canis lupus ligoni) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines. |
format | Online Article Text |
id | pubmed-9286827 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley & Sons, Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-92868272022-07-19 Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie Thorson, James T. Arimitsu, Mayumi L. Levi, Taal Roffler, Gretchen H. Ecology Statistical Reports Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R (mgcv and ggplot2) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins (Fratercula cirrhata) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves (Canis lupus ligoni) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines. John Wiley & Sons, Inc. 2022-03-16 2022-05 /pmc/articles/PMC9286827/ /pubmed/35060624 http://dx.doi.org/10.1002/ecy.3637 Text en © 2022 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America. This article has been contributed to by US Government employees and their work is in the public domain in the USA. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Statistical Reports Thorson, James T. Arimitsu, Mayumi L. Levi, Taal Roffler, Gretchen H. Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie |
title | Diet analysis using generalized linear models derived from foraging processes using R package
mvtweedie
|
title_full | Diet analysis using generalized linear models derived from foraging processes using R package
mvtweedie
|
title_fullStr | Diet analysis using generalized linear models derived from foraging processes using R package
mvtweedie
|
title_full_unstemmed | Diet analysis using generalized linear models derived from foraging processes using R package
mvtweedie
|
title_short | Diet analysis using generalized linear models derived from foraging processes using R package
mvtweedie
|
title_sort | diet analysis using generalized linear models derived from foraging processes using r package
mvtweedie |
topic | Statistical Reports |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9286827/ https://www.ncbi.nlm.nih.gov/pubmed/35060624 http://dx.doi.org/10.1002/ecy.3637 |
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