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The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees

1. Neighborhood competition models are powerful tools to measure the effect of interspecific competition. Statistical methods to ease the application of these models are currently lacking. 2. We present the forestecology package providing methods to (a) specify neighborhood competition models, (b) e...

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Autores principales: Kim, Albert Y., Allen, David N., Couch, Simon P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601886/
https://www.ncbi.nlm.nih.gov/pubmed/34824775
http://dx.doi.org/10.1002/ece3.8129
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author Kim, Albert Y.
Allen, David N.
Couch, Simon P.
author_facet Kim, Albert Y.
Allen, David N.
Couch, Simon P.
author_sort Kim, Albert Y.
collection PubMed
description 1. Neighborhood competition models are powerful tools to measure the effect of interspecific competition. Statistical methods to ease the application of these models are currently lacking. 2. We present the forestecology package providing methods to (a) specify neighborhood competition models, (b) evaluate the effect of competitor species identity using permutation tests, and (cs) measure model performance using spatial cross‐validation. Following Allen and Kim (PLoS One, 15, 2020, e0229930), we implement a Bayesian linear regression neighborhood competition model. 3. We demonstrate the package's functionality using data from the Smithsonian Conservation Biology Institute's large forest dynamics plot, part of the ForestGEO global network of research sites. Given ForestGEO’s data collection protocols and data formatting standards, the package was designed with cross‐site compatibility in mind. We highlight the importance of spatial cross‐validation when interpreting model results. 4. The package features (a) tidyverse‐like structure whereby verb‐named functions can be modularly “piped” in sequence, (b) functions with standardized inputs/outputs of simple features sf package class, and (c) an S3 object‐oriented implementation of the Bayesian linear regression model. These three facts allow for clear articulation of all the steps in the sequence of analysis and easy wrangling and visualization of the geospatial data. Furthermore, while the package only has Bayesian linear regression implemented, the package was designed with extensibility to other methods in mind.
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spelling pubmed-86018862021-11-24 The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees Kim, Albert Y. Allen, David N. Couch, Simon P. Ecol Evol Research Articles 1. Neighborhood competition models are powerful tools to measure the effect of interspecific competition. Statistical methods to ease the application of these models are currently lacking. 2. We present the forestecology package providing methods to (a) specify neighborhood competition models, (b) evaluate the effect of competitor species identity using permutation tests, and (cs) measure model performance using spatial cross‐validation. Following Allen and Kim (PLoS One, 15, 2020, e0229930), we implement a Bayesian linear regression neighborhood competition model. 3. We demonstrate the package's functionality using data from the Smithsonian Conservation Biology Institute's large forest dynamics plot, part of the ForestGEO global network of research sites. Given ForestGEO’s data collection protocols and data formatting standards, the package was designed with cross‐site compatibility in mind. We highlight the importance of spatial cross‐validation when interpreting model results. 4. The package features (a) tidyverse‐like structure whereby verb‐named functions can be modularly “piped” in sequence, (b) functions with standardized inputs/outputs of simple features sf package class, and (c) an S3 object‐oriented implementation of the Bayesian linear regression model. These three facts allow for clear articulation of all the steps in the sequence of analysis and easy wrangling and visualization of the geospatial data. Furthermore, while the package only has Bayesian linear regression implemented, the package was designed with extensibility to other methods in mind. John Wiley and Sons Inc. 2021-09-29 /pmc/articles/PMC8601886/ /pubmed/34824775 http://dx.doi.org/10.1002/ece3.8129 Text en © 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. 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 Research Articles
Kim, Albert Y.
Allen, David N.
Couch, Simon P.
The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees
title The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees
title_full The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees
title_fullStr The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees
title_full_unstemmed The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees
title_short The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees
title_sort forestecology r package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601886/
https://www.ncbi.nlm.nih.gov/pubmed/34824775
http://dx.doi.org/10.1002/ece3.8129
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