README.md
In NEON-biodiversity/Ostats: O-Stats, or Pairwise Community-Level Niche Overlap Statistics
Ostats: O-statistics, or Pairwise Community-Level Niche Overlap Statistics
The 'Ostats' package calculates overlap statistic to measure the degree of community-level trait overlap by fitting nonparametric kernel density functions to each species' trait distribution and calculating their areas of overlap (Mouillot et al. 2005, Geange et al. 2011, Read et al. 2018). For instance, the median pairwise overlap for a community is calculated by first determining the overlap of each species pair in trait space, and then taking the median overlap of each species pair in a community. This median overlap value is called the O-statistic (O for overlap). The Ostats() function calculates separate univariate overlap statistics for each trait, while the Ostats_multivariate() function calculates a single multivariate overlap statistic for all traits. O-statistics can be evaluated against null models to obtain standardized effect sizes. Grady et al. (2018) provide a teaching module that goes into detail about how to interpret the results presented in Read et al. (2018).
'Ostats' is part of the collaborative Macrosystems Biodiversity Project Local- to continental-scale drivers of biodiversity across the National Ecological Observatory Network (NEON). For more information on this project, see the Macrosystems Biodiversity Website.
Authors
- Quentin D. Read
- Arya Yue
- Isadora E. Fluck
- Benjamin Baiser
- John M. Grady
- Phoebe L. Zarnetske
- Sydne Record
How to install
To install the stable version of the package from CRAN, type the following into your R prompt.
install.packages('Ostats')
The development version of the package has more recent updates but may not be as thoroughly tested as the stable CRAN version. To install the development version, type the following into your R prompt.
remotes::install_github('NEON-biodiversity/Ostats')
Getting started
See the Ostats introduction vignette for more information.
Funding
National Science Foundation Division of Environmental Biology (Population & Community Ecology, MacroSysBIO & NEON-Enabled Science); Awards to P.L. Zarnetske (Michigan State University); S. Record (Bryn Mawr College); Ben Baiser (University of Florida); Angela Strecker (Western Washington University).
The National Ecological Observatory Network is a program sponsored by the National Science Foundation and operated under cooperative agreement by Battelle. This material is based in part upon work supported by the National Science Foundation through the NEON Program.
References
Geange, S.W., S. Pledger, K.C. Burns, and J.S. Shima. 2011. A unified analysis of niche overlap incorporating data of different types. Methods in Ecology and Evolution 2(2):175-184. https://doi.org/10.1111/j.2041-210X.2010.00070.x
Grady, J.M., Q.D. Read, S. Record, P.L. Zarnetske, B. Baiser, K. Thorne, and J. Belmaker. 2018. Size, niches, and the latitudinal diversity gradient. Teaching Issues and Experiments in Ecology 14: Figure Set #1.
Mouillot, D., W. Stubbs, M. Faure, O. Dumay, J.A. Tomasini, J.B. Wilson, and T. Do Chi. 2005. Niche overlap estimated based on quantitative functional traits: A new family of non-parametric indices. Oecologia 145(3):345-353. https://doi.org/10.1007/s00442-005-0151-z
Read, Q.D., J.M. Grady, P.L. Zarnetske, S. Record, B. Baiser, J. Belmaker, M.-N. Tuanmu, A. Strecker, L. Beaudrot, and K.M. Thibault. 2018. Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient. Ecography 41(10):1718-1727. https://doi.org/10.1111/ecog.03641
NEON-biodiversity/Ostats documentation built on Nov. 21, 2024, 4:01 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Ostats: O-statistics, or Pairwise Community-Level Niche Overlap Statistics
The 'Ostats' package calculates overlap statistic to measure the degree of community-level trait overlap by fitting nonparametric kernel density functions to each species' trait distribution and calculating their areas of overlap (Mouillot et al. 2005, Geange et al. 2011, Read et al. 2018). For instance, the median pairwise overlap for a community is calculated by first determining the overlap of each species pair in trait space, and then taking the median overlap of each species pair in a community. This median overlap value is called the O-statistic (O for overlap). The Ostats() function calculates separate univariate overlap statistics for each trait, while the Ostats_multivariate() function calculates a single multivariate overlap statistic for all traits. O-statistics can be evaluated against null models to obtain standardized effect sizes. Grady et al. (2018) provide a teaching module that goes into detail about how to interpret the results presented in Read et al. (2018).
'Ostats' is part of the collaborative Macrosystems Biodiversity Project Local- to continental-scale drivers of biodiversity across the National Ecological Observatory Network (NEON). For more information on this project, see the Macrosystems Biodiversity Website.
Authors
- Quentin D. Read
- Arya Yue
- Isadora E. Fluck
- Benjamin Baiser
- John M. Grady
- Phoebe L. Zarnetske
- Sydne Record
How to install
To install the stable version of the package from CRAN, type the following into your R prompt.
install.packages('Ostats')
The development version of the package has more recent updates but may not be as thoroughly tested as the stable CRAN version. To install the development version, type the following into your R prompt.
remotes::install_github('NEON-biodiversity/Ostats')
Getting started
See the Ostats introduction vignette for more information.
Funding
National Science Foundation Division of Environmental Biology (Population & Community Ecology, MacroSysBIO & NEON-Enabled Science); Awards to P.L. Zarnetske (Michigan State University); S. Record (Bryn Mawr College); Ben Baiser (University of Florida); Angela Strecker (Western Washington University).
The National Ecological Observatory Network is a program sponsored by the National Science Foundation and operated under cooperative agreement by Battelle. This material is based in part upon work supported by the National Science Foundation through the NEON Program.
References
Geange, S.W., S. Pledger, K.C. Burns, and J.S. Shima. 2011. A unified analysis of niche overlap incorporating data of different types. Methods in Ecology and Evolution 2(2):175-184. https://doi.org/10.1111/j.2041-210X.2010.00070.x
Grady, J.M., Q.D. Read, S. Record, P.L. Zarnetske, B. Baiser, K. Thorne, and J. Belmaker. 2018. Size, niches, and the latitudinal diversity gradient. Teaching Issues and Experiments in Ecology 14: Figure Set #1.
Mouillot, D., W. Stubbs, M. Faure, O. Dumay, J.A. Tomasini, J.B. Wilson, and T. Do Chi. 2005. Niche overlap estimated based on quantitative functional traits: A new family of non-parametric indices. Oecologia 145(3):345-353. https://doi.org/10.1007/s00442-005-0151-z
Read, Q.D., J.M. Grady, P.L. Zarnetske, S. Record, B. Baiser, J. Belmaker, M.-N. Tuanmu, A. Strecker, L. Beaudrot, and K.M. Thibault. 2018. Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient. Ecography 41(10):1718-1727. https://doi.org/10.1111/ecog.03641
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.