README.md

In atredennick/patches: Calculates metrics for analysis of alpha, beta, and gamma variability

patches

patches is an R package to calculate metrics of alhpa, beta, and gamma variability from species level time series data where the data is collected over several patches (plots) in a landscape or region. All metrics are based on equations derived in Wang and Loreau 2014, Ecology Letters.

The function patches_var() returns a list of metrics, currently including (note that all descriptions of the metrics described below are ver batim from Wang and Loreau 2014):

| Output name | Description | | ----------- | ----------- | | species_synchrony | Species synchrony within local patches | | species_var | Species-level variability within local patches: squared coefficient of temporal variation of species biomass | | plot_species_richness | Number of species observed in a focal plot, averaged over years | | weighted_patch_cv | Weighted average of coefficients of temporal variation across local patches | | alpha_var | Alpha variability: temporal variability at local scale | | patch_synchrony | Spatial synchrony among local patches | | beta_var | Multiplicative beta variability: spatial asynchrony or the reciprocal of spatial synchrony | | number_of_patches | Number of unique patches (plots) in the dataset | | gamma_var | Gamma variability: temporal variability at the metacommunity scale |

See Table 1 in Wang and Loreau 2014 for mathematical details.

License

The MIT License (MIT)

Copyright (c) 2015 Andrew Tredennick

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

atredennick/patches documentation built on May 10, 2019, 2:11 p.m.