readme.md

In cbrown5/BenthicLatent: Bayesian latent variable model

Estimating the footprint of pollution on coral reefs with models of species turnover

2018-01-23

Code in support of Brown, Hamilton. 2018. Estimating the footprint of pollution on coral reefs with models of species turnover. Conservation Biology. DOI: 10.1111/cobi.13079

For an open-access pre-print see: Brown, Hamilton. 2017. Estimating the footprint of pollution on coral reefs using models of species turn-over. doi: https://doi.org/10.1101/157297

You can install this package using devtools:

install.packages("devtools")
devtools::install_github("cbrown5/BenthicLatent")

Or just copy the whole thing to your local directory. Functions are in the folder "R", scripts to repeat analyses and data are in the folder "data-raw", scripts to generate the manuscript are in the folder "ms". Email Chris if you have any queries.

You can replicate my workflow by running the scripts in the data-raw folder in the order of the numbers that append file names.

Thanks to Rick Hamilton for making the data available. Please see the above reference and Hamilton et al. 2017 for citations of this data.

Hamilton RJ, Almany GR, Brown CJ, Pita J, Peterson NA, Choat JH. Logging degrades nursery habitat for an iconic coral reef fish. Biological Conservation. 2017 Jun 30;210:273-80.

cbrown5/BenthicLatent documentation built on Oct. 4, 2019, 6:40 p.m.