Beyond counts and averages: relating geodiversity to dimensions of biodiversity

posted on 21.05.2019 by Quentin Read, Phoebe L. Zarnetske, Sydne Record, Kyla Dahlin, Andrew O. Finley, John M. Grady, Martina Hobi, Sparkle Malone, Jennifer Costanza, Adam Wilson, Andrew M. Latimer, Keith Gaddis, Stephanie Pau, Scott V. Ollinger

Introduction. Code to accompany Read et al. manuscript on levels and dimensions of biodiversity, entitled "Beyond counts and averages: relating geodiversity to dimensions of biodiversity." Currently (21 May 2019) under consideration for publication in Global Ecology and Biogeography.

Model fitting. This code will allow the user to reproduce the models fit in the manuscript. For the model fitting steps, we are providing all the data used to fit the models in the manuscript, except for the true locations of the FIA plots due to confidentiality. FIA location data were provided through U.S Forest Service agreement No. 17-MU-11261919-021.

List of files:
model_fitting.r : R script that reproduces all model fitting, model validation, and extraction of summary statistics from model objects
bbs_biodiversity.csv : Biodiversity data for bird locations
bbs_geodiversity.csv : Geodiversity data for bird locations
fia_biodiversity.csv : Biodiversity data for tree locations
fia_geodiversity.csv : Geodiversity data for tree locations
tnc_adjacencymatrix.csv : Adjacency matrix (binary) of Nature Conservancy ecoregions in contiguous USA
ecoregion_folds.csv : List of ecoregions that are sequentially held out in model cross-validation procedure
prior_table.csv : Parameters for prior distributions used in model fitting

Modification history:

Originally created February 2019

Modified May 2019 to include changes in analysis from manuscript revisions


National Aeronautics and Space Administration (NASA) Ecological Forecasting Program, Earth Science Division, Grant #NNX16AQ44G