README.md

In James-Thorson/spatial_condition_factor: Package for estimating spatial and spatiotemporal variation in individual condition.

Description

SpatialCondition

• Is an R package for estimating spatial and spatiotemporal variation in individual condition using Gaussian random fields and potentially including covariates
• Is intended to allow rapid comparison of condition factor among multiple species.

Instructions

First, please install JAGS (Just Another Gibbs Sampler) here: http://mcmc-jags.sourceforge.net/

Next, please use R version >=3.1.1 and install the package:

# Install package
install.packages("devtools")
library("devtools")
install_github("James-Thorson/spatial_condition_factor")
# Load package
library(SpatialDeltaGLMM)

Please see examples folder for an example of how to run the model: https://github.com/James-Thorson/spatial_condition_factor/blob/master/examples/example_for_NWFSC_shelf-slope_data.R

Known installation/usage issues

none

Further reading

For more details regarding development and testing of this delta-GLMM software please see: Thorson, J. T., A. O. Shelton, E. J. Ward, and H. Skaug. In press. Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES Journal of Marine Science. Thorson, J. T., H. Skaug, K. Kristensen, A. O. Shelton, E. J. Ward, J. Harms, and J. Benante. In press. The importance of spatial models for estimating the strength of density dependence. Ecology.

James-Thorson/spatial_condition_factor documentation built on May 7, 2019, 10:20 a.m.