Description

SpatialDFA is an R package for implementing spatial dynamic factor analysis, a model for estimating spatiotemporal density dependence in community dynamics.

Usage

Please contact James Thorson if you're planning to use this package

Installation Instructions

This function depends on R version >=3.1.1 and a variety of other tools.

First, install the "devtools" package from CRAN

# Install and load devtools package
install.packages("devtools")
library("devtools")

Second, please install the following:

TMB (Template Model Builder): https://github.com/kaskr/adcomp
INLA (integrated nested Laplace approximations): http://www.r-inla.org/download

Note: at the moment, TMB and INLA can be installed using these commands:

# devtools command to get TMB from GitHub
install_github("kaskr/adcomp/TMB") 
# source script to get INLA from the web
source("http://www.math.ntnu.no/inla/givemeINLA.R")

Next, please install the SpatialDFA from this GitHub repository using a function in the "devtools" package:

# Install package
install_github("james-thorson/spatial_DFA") 
# Load package
library(spatial_DFA)

Works to read and cite if using the software

Thorson, J.T., Ianelli, J.N., Larsen, E., Ries, L., Scheuerell, M.D., Szuwalski, C. & Zipkin, E.F. (2016) Joint dynamic species distribution models: a tool for community ordination and spatiotemporal monitoring. Global Ecology and Biogeography, 25, 1144-1158. Abastract available here.

Further information

Thorson, J.T., Fonner, R., Haltuch, M., Ono, K. & Winker, H. (2016) Accounting for spatiotemporal variation and fisher targeting when estimating abundance from multispecies fishery data. Canadian Journal of Fisheries and Aquatic Sciences, 73, 1-14.
Thorson, J.T., Scheuerell, M.D., Shelton, A.O., See, K.E., Skaug, H.J. & Kristensen, K. (2015) Spatial factor analysis: a new tool for estimating joint species distributions and correlations in species range. Methods in Ecology and Evolution, 6, 627–637.
Thorson, J.T., Skaug, H.J., Kristensen, K., Shelton, A.O., Ward, E.J., Harms, J.H. & Benante, J.A. (2014) The importance of spatial models for estimating the strength of density dependence. Ecology, 96, 1202–1212.