Description

MIST

• Is an R package for implementing a Multispecies Interaction Spatio-Temporal (MIST) model.
• Uses identical input/output and model-diagnostic tools as VAST and other packages at www.FishStats.org

Background

• This tool is designed to estimate pairwise interactions among species using spatially referenced data from multiple years (spatio-temporal data)
• It decomposes variation into (1) covariance among species in a given year, and (2) impacts of species density on per-capita productivity of every other species
• Spatial and spatiotemporal variation are approximated as Gaussian Markov random fields (Thorson Skaug Kristensen Shelton Ward Harms Banante 2014 Ecology), which imply that correlations in spatial variation decay as a function of distance.

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 the 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/MIST") 
# Load package
library(MIST)

Known installation/usage issues

none

Example code

Please see examples folder for single-species and multi-species examples of how to run the model.

Description of package

Please cite if using the software

• 2017. Thorson, J., Munch, S, and Swain, D. Estimating partial regulation in community dynamics using spatio-temporal models. Ecology. 98(5): 1277-1289. DOI: 10.1002/ecy.1760. URL: http://onlinelibrary.wiley.com/doi/10.1002/ecy.1760/abstract