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
-
- 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