Spatial factor analysis: a tool for decomposing species density into a small number of latent maps
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 geostatistical_delta-GLMM package from this GitHub repository using a function in the "devtools" package:
# Install package
install_github("James-Thorson/spatial_factor_analysis")
# Load package
library(SpatialFA)
Please see the examples folder for an example of how to run the model: https://github.com/James-Thorson/spatial_factor_analysis/tree/master/examples
none
For more details regarding development and testing of this software please see:
For more details regarding estimating spatial variation via Gaussian random fields please see:
For more details regarding Template Model Builder please see:
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