VAST (Vector Autoregressive Spatio-Temporal model) is a spatio-temporal index standardization that can be used for single or multiple species.
Original scripts and documentation:
https://github.com/James-Thorson/VAST
http://www.FishStats.org
follow along in rtools_setup.r
install.packages("installr"); require(installr)
updateR()
Rtools allows you to access your computer's c++ compiler. Install the most recent version of Rtools from https://cran.rproject.org/bin/windows/Rtools/. While running the Rtools setup .exe, there will be an option to 'Select Additional Tasks' - check the box below the 'Current value' to ensure that Rtools is listed in the system path. Use the default is to save Rtools directly to your C: drive.
For details: https://github.com/stan-dev/rstan/wiki/Install-Rtools-for-Windows
install.packages("devtools")
library(devtools)
Once devtools is installed, run install_github("kaskr/adcomp/TMB"). STOP the operation when it starts downloading the Rtools.exe. You will receive an error msg saying it cancelled and didn't install properly. Run install_github() again.
install_github("kaskr/adcomp/TMB") # Don't forget to hit the stop sign the first time!
library(TMB)
In rtools_setup.r, we're using a simple linear mixed effects model example from https://github.com/James-Thorson/mixed-effects/tree/master/linear_mixed_model.
Map system path to Rtools in your environmental vars From Start menu, right click on 'Computer', select 'Properties', select 'Advanced system settings', select 'Environment Variables'. Under 'System variables,' scoll down to 'PATH' (or 'Path'), highlight it and select 'Edit.' Scroll to end of listed paths, and add the following paths to end of existing list using a semicolon to separate paths: "; C:\Rtools\gcc-4.6.3\bin") WARNING do not delete existing paths, just add the new one to the end of the existing list. Restart R or Rstudio before trying STEP 3 again.