multispecies VAST

[EllenY]

I am running VAST with 1000 knots for 11 species in RStudio. How can I speed up the Optimize process for estimating the final model?

#5.2 Estimate fixed effect and predict random variables
Opt = TMBhelper::Optimize( obj=Obj, lower=TmbList[["Lower"]],
upper=TmbList[["Upper"]], getsd=TRUE, savedir=DateFile,
bias.correct=FALSE )

[James-Thorson]

Easiest fix: Install and use Revolution R, which will speed up by factor approx. equal to number of processors on machine.

Other fixes:

• Decrease number of knots
• Decrease number of species
• Decrease number of years
• Decrease / change number of factors, e.g., to start with 1 factor for each component and increase slowly until new factors explain small proportion of total variance, as I did in Thorson et al. 2016 Global Ecology and Biogeography
• Use bigger machine
• Use amazon cloud computer