In atredennick/sageAbundance: Fits population model for sagebrush based on remote sensing data.

Check preliminary results from Rstan MCMC. Took 19 days and 9 hours to fit the full spatial dataset at 2000 iterations with 3 chains in parallel.

library(ggmcmc)
library(ggplot2)
mcmc <- readRDS("../../results/stanmcmc_sage.RDS")
ggplot(subset(mcmc, Parameter=="beta_mu"),
       aes(x=Iteration, y=value, color=as.factor(Chain)))+
  geom_line()
ggplot(subset(mcmc, Parameter=="int_mu"),
       aes(x=Iteration, y=value, color=as.factor(Chain)))+
  geom_line()
ggplot(subset(mcmc, Parameter=="alpha[1]"),
       aes(x=Iteration, y=value, color=as.factor(Chain)))+
  geom_line()

The slope mixed well, but clearly the alphas and the intercept are fighting. Need to work this out with Mevin.

atredennick/sageAbundance documentation built on May 10, 2019, 2:11 p.m.