library(R2admb)
library(MCMCpack)
library(coda)

setup_admb()
source("wildflower_ADMB_funs.R")
sessionInfo()

fdat=read.csv("../DATA/wildflower_pods_complete.csv")

data4ADMB=setup_wildflower_data(fdat)
	
write_dat("wildflowers_mcmc", L=data4ADMB)

params4ADMB=setup_wildflower_params(data4ADMB$nfixed, data4ADMB$nplants, data4ADMB$nyears)
		
write_pin("wildflowers_mcmc", L=params4ADMB)

compile_admb("wildflowers_mcmc", safe=TRUE, re=TRUE, verbose=TRUE)

run_admb("wildflowers_mcmc", verbose=TRUE, extra.args="-shess -noinit -nox",
	mcmc=TRUE,mcmc.opts=mcmc.control(mcmc=1000,
                    mcmcpars=c("plant_int_std", "plant_slope_std", "year_int_std")))

fit_mcmc <- read_admb("wildflowers_mcmc",mcmc=TRUE)
## ,mcmc.opts=mcmc.control(mcmcpars=c("plant_int_std", "plant_slope_std", "year_int_std")))

mmc <- as.mcmc(fit_mcmc$mcmc)

xyplot(mmc[,1:16],layout=c(4,4),asp="fill")

library(coefplot2)
coefplot2(mmc[,1:9])
save("fit_mcmc",file="fit_mcmc.RData")
clean_admb("wildflowers_mcmc")