## READ DATA from file!

library(lme4)
fruitdat1 = read.csv("C:\\Users\\ecrone\\Desktop\\NCEAS\\projects\\wildflower\\DATA\\wildflower_pods_complete.csv")

sessionInfo()


t1 <- system.time(nfit <- lmer(toF ~ State + Pods + (1|PlantID) + (-1 + Pods|PlantID) + (1|Year), family = binomial, data = fruitdat1))["elapsed"]

if (class(nfit)=="try-error")  {  # or if (inherits(nfit,"try-error"))
  results <- list(obj=NA,coef=rep(NA,4),
                  sd=rep(NA,4))
} else {
  results <- list(obj=-logLik(nfit),  ## objective function/Neg log likelihood (NULL for MCMC)
                coef=slot(summary(nfit), "coefs")[,1],  ## coefficients
                rcoef = as.numeric(slot(summary(nfit), "REmat")[,4]),
                sd=slot(summary(nfit), "coefs")[,2],
                vcov=vcov(nfit)
#                confint.quad=confint.default(nfit),
 #               confint.profile=confint(nfit),
 #               time=c(fit=unname(t1))
                )
}

save("results",file="fit.RData")