## ----knitr_setup, include=FALSE, message=FALSE--------------------------------
library(knitr)
opts_chunk$set(echo = TRUE,
               eval = identical(Sys.getenv("NOT_CRAN"), "true"))
rc <- knitr::read_chunk
rc(system.file("vignette_data","mcmc.R",package="glmmTMB"))

## ----libs,message=FALSE-------------------------------------------------------
#  library(glmmTMB)
#  library(coda)     ## MCMC utilities
#  library(reshape2) ## for melt()
#  ## graphics
#  library(lattice)
#  library(ggplot2); theme_set(theme_bw())

## ----fit1---------------------------------------------------------------------
#  data("sleepstudy",package="lme4")
#  fm1 <- glmmTMB(Reaction ~ Days + (Days|Subject),
#                 sleepstudy)

## ----setup--------------------------------------------------------------------
#  ## FIXME: is there a better way for user to extract full coefs?
#  rawcoef <- with(fm1$obj$env,last.par[-random])
#  names(rawcoef) <- make.names(names(rawcoef),unique=TRUE)
#  ## log-likelihood function
#  ## (MCMCmetrop1R wants *positive* log-lik)
#  logpost_fun <- function(x) -fm1$obj$fn(x)
#  ## check definitions
#  stopifnot(all.equal(c(logpost_fun(rawcoef)),
#                      c(logLik(fm1)),
#            tolerance=1e-7))
#  V <- vcov(fm1,full=TRUE)

## ----run_MCMC-----------------------------------------------------------------
#  ##' @param start starting value
#  ##' @param V variance-covariance matrix of MVN candidate distribution
#  ##' @param iterations total iterations
#  ##' @param nsamp number of samples to store
#  ##' @param burnin number of initial samples to discard
#  ##' @param thin thinning interval
#  ##' @param tune tuning parameters; expand/contract V
#  ##' @param seed random-number seed
#  run_MCMC <- function(start,
#                       V,
#                       logpost_fun,
#                       iterations = 10000,
#                       nsamp = 1000,
#                       burnin = iterations/2,
#                       thin = floor((iterations-burnin)/nsamp),
#                       tune = NULL,
#                       seed=NULL
#                       ) {
#      ## initialize
#      if (!is.null(seed)) set.seed(seed)
#      if (!is.null(tune)) {
#          tunesq <- if (length(tune)==1) tune^2 else outer(tune,tune)
#          V <-  V*tunesq
#      }
#      chain <- matrix(NA, nsamp+1, length(start))
#      chain[1,] <- cur_par <- start
#      postval <- logpost_fun(cur_par)
#      j <- 1
#      for (i in 1:iterations) {
#          proposal = MASS::mvrnorm(1,mu=cur_par, Sigma=V)
#          newpostval <- logpost_fun(proposal)
#          accept_prob <- exp(newpostval - postval)
#          if (runif(1) < accept_prob) {
#              cur_par <- proposal
#              postval <- newpostval
#          }
#          if ((i>burnin) && (i %% thin == 1)) {
#              chain[j+1,] <- cur_par
#              j <- j + 1
#          }
#      }
#      chain <- na.omit(chain)
#      colnames(chain) <- names(start)
#      chain <- coda::mcmc(chain)
#      return(chain)
#  }

## ----do_run_MCMC,eval=FALSE---------------------------------------------------
#  t1 <- system.time(m1 <- run_MCMC(start=rawcoef,
#                                   V=V, logpost_fun=logpost_fun,
#                                   seed=1001))

## ----load_MCMC, echo=FALSE, eval=TRUE-----------------------------------------
L <- load(system.file("vignette_data", "mcmc.rda", package="glmmTMB"))

## ----add_names----------------------------------------------------------------
#  colnames(m1) <- c(names(fixef(fm1)[[1]]),
#                    "log(sigma)",
#                    c("log(sd_Intercept)","log(sd_Days)","cor"))
#  m1[,"cor"] <- sapply(m1[,"cor"], get_cor)

## ----traceplot,fig.width=7----------------------------------------------------
#  xyplot(m1,layout=c(2,3),asp="fill")

## ----effsize------------------------------------------------------------------
#  print(effectiveSize(m1),digits=3)

## ----violins,echo=FALSE-------------------------------------------------------
#  ggplot(reshape2::melt(as.matrix(m1[,-1])),aes(x=Var2,y=value))+
#           geom_violin(fill="gray")+coord_flip()+labs(x="")

## ----do_tmbstan,eval=FALSE----------------------------------------------------
#  ## install.packages("tmbstan")
#  library(tmbstan)
#  t2 <- system.time(m2 <- tmbstan(fm1$obj))

## ----show_traceplot,echo=FALSE,fig.width=8,fig.height=5-----------------------
#  library(png)
#  library(grid)
#  img <- readPNG(system.file("vignette_data","tmbstan_traceplot.png",package="glmmTMB"))
#  grid.raster(img)