## ----setup, include=FALSE---------------------------------------------------------------
library(knitr)
options(rmarkdown.html_vignette.check_title = FALSE,
        # formatR.arrow = TRUE, 
        # scipen=999, 
        # digits=5,
        width=90) 
#thm <- knit_theme$get("edit-kwrite")   # whitengrey, bright, print, edit-flashdevelop, edit-kwrite
#knit_theme$set(thm)
knit_hooks$set(
   par = function(before, options, envir) {
      if (before && options$fig.show != 'none')
         par(mar = c(0, 0, 0, 0), # bottom, left, top, and right
             oma = c(0, 0, 0, 0))}
)
knitr::opts_chunk$set(
   # collapse = TRUE,
   comment = "#>",
   fig.align = 'center',
   fig.width = 9,
   fig.height = 5,
   fig.show = 'hold',
   out.extra = 'style="max-width:100%;"',
   # tidy = TRUE,
   # prompt=T,
   # comment=NA,
   cache = F
   # background = "red"
)
library(magrittr)
library(dplyr)

## ---------------------------------------------------------------------------------------
library(MDP2)

## ----echo=FALSE, fig.cap="The state-expanded hypergraph of the first stage of a hierarchical MDP. Level 0 indicate the founder level, and the nodes indicates states at the different levels. A child process (oval box) is represented using its state-expanded hypergraph (hyperarcs not shown) and is uniquely defined by a given state and action of its parent process."----
knitr::include_graphics("vignette_files/hmdp_index.png")

## ----par=TRUE---------------------------------------------------------------------------
prefix <- paste0(system.file("models", package = "MDP2"), "/cow_")
mdp <- loadMDP(prefix)
mdp 

## ----plotHMDP, message=FALSE, par=TRUE--------------------------------------------------
hgf <- getHypergraph(mdp)
## Rename labels
dat <- hgf$nodes %>% 
   dplyr::mutate(label = dplyr::case_when(
      label == "Low yield" ~ "L",
      label == "Avg yield" ~ "A",
      label == "High yield" ~ "H",
      label == "Dummy" ~ "D",
      label == "Bad genetic level" ~ "Bad",
      label == "Avg genetic level" ~ "Avg",
      label == "Good genetic level" ~ "Good",
      TRUE ~ "Error"
   ))
## Set grid id
dat$gId[1:3]<-85:87
dat$gId[43:45]<-1:3
getGId<-function(process,stage,state) {
   if (process==0) start=18
   if (process==1) start=22
   if (process==2) start=26
   return(start + 14 * stage + state)
}
idx<-43
for (process in 0:2)
   for (stage in 0:4)
      for (state in 0:2) {
         if (stage==0 & state>0) break
         idx<-idx-1
         #cat(idx,process,stage,state,getGId(process,stage,state),"\n")
         dat$gId[idx]<-getGId(process,stage,state)
      }
hgf$nodes <- dat
## Rename labels
dat <- hgf$hyperarcs %>% 
   dplyr::mutate(label = dplyr::case_when(
      label == "Replace" ~ "R",
      label == "Keep" ~ "K",
      label == "Dummy" ~ "D",
      TRUE ~ "Error"
      ),
      col = dplyr::case_when(
         label == "R" ~ "deepskyblue3",
         label == "K" ~ "darkorange1",
         label == "D" ~ "black",
         TRUE ~ "Error"
      ),
      lwd = 0.5,
      label = ""
   ) 
hgf$hyperarcs <- dat
## Make the plot
plotHypergraph(hgf, gridDim = c(14, 7), cex = 0.8, radx = 0.02, rady = 0.03)

## ----Optimize (cow)---------------------------------------------------------------------
wLbl<-"Net reward"         # the weight we want to optimize (net reward)
durLbl<-"Duration"         # the duration/time label
runPolicyIteDiscount(mdp, wLbl, durLbl, rate = 0.1)

## ----plotPolicy, results='hide', message=FALSE, par=TRUE--------------------------------
hgf$hyperarcs <- right_join(hgf$hyperarcs, getPolicy(mdp), by = c("sId", "aIdx"))
plotHypergraph(hgf, gridDim = c(14, 7), cex = 0.8, radx = 0.02, rady = 0.03)

## ----eval=FALSE, include=FALSE----------------------------------------------------------
# # getPolicy(mdp)
# # rpo<-calcRPO(mdp, wLbl, iA=rep(0,42), criterion="discount", dur=durLbl, rate=rate, rateBase=rateBase)
# # policy<-merge(policy,rpo)
# # policy

## ----avePerLac, tidy.opts=list(comment=FALSE)-------------------------------------------
wLbl<-"Net reward"         # the weight we want to optimize (net reward)
durLbl<-"Duration"         # the duration/time label
runPolicyIteAve(mdp, wLbl, durLbl)
getPolicy(mdp)

## ----echo=TRUE--------------------------------------------------------------------------
runCalcWeights(mdp, w=wLbl, criterion="average", dur = "Yield")

## ----Reward/piglet (sow rep), echo=TRUE-------------------------------------------------
runCalcWeights(mdp, w="Yield", criterion="average", dur = durLbl)

## ----Delete bin, include=FALSE----------------------------------------------------------
do.call(file.remove,list(list.files(pattern = ".bin")))