#Randomization scheme for the Nutnet experiment.
# nutnet_rand 1.0, 29 Apr 07, Brett Melbourne.
# R: www.r-project.org
#
#Hierarchical randomization for a single site.
# One constraint is allowed:
# The number of blocks (1-k; standard is 3)

#Set this constraints for each site by changing these values:
nblocks <- 3      #How many blocks?
sitename <- "SITENAME_HERE"

#To run the randomization program:
# 1) Use a text editor to modify the constraints above to match your site
#    and SAVE THE FILE.
# 2) Change the R working directory to the one containing the saved
#    file (nutnet_rand10.r).
# 3) Enter 'source("nutnetrand10.r")' at the R prompt.
#
#The following files are created in the current working directory:
# RandDesign_SITENAME_HERE.csv - a comma separated values spreadsheet that can be opened 
#                  in Excel.
# DRAGNet-plan-SITENAME_HERE


#----Program begins----
# DRAGNet treatments
trt_labelsd<-c("Control", "Disturbance", "NPK", "NPK+Disturbance", "NPK_Cessation") # Dist = Disturbance

NPKud       <- c(0, 0, 1, 1, 1)
Disturbanced <- c(0, 1, 0, 1, 0)
Cessationd   <- c(0, 0, 0, 0, 1)

#Function to expand labels for all 4 subplots
subplotrep <- function(x) {
  rep(x,rep(4,length(x)))
}

numerics <- NULL #To hold numerical labels
chars <- NULL    #To hold character labels

n <- 1

for (Block in 1:nblocks) {
  # number of plots: 
  np <- length(trt_labelsd) # number of plots (np)
# Randomize treatments among plots within blocks
  block <- subplotrep( rep(Block,np) )
  plot <- subplotrep( n:(n+np-1) )
  #This is the random draw for plots
  rand<-sample(1:np)
  plot_trt <- subplotrep( rand )
  NPKu <- subplotrep( NPKud[rand] )
  Disturbance <- subplotrep( Disturbanced[rand] )
  Cessation <- subplotrep( Cessationd[rand] )
  trt_labels <- subplotrep(trt_labelsd[rand] )
  n <- n + np
# Randomize subplots
  nsubplots <- length(plot)
  subplot <- rep(1:4,nsubplots/4)
  subplot_lab <- rep(c("A","B","C","D"),nsubplots/4)
  subplot_trt <- integer(nsubplots)
  subplot_trt_lab <- character(nsubplots)
  for (i in seq(1,nsubplots-3,by=4)) {
    rand <- sample(1:4)           #This is the random draw for subplots
    subplot_trt[i:(i+3)] <- rand
    subplot_trt_lab[i:(i+3)] <- c("Core","Future1","Future2","Site")[rand]
  }
  numerics <- rbind(numerics,cbind(block,plot,plot_trt,NPKu,Disturbance,Cessation,subplot,subplot_trt))
  chars <- rbind(chars,cbind(trt_labels,subplot_lab,subplot_trt_lab))
}


remove(block,plot,plot_trt,NPKu,Disturbance,Cessation,
       subplot,subplot_trt,trt_labels,subplot_lab,subplot_trt_lab)

design <- cbind(as.data.frame(numerics),as.data.frame(chars))

design$plot_trt<-NULL
design$subplot<-NULL

design <- design[,c("block", "plot", "trt_labels",  
                    "NPKu", "Disturbance", "Cessation", 
                    "subplot_lab","subplot_trt_lab", "subplot_trt")] #reorder columns

write.csv(design[,!names(design) %in% c("subplot_trt")],file=paste0("~/Desktop/RandDesign_", sitename, ".csv"))  #Write to comma separated values file; can open in Excel


#----Plot the design----
library(grid) #Low level graphics utilities

plotspecs

drawplot <- function(plotspecs, row, col){
  pushViewport(viewport(layout.pos.row=row,layout.pos.col=col))
  fillcol <- ifelse(plotspecs$trt_labels == "NPK", "#E2D859", 
                    ifelse(plotspecs$trt_labels == "NPK+Disturbance", "#7EA359", 
                           ifelse(plotspecs$trt_labels == "Disturbance", "#7DA9BC", 
                                  ifelse(plotspecs$trt_labels == "NPK_Cessation", "#DD542F", "gray80"))))
  grid.rect(width=0.75,height=0.75, gp=gpar(fill=fillcol))
  #Annotate the plot
  grid.text(x=0.5,y=1,paste("Plot",plotspecs$plot[1],sep=" "))
  grid.text(x=0.5,y=.93,plotspecs$trt_labels[1])
  #Draw subplots
  subplotspecs<-plotspecs[,c("subplot_trt_lab", "subplot_lab", "subplot_trt")]
  drawsubplots(subplotspecs)
  popViewport()
}

#Function to draw subplots
drawsubplots <- function(subplotspecs){
  plot.vp <- viewport(width=0.75,height=0.75,layout=grid.layout(2,2))
  pushViewport(plot.vp)
  pos <- cbind(row=c(1,1,2,2),col=c(1,2,1,2))
  for (i in 1:4) {
    pushViewport(viewport(layout.pos.row=pos[i,"row"],layout.pos.col=pos[i,"col"]))
    fillcol <- switch(subplotspecs[i,"subplot_trt"],
                      alpha('white', 0.8), 
                      alpha('white', 0.1), 
                      alpha('white', 0.1), 
                      alpha('white', 0.1))
    grid.rect(width=0.9,height=0.9,gp=gpar(fill=fillcol))
    #Annotate the plot
    grid.text(x=0.2,y=0.8,subplotspecs[i,"subplot_lab"],gp=gpar(cex = 0.6))
    grid.text(subplotspecs[i,"subplot_trt_lab"],gp=gpar(cex = 0.8))
    popViewport()
  }
  popViewport()
}


#Draw the diagrams
dev.off()
pdf(paste0('~/Desktop/DRAGNet-plan-', sitename, ".pdf"), height = 8.5, width = 11)

plot.new()
nplots <- nrow(design)/4
ntrt <- length(unique(design$trt_labels))
pos <- cbind(row=rep(1:max(design$block),
                     each = ntrt), col=1:ntrt)
site.vp <- viewport(y=0.5,
                    x=0.5,
                    height=0.8,
                    width=1,
                    layout=grid.layout(nrow = max(design$block), # blocks in rows
                                       ncol = length(unique(design$trt_labels)))) # treatments in columns
pushViewport(site.vp)


for (i in 1:nplots) {
    plotspecs <- subset(design,plot==i)
    drawplot(plotspecs,pos[i,"row"],pos[i,"col"])
}
grid.text(x=0.5,y=1.05,sitename)
popViewport()
dev.off()