R/DRRC.r

   1
   2 args=commandArgs(TRUE)
   3
   4 ##args is now a list of character vectors
   5 ## First check to see if arguments are passed.
   6 ## Then cycle through each element of the list and evaluate the expressions.
   7
   8 if(length(args)==0){
   9     print("No arguments supplied.")
  10     ##supply default values
  11     paramfile=''
  12 } else {
  13     for(i in 1:length(args)){
  14         print(paste("Processing arg ", args[[i]]));
  15         eval(parse(text=args[[i]]))
  16     }
  17 }
  18
  19 library(reshape2)
  20 library(dplyr)
  21 library(blocksdesign)
  22
  23 source(paramfile)
  24 ## 1) Preparing dataframe
  25 all.clones <- treatments
  26 nTrt <- length(all.clones)
  27 nRep <- nRep
  28 nRows <- nRow
  29 nCols <- nCol
  30 # nCols <- nTrt*nRep/nRows
  31 rowsPerBlock <- nTrt/nCols
  32 colsPerBlock <- nTrt/nRows
  33 superCols <- nCols/colsPerBlock
  34 totalPlots <- nTrt*nRep
  35
  36 plot_type <- plot_type
  37 plot_start <- plot_start
  38
  39 blocks = data.frame(block_number = gl(nRep,nTrt),
  40                     Cols = gl(superCols,colsPerBlock,totalPlots),
  41                     row_number = gl(nRows,nCols,totalPlots),
  42                     col_number = gl(nCols,1,totalPlots))
  43
  44 ## Setting rep number orthogonal to block number
  45 rep_number = as.numeric(blocks$Cols)
  46
  47
  48 # treatments = data.frame(treatments =gl(nTrt,1,totalPlots))
  49 Z=design(all.clones,blocks, searches = 50, weighting=0.5)
  50 fieldBook <- Z$Design
  51
  52 trialMatrix <- matrix(0,nRows,nCols)
  53
  54 for(i in 1:nrow(fieldBook)){
  55   trialMatrix[fieldBook$subRows[i],fieldBook$subCols[i]]<-fieldBook$treatments[i]
  56 }
  57 trialMatrix
  58
  59 ## Adding plot number
  60 colnames(fieldBook)[5] <- "plot_number"
  61
  62 fieldBook$block_number <- as.integer(fieldBook$block_number)
  63 fieldBook$row_number <- as.integer(fieldBook$row_number)
  64 fieldBook$col_number <- as.integer(fieldBook$col_number)
  65
  66 # Load dplyr
  67 library(dplyr)
  68
  69 # Arrange fieldBook by row_number and col_number
  70 fieldBook <- fieldBook %>% arrange(row_number, col_number)
  71 fieldBook$plot_number <- c(1:totalPlots)
  72 fieldBook$plot_id <- c(1:nTrt)
  73
  74
  75
  76 ## Number start
  77 ## 00101 will be added for NCSU
  78 if(plot_start == "00101"){
  79   fieldBook$plot_number = paste0(formatC(fieldBook$block_number,width=3,flag="0"),
  80                               formatC(fieldBook$plot_id,width=2,flag="0"))
  81 }else if (plot_start == 1001){
  82   fieldBook$plot_number <- (1000*fieldBook$block_number)+fieldBook$plot_id
  83 }else if (plot_start == 101) {
  84   fieldBook$plot_number <- (100*fieldBook$block_number)+fieldBook$plot_id
  85 }
  86
  87 cat("plot start is ", plot_start,"\n")
  88 cat("plot type is ", plot_type,"\n")
  89
  90 plot_type = "serpentine"
  91 ## Plot number format
  92 if(plot_type == "serpentine"){
  93   for(i in 1:nRows){
  94     if(i%%2==0){
  95       fieldBook[fieldBook$row_number == i, "plot_number"] <- rev(fieldBook[fieldBook$row_number==i,"plot_number"])
  96     }
  97   }
  98 }
  99
 100 fieldBook$rep_number <- rep_number
 101
 102
 103 #### create is_a_control
 104 names(fieldBook)[names(fieldBook) == "treatments"] <- "accession_name"
 105 fieldBook <- transform(fieldBook, is_a_control = ifelse(fieldBook$accession_name %in% controls, 1, 0))
 106
 107 design <- fieldBook %>% dplyr::select(block_number, rep_number, row_number, col_number, plot_number, accession_name, is_a_control)
 108
 109 head(design)
 110
 111 # save result files
 112 basefile <- tools::file_path_sans_ext(paramfile)
 113 outfile = paste(basefile, ".design", sep="");
 114 sink(outfile)
 115 write.table(design, quote=F, sep='\t', row.names=FALSE)
 116 sink();