Multi trial allocation tool

R/DRRC.r

@@ -1,16 +1,16 @@
 
 args=commandArgs(TRUE)
 
 ##args is now a list of character vectors
 ## First check to see if arguments are passed.
 ## Then cycle through each element of the list and evaluate the expressions.
 
 if(length(args)==0){
     print("No arguments supplied.")
     ##supply default values
     paramfile=''
 } else {
     for(i in 1:length(args)){
         print(paste("Processing arg ", args[[i]]));
         eval(parse(text=args[[i]]))
     }
@@ -22,7 +22,8 @@
 
 source(paramfile)
 ## 1) Preparing dataframe
-all.clones <- treatments
+if (!exists("engine", inherits = FALSE)) engine <- "breedbase"
+if(engine == 'trial_allocation'){ all.clones <- c(treatments, controls) } else { all.clones <- treatments }
 nTrt <- length(all.clones)
 nRep <- nRep
 nRows <- nRow
@@ -34,7 +35,10 @@
 totalPlots <- nTrt*nRep
 
 plot_type <- plot_type 
-plot_start <- plot_start
+
+plot_start = 1
+if( serie == 2){ plot_start <- 101 }
+if( serie == 3){ plot_start <- 1001 }
 
 blocks = data.frame(block_number = gl(nRep,nTrt),
                     Cols = gl(superCols,colsPerBlock,totalPlots),
@@ -106,6 +110,13 @@
 
 design <- fieldBook %>% dplyr::select(block_number, rep_number, row_number, col_number, plot_number, accession_name, is_a_control)
 
+if(engine == 'trial_allocation'){
+  design <- design %>% dplyr::select(plot_number, block_number, accession_name, rep_number, is_a_control)
+  colnames(design) <- c("plots", "block", "all_entries", "rep", "is_control")
+}
+
+
+
 head(design)
 
 # save result files

R/RCBD.R

@@ -0,0 +1,60 @@
+## Create Randomized Complete Block Designs
+args = commandArgs(TRUE)
+
+if(length(args)==0){
+    print("No arguments supplied.")
+    ##supply default values
+    paramfile=''
+} else {
+    for(i in 1:length(args)){
+        print(paste("Processing arg ", args[[i]]));
+        eval(parse(text=args[[i]]))
+    }
+}
+
+source(paramfile)
+basefile <- tools::file_path_sans_ext(paramfile)
+
+# Printing variables:
+print(treatments)
+print(controls)
+print(n_rep)
+print(n_row)
+print(n_col)
+print(n_blocks)
+print(serie)
+
+## Preparing design
+library(FielDHub)
+library(dplyr)
+
+all_entries <- c(treatments, controls)
+new_seed <- sample(1:1e6, 1)
+
+init_plot = 1
+if( serie == 2 ){ init_plot = 101}
+if( serie == 3 ){ init_plot = 1001}
+
+
+## Design
+outdesign <- RCBD(t = length(all_entries), reps = n_blocks, plotNumber = init_plot, seed = new_seed)
+
+## Extracting field book
+book <- outdesign$fieldBook
+
+## Adding treatment names
+book$TREATMENT <- all_entries[match(book$TREATMENT, paste0("T", seq_along(all_entries)))]
+book$block <- book$REP
+
+## setting controls
+book$is_control <- 0
+book[book$TREATMENT %in% controls, "is_control"] <- 1
+book <- book %>% select(PLOT, block, TREATMENT, REP, is_control)
+
+colnames(book) <- c("plots", "block", "all_entries", "rep", "is_control")
+head(book, 10)
+
+outfile <- paste0(basefile, ".design")
+sink(outfile)
+write.table(book, quote = FALSE, sep = '\t', row.names = FALSE)
+sink()