R/makeHarvMasterFile.R

In nsantantonio/fieldMapR: fieldMapR

#' makeHarvMasterFile function
#'
#' function to (do something)
#'
#' @param block [value] Object of class 'fieldBlock'
#' @param printPlotNo [value]. Should plot number be printed? Default is TRUE
#' @param rmBorderRanges [value]. Should all border ranges be removed? Default is FALSE
#' @param rmBorderPasses [value]. Should all border passes be removed? Default is FALSE
#' @return [value]
#' @details [fill in details here]
#' @examples # none
#' @export

makeHarvMasterFile <- function(block, printPlotNo = TRUE, rmBorderPasses = TRUE, rmBorderRanges = FALSE){
	# block <- blocks[[5]]; rmBorderRanges = TRUE; rmBorderPasses = TRUE
	block@long[["plotName"]] <- paste0(block@long[["Trial"]], "_", block@long[["plotNo"]])
	harvM <- block@long[c("plotName", "range", "pass", "Trial", "Line", "Entry")]
	names(harvM) <- c("Plot ID", "Range", "Row", "Study", "Line", "Entry")
	harvM$blockName <- block@blockName
	if(rmBorderPasses) {
		harvM <- harvM[!harvM$Row %in% block@borderPasses,]
		shiftRow <- min(harvM$Row) - 1
		harvM$Row <- harvM$Row - shiftRow
	}
	if(rmBorderRanges){
		# fillRanges <- which(apply(block@fill, 1, all))
		fillRanges <- which(apply(block@fill[nrow(block@fill):1, , drop = FALSE], 1, all)) # this was backwards because the range index is human readable matrix (first row is at back), but block@long range index is correct.
		harvM <- harvM[!harvM$Range %in% fillRanges,]
		# isBorder <- gsub(".*_[0-9]*", "", harvM[["Plot ID"]]) != "" # relies on border plots starting with letter, others integer
		# harvM <- harvM[!isBorder,]
		shiftRange <- min(harvM$Range) - 1
		harvM$Range <- harvM$Range - shiftRange
	}

	if(printPlotNo) harvM$plotNo <- gsub(".*_", "", harvM[["Plot ID"]])
	return(harvM)
}