R/int.order.R

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

#' Ordering the rows of the data frames contained in an ecogen or ecopop object
#' 
#' @details This program generates an ecogen/ecopop object with the rows of all
#' the data frames ordered using a reference row names vector.
#' This is useful when the data frames are loaded into the n object,
#' but were not ordered previously. Also, this tool can be useful 
#' for reorder rows when is needed. 
#' The program used the row names data that was set during the
#' construction of the object. Then, the program then aligns 
#' all the data frames by coincidence of row names of the reference vector.
#' 
#' @param eco Object of class "ecogen".
#' @author Leandro Roser \email{learoser@@gmail.com}
#' 
#' @keywords internal

 
# example
# data(eco.test)
# eco1 <- eco
# eco1[["P"]] <- eco[["P"]][sample(1:225), ]  #object with shuffled rows
# eco1[["E"]] <- eco[["E"]][sample(1:225), ]
# ordered <- int.order(eco1)
# head(ordered[["P"]]); head(eco[["P"]])


setGeneric("int.order", 
           function(eco) {
             
             ord <- 0
             #function to order rows
             .order <- function(.refnames, df_to_order) {
               
               this_order <- match(.refnames, rownames(df_to_order), nomatch = 0)
               if(length(this_order) != length(.refnames)) {
                 stop("invalid object: some row names do not match")
               }
               
               if(!all(this_order == seq_len(length(.refnames))) && !all(this_order == 0)) {
                 df_to_order <- df_to_order[this_order, , drop = FALSE]
                 ord <<- ord + 1
               }
               df_to_order
             }
             
             if(is.ecogen(eco)) {
               refnames <- eco@ATTR$names
               if(length(refnames) != 0) {
               
               eco@XY <- .order(refnames, eco@XY)
               eco@P <- .order(refnames, eco@P)
               eco@G <- .order(refnames, eco@G)
               eco@A <- .order(refnames, eco@A)
               eco@E <- .order(refnames, eco@E)
               eco@S <- .order(refnames, eco@S)
               eco@C <- .order(refnames, eco@C)
               
               #ordering missing cells
               dum <- as.matrix(eco@A - eco@A)
               dum[eco@INT@missing.cells] <- NA
               dum <- .order(refnames, dum)
               eco@INT@missing.cells <- which(is.na(dum))
             }
             } else {
               
               refnames <- eco@ATTR$names
               if(length(refnames) != 0) {
                 
                 eco@XY <- .order(refnames, eco@XY)
                 eco@P <- .order(refnames, eco@P)
                 eco@GF <- .order(refnames, eco@GF)
                 eco@E <- .order(refnames, eco@E)
                 eco@C <- .order(refnames, eco@C)
               }
               
             }
             
             if(ord != 0) {
               message("Note: ordered rows")
             }
             
             eco
           })