R/deltPointOrSp.R

In alarconvv/geocleaMT: A Package to Clean/Test Georeferenced Data

#'@name delPointsOrSp
#'
#'@title  Delete some/all records of a given species
#'
#'@description The area of interest is framed as the four coordinates (North, 
#'South, West and East), if the species has some points outside of this area the user
#'will be asked to decide whether delete the point or delete the  species.
#'
#'@param data Vector of characters. Name of the input file.
#'
#'@param rd.frmt Vector of characters. The file format to read. 
#'By default it will be read  as a  R object using the
#' \code{'readRDS'} argument, but it can be read as plain text using the
#' \code{'readTXT'} argument. See details.
#'
#'@param path Vector of characters. Path to the input file.
#'
#'@param west Numeric vector. Western coordinate in decimal longitude format.
#'
#'@param east Numeric vector. Eastern coordinate in decimal longitude format.
#'
#'
#'@param south Numeric vector. Southern coordinate in decimal latitude format.
#'
#'
#'@param north Numeric vector. Northern coordinate in decimal latitude format.
#'
#'
#'@param plot.distrib Logical vector. If \code{'TRUE'}, the distribution of the species will 
#'be plotted in red on a world map.
#'
#'@param wrt.frmt Vector of characters. Format to save output
#'file. By default it will be written  as a  R object using 
#' \code{'saveRDS'} argument, but it can be saved as plain text using 
#' \code{'saveTXT'} argument. See details.
#' 
#'@param save.file Vector of characters. Path to the output 
#'file for each  species.
#'
#'@details
#'The headers of the input file must follow the Darwin Core standard [1]. 
#'The user can see the guide using data('ID_DarwinCore) command.
#'For  more details about the formats to read and/or write, see 
#'\code{\link{readAndWrite}} function.
#'
#'@return A file for each species as data frame class.
#'
#'@author R-Alarcon Viviana and Miranda-Esquivel Daniel R.
#'
#'@note See:
#'R-Alarcon V. and Miranda-Esquivel DR.(submitted) geocleaMT: An R package to
#'cleaning geographical data from electronic biodatabases.
#'
#'@seealso \code{\link{readAndWrite}}
#'
#'@references
#' [1] Wieczorek, J. et al. 2012. Darwin core: An evolving community-developed biodiversity data standard. 
#' PloS One 7: e29715.




delPointsOrSp <- function (data = NULL, 
                            rd.frmt = "readRDS", 
                            path = NULL, 
                            west = -120, 
                            east = -65, 
                            south = -25, 
                            north = 25, 
                            plot.distrib = T, 
                            wrt.frmt = "saveRDS", 
                            save.file = NULL) 
{
  tab.info <- as.data.frame(matrix(NA, length(data), 5))
  colnames(tab.info) <- c("Sp", "Initial.Sp", "Initial.Occ", 
                          "Final.Sp", "Final.Occ")
  i<-2
  for (i in 1:length(data)) {
    sp.table <- readAndWrite(action = "read", frmt = rd.frmt, 
                             path = path, name = data[i])
    tab.info$Sp[i] <- data[i]
    tab.info$Initial.Sp[i] <- length(unique(sp.table$species))
    tab.info$Initial.Occ[i] <- nrow(sp.table)
    y <- which(as.numeric(sp.table$decimalLongitude) < west | 
                 as.numeric(sp.table$decimalLongitude) > east)
    x <- which(as.numeric(sp.table$decimalLatitude) < south | 
                 as.numeric(sp.table$decimalLatitude) > north)
    total <- unique(c(y, x))
    names <- unique(sp.table$species[total])
    if (!length(total) == 0) {
      if (plot.distrib == T) {
        data(wrld_simpl)
        plot(wrld_simpl)
        points(x = as.numeric(sp.table$decimalLongitude[-total]), 
               y = as.numeric(sp.table$decimalLatitude[-total]), col = "blue", 
               pch = 20)
        points(x = as.numeric(sp.table$decimalLongitude[total]), 
               y = as.numeric(sp.table$decimalLatitude[total]), col = rainbow(length(names)), 
               pch = 20)
      }
      for (sp in 1:length(names)) {
        message("There are points inside of the range, you can see them in red color")
        print(paste("Check the distribution:", names[sp]))
        input1 <- readline("Delete points? \n (yes: y or not: n)= ")
        if (input1 == "y" | input1 == "yes") {
          find.points <- which(sp.table$species[total] == 
                                 as.character(names[sp]))
          total <- total[find.points]
          sp.table <- as.data.frame(sp.table[-total, 
                                             ])
        }
        else {
          input2 <- readline("Delete species? \n (yes: y or not: n)= ")
          if (input2 == "y" | input1 == "yes") {
            find.points <- which(sp.table$species == 
                                   as.character(names[sp]))
            sp.table <- as.data.frame(sp.table[-find.points, 
                                               ])
          }
        }
        y <- which(as.numeric(sp.table$decimalLongitude) < 
                     west | as.numeric(sp.table$decimalLongitude) > 
                     east)
        x <- which(as.numeric(sp.table$decimalLatitude) < 
                     south | as.numeric(sp.table$decimalLatitude) > 
                     north)
        total <- unique(c(y, x))
        if (plot.distrib == T) {
        dev.off()
        }
      }
    }
    else {
      print(paste(data[i], ": There are no points in the range", 
                  sep = ""))
    }
    if (!nrow(sp.table) == 0) {
      readAndWrite(action = "write", frmt = wrt.frmt, object = sp.table, 
                   path = save.file, name = data[i])
    }
    tab.info$Final.Sp[i] <- length(unique(sp.table$species))
    tab.info$Final.Occ[i] <- nrow(sp.table)
  }
  return(tab.info)
}