R/cor_spatial.R

In Pintademijote/multipack: What the Package Does (One Line, Title Case)

#' Produce a tab containing the value selected each x pixel on the map generated by Chloe per metric.
#'
#' `cor_spatial()` Return a tab containing a the value selected each x pixel on the map generated by Chloe per metric.
#'
#' This fonction is to used when you search to find correlation between metrics
#' at multiple scales and when your sampling is randomly selected across
#' the the landscape and patches. To test the correlation, you must used after that the
#' 'temp()' function.
#' @param directory The directory where your ascii generated with Chloe are stored
#'
#' @param dist Vector of scales you choosed in Chloe when you created the ascii whith Cloe
#' @param metrics Vector of metrics you choosed in Chloe when you created the ascii whith Cloe
#'
#' @section Warning:
#' This process can take some time depending of the size of your ascii and the numbers of your metrics
#'
#' @return Return a tab containing a the value selected each x pixel on the map generated by Chloe per metric
#' @author Pierre-Gilles Lemasle <pg.lemasle@gmail.com>
#' @export
cor_spatial=function(directory,metrics,dist){



  metrics_temp=metrics
  files=list.files(directory,pattern = "\\.asc$")
  metrics=gsub('.', "-", metrics, fixed=TRUE)
  distname=paste("w",dist,"_",sep = "")
  metrics=metrics[rev(order(metrics))]

  temp=files[grep(distname[1],files)]
  temp=temp[grep(metrics[1],temp)]
  temp=paste(directory,temp,sep = "")
  r=raster(temp)

  columnames=NULL
  for (metric in metrics) {
    columnames=c(columnames,(paste(distname,"_",metric,sep="")))
  }

  test=matrix(nrow = length(seq(1,ncol(r),10))*length(seq(1,nrow(r),10)),ncol = length(metrics)*length(distname))
  test=as.data.frame(test)
  colnames(test)=columnames

  start_time <- Sys.time()
  pb <- txtProgressBar(min = 0, max = length(distname)*length(metrics), style = 3)
  repet=0
  shin_progress=length(distname)*length(metrics)

  for (dist in distname) {
    tempdist=files[grep(dist,files)]
    a=0
    for (metric in metrics) {
      repet=repet+1
      Sys.sleep(0.1)
      # update progress bar
      setTxtProgressBar(pb, repet)


      temp=tempdist[grep(metric,tempdist)]
      temp=paste(directory,temp,sep = "")
      r=raster(temp)

      test[,paste(dist,"_",metric,sep="")]=as.vector(r[seq(1,nrow(r),10),seq(1,ncol(r),10)])

      tempdist=tempdist[-grep(metric,tempdist)]

      Sys.sleep(0.1)
      incProgress(1/shin_progress)

    }
  }
  end_time <- Sys.time()
  end_time - start_time

  metrics=metrics_temp
  columnames=NULL
  for (metric in metrics) {
    columnames=c(columnames,(paste(distname,"_",metric,sep="")))
  }
  colnames(test)=columnames
  return(test)
}