global.polygon <- "/Volumes/Albacora/Dropbox/Raw Data/Shapefiles/World Present/Global_CostLine_HD_Polygon.shp"
contour( global.polygon = global.polygon , file= "Data/sampling_sites.txt" , file.sep = ";" , file.dec = "." , file.strucutre = 1 , file.header = FALSE , resolution = 0.01 , buffer = c(1,1,1,1) , export.file = TRUE )

## -----------------

contour <- function (global.polygon , file , file.sep , file.dec , file.header, resolution, buffer , file.strucutre,export.file) {

            site.names <- as.character(read.table(file,sep=file.sep,dec=file.dec,header = file.header)[,1])

            if(file.strucutre == 1) {
              site.xy <- read.table(file,sep=file.sep,dec=file.dec,header = file.header)[,c(2,3)]
            }
            if(file.strucutre == 2) {
              site.xy <- read.table(file,sep=file.sep,dec=file.dec,header = file.header)[,c(3,2)]
            }

            ## ---------

            if( !"wordcloud" %in% names(installed.packages()[,1]) ) {

              cat( "\r" , "\r" , "Installing Dependences.", "\r", "\r")
              suppressMessages(suppressWarnings( try(install.packages("wordcloud" , verbose=FALSE , quiet = TRUE) , silent = TRUE) ) )

            }
            if( !"raster" %in% names(installed.packages()[,1]) ) {

              cat( "\r" , "\r" , "Installing Dependences.", "\r", "\r")
              suppressMessages(suppressWarnings( try(install.packages("raster" , verbose=FALSE , quiet = TRUE) , silent = TRUE) ) )

            }
            if( !"rgeos" %in% names(installed.packages()[,1]) ) {

              cat( "\r" , "\r" , "Installing Dependences.", "\r", "\r")
              suppressMessages(suppressWarnings( try(install.packages("rgeos" , verbose=FALSE , quiet = TRUE) , silent = TRUE) ) )

            }
            if( !"gdistance" %in% names(installed.packages()[,1]) ) {

              cat( "\r" , "\r" , "Installing Dependences.", "\r", "\r")
              suppressMessages(suppressWarnings( try(install.packages("gdistance" , verbose=FALSE , quiet = TRUE) , silent = TRUE) ) )

            }
            cat( "\r" , "\r" ,   "                                         ", "\r", "\r")
            cat( " ", "\n")

            cat( " " ,   "Loading Dependences.")
            suppressMessages(suppressWarnings(try( library(raster) , silent = TRUE) ))
            suppressMessages(suppressWarnings(try( library(rgeos) , silent = TRUE) ))
            suppressMessages(suppressWarnings(try( library(gdistance) , silent = TRUE) ))
            suppressMessages(suppressWarnings(try( library(wordcloud) , silent = TRUE) ))

            ## ---------------------------------------------------------------------------------------------

            if(length(buffer) == 1) { buffer <- rep(buffer,4)}
            xmin <- min(site.xy[,1]) - buffer[1]
            xmax <- max(site.xy[,1]) + buffer[2]
            ymin <- min(site.xy[,2]) - buffer[3]
            ymax <- max(site.xy[,2]) + buffer[4]

            if (xmin <= -180) { xmin <- -180}
            if (xmax >= 180) { xmin <- 180}
            if (ymin <= -90) { xmin <- -90}
            if (ymax >= 90) { ymax <- 90}

            cat( " ", "\n")
            cat( " " , " ", "\n")
            cat( " " , ".....................................................................", "\n")
            cat( " " , "Generating region of interest.","\n")
            cat( " " , "This step may take a while depending on the resolution chosen and distance between sites.")

            ocean <- shapefile(global.polygon)
            ocean <- crop(ocean, extent(xmin, xmax, ymin, ymax))

            region.as.table <- matrix( NA ,nrow= ((ymax-ymin)/resolution) ,ncol= ((xmax-xmin)/resolution) )
            region.as.raster <- raster(region.as.table)
            extent(region.as.raster) <- c(xmin,xmax,ymin,ymax)

            ocean.r <- rasterize(ocean, region.as.raster)
            ocean.r[!is.na(ocean.r)] <- 0
            ocean.r[is.na(ocean.r)] <- 1

            ## ---------------------------------------------------------------------------------------------
            ## Relocate sites if needed

            sites.to.relocate <- extract(ocean.r,site.xy[,1:2]) == 0
            sites.to.relocate.xy <- site.xy[sites.to.relocate,]

            if( nrow(sites.to.relocate.xy) > 0 ) {

              cat(  " ", "\n")
              cat( " " , ".....................................................................", "\n")
              cat(  " ", "\n")

                    if(nrow(sites.to.relocate.xy) == 1 ) {

                      cat( " " , " 1 site to be relocated.")

                    }
                    if( nrow(sites.to.relocate.xy) > 1 ) {

                        cat( " " ,  nrow(sites.to.relocate.xy) , "sites to be relocated.")
                    }

                    ocean.r.sites <- as.data.frame(ocean.r,xy=TRUE)[,1:2]
                    ocean.r.sites <- cbind(ocean.r.sites,extract(ocean.r,ocean.r.sites))
                    ocean.r.sites <- ocean.r.sites[ocean.r.sites[,3] == 1 , 1:2 ]

                    for (i in 1:nrow(sites.to.relocate.xy)) {

                      near.cells <- as.data.frame( sort( spDistsN1( as.matrix(ocean.r.sites), as.matrix(sites.to.relocate.xy[i,1:2]),longlat=TRUE), decreasing = FALSE,index.return = TRUE))
                      site.xy[ which(sites.to.relocate)[i] ,  ] <- ocean.r.sites[ near.cells[1,2] , 1:2 ]

                    }
            }

            ## -------------------------

            pdf(file="Contour _ Study Region.pdf", width=200, height=200)

            plot(ocean.r , col=c("#fffafa","#87ceeb"), legend=FALSE)
            points(site.xy[,1] , site.xy[,2],  col="black",cex=10)
            textplot(site.xy[,1] , site.xy[,2]  , site.names , cex=15, show.lines=TRUE,new=FALSE)

            suppressMessages( dev.off())

            ## -------------------------

            cost.surface <- ocean.r
            projection(cost.surface) <- CRS("+proj=longlat +datum=WGS84")

            raster_tr <- transition(cost.surface, mean, directions=8)
            raster_tr_corrected <- geoCorrection(raster_tr, type="c", multpl=FALSE)

            example.sites.to.plot <- sample(1:nrow(site.xy),2,replace=FALSE)

            pdf(file="Contour _ Example.pdf", width=200, height=200)
            plot(ocean.r , col=c("#fffafa","#87ceeb"), legend=FALSE)
            lines( shortestPath(raster_tr_corrected, as.matrix(site.xy[example.sites.to.plot[1],]) , as.matrix(site.xy[example.sites.to.plot[2],]) , output="SpatialLines") )
            points(site.xy[example.sites.to.plot,1] , site.xy[example.sites.to.plot,2],  col="black",cex=10)
            textplot( site.xy[example.sites.to.plot,1] , site.xy[example.sites.to.plot,2] , site.names[example.sites.to.plot] ,cex=15, show.lines=TRUE, new=FALSE)
            suppressMessages( dev.off())

            raster_cosDist <- costDistance(raster_tr_corrected,  as.matrix(site.xy) ,  as.matrix(site.xy) )
            distance.marine <- as.matrix(raster_cosDist) / 1000
            colnames(distance.marine) <- as.factor(site.names)
            rownames(distance.marine) <- as.factor(site.names)

            cat( " ", "\n")
            cat( " " , ".....................................................................", "\n")
            cat( " " , "Job is done.", "\n")
            cat( " ", "\n")
            cat( " " , "Comments or doubts?", "\n")
            cat( " " , "Please contact jorgemfa@gmail.com", "\n")

            if(export.file) { write.table(distance.marine, file = "Contour _ Pairwise Marine Distances.txt" , quote = FALSE , sep = file.sep, row.names = TRUE, col.names = TRUE, na = "NA", dec = file.dec) }

            if(!export.file) { print(distance.marine) }
}

## ------------------------------------------------------------------------------
## End of function
## ------------------------------------------------------------------------------