inst/deprecated/convert2poly.R

In Maritimes/Mar.utils: A suite of functions used by a variety of Maritimes packages

#' @title convert2poly
#' @description This function will accept a PBSMapping style csv, a df or a 
#' spatialpolygondataframe and turn it into an  sf object, an sp object or a shapefile.
#' @param input a shapefile, SpatialPolygonsDataFrame, or PBSMapping PolySet to be converted (csv or df).
#' @param header indicates whether or not the input data has an initial row
#' describing the data.
#' @param out default is \code{'sf'}.  This indicates whether an \code{sf} object, 
#' \code{'sp'} (SpatialPolygonsDataFrame) or \code{'shp'} (shapefile) should be created.
#' @param lat.field the default is \code{"X"}. the name of the field holding latitude values
#' (in decimal degrees)
#' @param lon.field the default is \code{"Y"}.  the name of the field holding longitude
#' values (in decimal degrees)
#' @param PID the default is \code{"PID"}.  the name of the field holding primary 
#' identifiers for polygons 
#' @param SID the default is \code{"SID"}.  the name of the field holding secondary 
#' identifiers for polygons 
#' @param POS the default is \code{"POS"}.  the name of the field holding the 
#' order in which the provided coordinates should be joined
#' @param shp.path if \code{out ='shp'}, this is the path to where the shapefile 
#' should be saved.  sf and sp objects are just created in the environment
#' @return an sf object, a SpatialPolygonsDataFrame,or a shapefile
#' @note if no  PID or POS is provided, it is assumed that the provided positions
#' are for a single polygon and the position are in the correct order.
#' @family general_use
#' @author  Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
convert2poly <- function(input=NULL, 
                         header = TRUE,
                         out='sf', 
                         lat.field = 'X', lon.field = 'Y',
                         PID = "PID", SID = "SID", POS= "POS",
                         shp.path = NULL){
  .Deprecated("Mar.utils::convert2poly", msg="Mar.utils::convert2poly() is now deprecated - please use Mar.utils::df_to_sf instead.")
  
  if (inherits(input,"sf") && out =="shp"){
 
    nm <- deparse(substitute(input))
    thePath <- ifelse(is.null(shp.path), getwd(), shp.path)
    
    filePath <- file.path(thePath,paste0(nm,".shp"))
    
    sf::st_write(input, dsn = filePath, layer = filePath, driver = "ESRI Shapefile")
    print(paste0("Saved shapefile to ",thePath,"/",nm,".shp"))
    return(NULL)
  }
  skip <- FALSE
  if (is.character(input)){
    nm <- gsub(".csv|.dat","", basename(input))
    theInput <- utils::read.csv(input, header = header)
    if(ncol(theInput)<2) {
      theInput <- utils::read.table(input, header = header)
      
      if (!all(c(lat.field,lon.field) %in% names(theInput)) && all(c("V1","V2") %in% names(theInput))){
        if (mean(theInput$V1)<0){
          colnames(theInput)[colnames(theInput)=="V1"] <- "X"
          colnames(theInput)[colnames(theInput)=="V2"] <- "Y"
        }else{
          colnames(theInput)[colnames(theInput)=="V1"] <- "Y"
          colnames(theInput)[colnames(theInput)=="V2"] <- "X"
        }
      }
    }
  }else if (inherits(input,"data.frame")){
    
    nm <- deparse(substitute(input))
    theInput <- input
  }else if (inherits(input,"SpatialPolygonsDataFrame")){
    nm <- deparse(substitute(input))
    polySpDf<- input
    skip <- TRUE
  }
  if (!skip){
    if(!PID %in% colnames(theInput)) theInput$PID <- 1
    if(!SID %in% colnames(theInput)) theInput$SID <- 1
    if(!POS %in% colnames(theInput)) theInput$POS <- seq(1:nrow(theInput))
    colnames(theInput)[colnames(theInput)==lat.field] <- "X"
    colnames(theInput)[colnames(theInput)==lon.field] <- "Y"
    colnames(theInput)[colnames(theInput)==PID] <- "PID"
    colnames(theInput)[colnames(theInput)==SID] <- "SID"
    colnames(theInput)[colnames(theInput)==POS] <- "POS"
    theInput <- PBSmapping::as.PolySet(theInput, projection = "LL")
    polySp = suppressWarnings(maptools::PolySet2SpatialPolygons(theInput))
    thisdata = data.frame(PID = unique(theInput$PID))
    
    thisdata$ID = seq(1:nrow(thisdata))
    polySpDf <- tryCatch({
      rownames(thisdata) <- thisdata$PID
      polySpDf <- sp::SpatialPolygonsDataFrame(Sr = polySp, data =thisdata)
    },
    error = function(cond) {
      rownames(thisdata) <- thisdata$ID
      polySpDf <- sp::SpatialPolygonsDataFrame(Sr = polySp, data =thisdata)
    })
  }
  if (out == 'sp'){
    return(polySpDf) 
  } else if ( tolower(out)=="shp"){
    thePath <- ifelse(is.null(shp.path), getwd(), shp.path)
    rgdal::writeOGR(obj = polySpDf, layer = nm, dsn = thePath, driver="ESRI Shapefile", overwrite_layer=TRUE)
    print(paste0("Saved shapefile to ",thePath,"/",nm,".shp"))
    return(NULL)
  }else if ( tolower(out)=="sf"){
    #preventing weird orphaned hole issue
    methods::slot(polySpDf, "polygons") <- lapply(methods::slot(polySpDf, "polygons"), maptools::checkPolygonsHoles)
    polySf <- sf::st_as_sf(polySpDf) 
    return(polySf)
  }
  
}