https://github.com/cran/RandomFields
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Tip revision: fab3d29ef16569604858ee648b9e1f6f7d4a7c96 authored by Martin Schlather on 21 September 2014, 00:00:00 UTC
version 3.0.42
Tip revision: fab3d29
Methods-RFsp.R

## Coerce Objects #########################################################

as.data.frame.RFspatialPointsDataFrame <- function(x, ...) {
  #str(x); kkkk
  cbind(x@data, x@coords)
}
as.data.frame.RFspatialGridDataFrame <- function(x, ...) 
  spatialGridObject2conventional(x, TRUE)

setAs("RFspatialPointsDataFrame", "data.frame",
      function(from, to) from@data
)
setAs("RFspatialGridDataFrame", "data.frame",
      function(from, to) spatialGridObject2conventional(from, TRUE)$data
)


setAs("SpatialPointsDataFrame", "RFspatialPointsDataFrame",
      function(from, to) sp2RF(from))
setAs("SpatialGridDataFrame", "RFspatialGridDataFrame",
      function(from, to) sp2RF(from))

setAs("RFspatialGridDataFrame", "RFspatialPointsDataFrame",
      function(from, to) RFspatialPointsDataFrame(coords=coordinates(from),
                                                  data=from@data,
                                                  RFparams=from@.RFparams))
setAs("RFspatialPointsDataFrame", "RFspatialGridDataFrame",
      function(from, to) RFspatialGridDataFrame(grid=sp::points2grid(from),
                                                data=from@data,
                                                RFparams=from@.RFparams))

setAs("RFpointsDataFrame", "RFgridDataFrame",
      function(from, to) {
        tmp.coord <- sp::SpatialPoints(cbind(from@coords, 1:length(from@coords)))
        tmp.grid <- sp::points2grid(tmp.coord)
        grid <- convert2GridTopology(tmp.grid[,1, drop=FALSE])
        RFgridDataFrame(data=from@data, grid=grid, RFparams=from@.RFparams)
      })
setAs("RFgridDataFrame", "RFpointsDataFrame", 
      function(from, to) {
        coords <- GridTopology2gridVectors(from@grid)[[1]]
        RFpointsDataFrame(data=from@data, coords=coords,
                          RFparams=from@.RFparams)
      })



## methods 'as.matrix' and 'cbind' as in the 'sp' package

as.matrix.RFgridDataFrame <- 
 as.matrix.RFspatialGridDataFrame <- function(x, ...) {
  z <- as.array.RFgridDataFrame(x, ...) 
  if (length(dim(z)) > 2)
    stop("the data set cannot be turned into a matrix. Try 'as.array'")
  z
}

as.array.RFgridDataFrame <-
  as.array.RFspatialGridDataFrame <- function(x, ...) {
    z <- as.matrix(x@data)    
    dim <- c(x@grid@cells.dim, x@.RFparams$vdim, x@.RFparams$n)
    dim <- dim[dim > 1]
    if (length(dim) == 1) return(as.vector(z))
    dim(z) <- dim
    if ((l <- length(x@grid@cells.dim)) > 1) {
      idx <- as.list(rep(TRUE, length(dim)))
      idx[[2]] <- (dim[2]) : 1
      #Print(idx, c(list(z), drop=FALSE, idx))
      do.call("[", c(list(z), drop=FALSE, idx))
    } else z
  }


as.vector.RFgridDataFrame <-
  as.vector.RFspatialGridDataFrame <- function(x, ...) {
    as.vector(as.array.RFgridDataFrame(x))
  }

#setAs("RFgridDataFrame", "matrix", gridtomatrix)
#setAs("RFspatialGridDataFrame", "matrix", gridtomatrix)


cbind.RFspatialGridDataFrame <- function(...)
  cbind_RFsp(...)
cbind.RFgridDataFrame <- function(...)
  cbind_RFsp(...)

cbind.RFspatialPointsDataFrame <- function(...)
  cbind_RFspPoints(...)
cbind.RFpointsDataFrame <- function(...)
  cbind_RFspPoints(...)



## convert 'RFsp' objects to conventional format of 'RFsimulate',
## i.e. data is an array and x a matrix of coordinates or gridtriple defs.

setGeneric(name = "RFspDataFrame2conventional", 
           def = function(obj) standardGeneric("RFspDataFrame2conventional"))
setMethod("RFspDataFrame2conventional",
          signature=c("RFspatialGridDataFrame"),
          function(obj) spatialGridObject2conventional(obj))
setMethod("RFspDataFrame2conventional", signature=c("RFgridDataFrame"),
          function(obj) spatialGridObject2conventional(obj))
setMethod("RFspDataFrame2conventional",
          signature=c("RFspatialPointsDataFrame"),
          function(obj) spatialPointsObject2conventional(obj))
setMethod("RFspDataFrame2conventional", signature=c("RFpointsDataFrame"),
          function(obj) spatialPointsObject2conventional(obj))


rfspDataFrame2dataArray_generic <- function(obj) {
  has.variance <- !is.null(obj@.RFparams$has.variance) && obj@.RFparams$has.variance
  arr <- unlist(obj@data)
  names(arr) <- NULL
  grid.length.v <- obj@grid@cells.dim
  dim(arr) <- c(grid.length.v,         # spatial and time dim
                obj@.RFparams$vdim,    # vdim
                obj@.RFparams$n + has.variance)       # repetitions
  timespacedim <- length(grid.length.v)
  if (timespacedim > 1)
    arr <- reflection(arr, 2, drop=FALSE)
    ## re-ordering of 2nd space dimension since in sp objects, the 2nd dimension
    ## is in decreasing order
  return(arr)
}      

setGeneric(name = "RFspDataFrame2dataArray", 
           def = function(obj) standardGeneric("RFspDataFrame2dataArray"))
setMethod("RFspDataFrame2dataArray", signature=c("RFspatialGridDataFrame"),
          function(obj) rfspDataFrame2dataArray_generic(obj))
          ## used in plot method
setMethod("RFspDataFrame2dataArray", signature=c("RFgridDataFrame"),
          function(obj) rfspDataFrame2dataArray_generic(obj))



##  convert GridTopology or 3-row matrix to list of vectors
setGeneric(name = "GridTopology2gridVectors", 
           def = function(grid) standardGeneric("GridTopology2gridVectors"))
setMethod("GridTopology2gridVectors",
          signature=c("GridTopology"),
          function(grid) {
            len <- length(grid@cells.dim)
            x <- list()
            for (i in 1:len)
              x[[i]] <- seq(from   = grid@cellcentre.offset[i],
                            to     = grid@cellcentre.offset[i] +
                                     ((grid@cells.dim[i]-1) * grid@cellsize[i]),
                            length = grid@cells.dim[i])
            return(x)
          })
setMethod("GridTopology2gridVectors",
          signature=c("matrix"),
          function(grid) {
            stopifnot(nrow(grid)==3)
            x <- list()
            for (i in 1:ncol(grid))
              x[[i]] <- seq(from  = grid[1,i],
                            to    = grid[1,i] + (grid[3,i]-1) * grid[2,i],
                            length= grid[3,i])
            return(x)
          })
##  convert GridTopology to 3-row matrix
as.matrix.GridTopology <- function(x, ...)
  return(rbind(x@cellcentre.offset, x@cellsize, x@cells.dim))



## extract or calculate! coordinates; 
                                                
setMethod(f = "coordinates", signature="RFpointsDataFrame",
          definition=function(obj) return(obj@coords) )
setMethod(f = "coordinates", signature="RFgridDataFrame",
          definition=function(obj) coordinates(as(obj, "RFpointsDataFrame")) )


extract.kriging.variance <- function(x){
  stopifnot(is(x, "RFsp"))
  has.variance <- !is.null(x@.RFparams$has.variance) && x@.RFparams$has.variance
  if (!has.variance) return(NULL)
  return(x[(x@.RFparams$n*x@.RFparams$vdim + 1):(ncol(x@data))])
}

  
setGeneric(name = "variance", 
           def = function(obj) standardGeneric("variance"))
setMethod(f = "variance", signature="RFsp",
          definition=function(obj) extract.kriging.variance(obj))




## conventional 'RFsimulate' output to 'RFsp' class

summary.RFpointsDataFrame <- function(object, digits = 6, ...) {
  df = data.frame(coordinates=signif(coordinates(object), digits), object@data)
  row.names(df) = row.names(object@data)
  class(df) <- "summary.RFpointsDataFrame"
  df
}
print.summary.RFpointsDataFrame <- function(x, ...)
  print.data.frame(x, ...)#

print.RFpointsDataFrame <- function(x, ...) {
  sx <- summary.RFpointsDataFrame(x, ...)
  cat("Object of class RFpointsDataFrame\n")
  print.summary.RFpointsDataFrame(sx) #
  invisible(sx)
}

setMethod(f="show", signature="RFpointsDataFrame",
          definition=function(object) print.RFpointsDataFrame(object))

summary.RFgridDataFrame <- function(object, ...) {
  if (ncol(object@data) > 1) summary(object@data) else summary(object@data[[1]])
} 
print.RFgridDataFrame <- function(x, ...) {
  cat("Object of class RFgridDataFrame\n")
  cat("Grid topology:\n")
  print.data.frame(data.frame(cellcentre.offset=x@grid@cellcentre.offset, #
                   cellsize=x@grid@cellsize,
                   cells.dim=x@grid@cells.dim, row.names=""))
  cat("Points:\n")
  print.data.frame(data.frame(coordinates=coordinates(x), x@data)) #
  cat("Data summary:\n")
  summary.RFgridDataFrame(x, ...)
  invisible(x)
}
setMethod(f="show", signature="RFgridDataFrame", 
	  definition=function(object) print.RFgridDataFrame(object))

summary.RFspatialPointsDataFrame <- function(object, ...) summary(object@data)
print.RFspatialPointsDataFrame <- function(x, ...){
  if (!hasArg("silent") || !list(...)$silent) {
    cat("Object of class 'RFspatialPointsDataFrame'\n")
    str(x@data, no.list=TRUE, give.attr=FALSE)#
  }
  invisible(x@data)
}
setMethod(f="show", signature="RFspatialPointsDataFrame", 
	  definition=function(object) print.RFspatialPointsDataFrame(object))


summary.RFspatialGridDataFrame <- function(object, ...) summary(object@data)
print.RFspatialGridDataFrame <- function(x,...) {
 if (!hasArg("silent") || !list(...)$silent) {
    cat("Object of class 'RFspatialGridDataFrame'\n")
    utils::str(x@data, no.list=TRUE, give.attr=FALSE)#
  }
  invisible(x@data)
}
setMethod(f="show", signature="RFspatialGridDataFrame", 
	  definition=function(object) print.RFspatialGridDataFrame(object))


## extend methods for 'Spatial' to class 'RFsp'
if (!isGeneric("isGridded"))
  setGeneric(name = "isGridded", 
             def = function(obj)
             standardGeneric("isGridded") )

setMethod(f="isGridded", signature="RFsp", 
	  definition=function(obj)
          (is(obj, "RFgridDataFrame") || is(obj, "RFspatialGridDataFrame")))

setMethod(f="dimensions", signature="RFsp", 
	  definition=function(obj) {
            (getMethod("dimensions", "Spatial")@.Data)(obj)
          })
          
setMethod(f="dimensions", signature="RFspatialDataFrame", 
	  definition=function(obj) {
            if (is(obj, "RFdataFrame")) return(1)
            else (getMethod("dimensions", "Spatial")@.Data)(obj)
          })
setMethod(f="dimensions", signature="RFdataFrame", 
	  definition=function(obj) return(1))


summary.RFsp <- function(object, ...) {
  if (is(object, "Spatial"))
    return((getMethod("summary", "Spatial")@.Data)(object))
  
  obj = list()
  obj[["class"]] = class(object)
            #obj[["bbox"]] = bbox(object)
            #obj[["is.projected"]] = is.projected(object)
            #obj[["proj4string"]] = object@proj4string@projargs
  if (is(object, "RFpointsDataFrame")) 
    obj[["npoints"]] = nrow(object@coords)
  if (is(object, "RFgridDataFrame")) {
    gr <- object@grid
    obj[["grid"]] =
      data.frame(cellcentre.offset = gr@cellcentre.offset, 
                 cellsize = gr@cellsize,
                 cells.dim = gr@cells.dim)
  }
  if ("data" %in% slotNames(object))
    if (nrow(object@data) > 0)
      if (ncol(object@data) > 1) 
        obj[["data"]] = summary(object@data)
      else obj[["data"]] = summary(object@data[[1]])
  class(obj) = "summary.RFsp"
  return(obj)
}

print.summary.RFsp <- function(x, ...){
  x <- summary.RFsp(x)
  str(x, give.attr=FALSE) #
  invisible(x)
}

print.RFsp <- function(x, ...) print.summary.RFsp(summary.RFsp(x, ...))#

## plot methods
## for 1-dim coordinates for grid and points
## for 2-or more dimensional coordinates for grid only

#for (.x in c("RFgridDataFrame", "RFpointsDataFrame"))
#  for (.y in c("missing", "RFgridDataFrame", "RFpointsDataFrame"))
#  setMethod(f="plot", signature(x=.x, y=.y),
#            definition=function(x, y, nmax = 6,
#              plot.variance = (!is.null(x@.RFparams$has.variance) &&
#                               x@.RFparams$has.variance),
#              ...)
#            plotRFdataFrame(x, y=y, nmax=nmax, plot.variance=plot.variance, ...)
#            )


setMethod(f="plot", signature(x="RFdataFrame", y="missing"),
          definition=function(x, y, nmax = 6,
            plot.variance = (!is.null(x@.RFparams$has.variance) &&
                             x@.RFparams$has.variance),legend=TRUE, 
            ...)
          plotRFdataFrame(x, y=y, nmax=nmax, plot.variance=plot.variance,
                          legend=legend, ...)
          )

setMethod(f="plot", signature(x="RFdataFrame", y="RFdataFrame"),
          definition=function(x, y, nmax = 6,
            plot.variance = (!is.null(x@.RFparams$has.variance) &&
                             x@.RFparams$has.variance),legend=TRUE, 
            ...)
          plotRFdataFrame(x, y=y, nmax=nmax, plot.variance=plot.variance,
                          legend=legend, ...)
          )



setMethod(f="plot", signature(x="RFspatialDataFrame", y="missing"),
	  definition=function(
            x, y, MARGIN = c(1, 2),
            MARGIN.slices = NULL,
            n.slices= if (is.null(MARGIN.slices)) 1 else 10,
            nmax = 6,
            plot.variance = (!is.null(x@.RFparams$has.variance) &&
                             x@.RFparams$has.variance),
            select.variables, # = 1:vdim,
            zlim,
            legend=TRUE,  MARGIN.movie = NULL, ...)
          plotRFspatialDataFrame(x=x, y=y, MARGIN=MARGIN,
                                 MARGIN.slices=MARGIN.slices,
                                 n.slices=n.slices, nmax=nmax,
                                 plot.variance = plot.variance,
                                 select=select.variables,
                                 zlim=zlim,
                                 legend=legend,
                                 MARGIN.movie = MARGIN.movie,
                                 ...))

setMethod(f="plot",
          signature(x="RFspatialDataFrame", y="RFspatialGridDataFrame"),
	  definition=function(
            x, y, MARGIN = c(1, 2),
            MARGIN.slices = NULL,
            n.slices= if (is.null(MARGIN.slices)) 1 else 10,
            nmax = 6,
            plot.variance = (!is.null(x@.RFparams$has.variance) &&
                             x@.RFparams$has.variance),
            select.variables, # = 1:vdim,
            zlim,
            legend=TRUE,
            MARGIN.movie = NULL,
            ...)
          plotRFspatialDataFrame(x=x, y=y, MARGIN=MARGIN,
                                 MARGIN.slices=MARGIN.slices,
                                 n.slices=n.slices, nmax=nmax,
                                 plot.variance = plot.variance,
                                 select=select.variables,
                                 zlim=zlim,
                                 legend=legend,
                                 MARGIN.movie = MARGIN.movie,
                                 ...))

setMethod(f="plot",
          signature(x="RFspatialDataFrame", y="RFspatialPointsDataFrame"),
	  definition=function(
            x, y, MARGIN = c(1, 2),
            MARGIN.slices = NULL,
            n.slices= if (is.null(MARGIN.slices)) 1 else 10,
            nmax = 6,
            plot.variance = (!is.null(x@.RFparams$has.variance) &&
                             x@.RFparams$has.variance),
            select.variables, # = 1:vdim,
            zlim,
            legend=TRUE,
            MARGIN.movie = NULL,
            ...)
          plotRFspatialDataFrame(x=x, y=y, MARGIN=MARGIN,
                                 MARGIN.slices=MARGIN.slices,
                                 n.slices=n.slices, nmax=nmax,
                                 plot.variance = plot.variance,
                                 select=select.variables,
                                 zlim=zlim,
                                 legend=legend,
                                 MARGIN.movie = MARGIN.movie,
                                 ...))
setMethod(f="plot",
          signature(x="RFspatialDataFrame", y="matrix"),
	  definition=function(
            x, y, MARGIN = c(1, 2),
            MARGIN.slices = NULL,
            n.slices= if (is.null(MARGIN.slices)) 1 else 10,
            nmax = 6,
            plot.variance = (!is.null(x@.RFparams$has.variance) &&
                             x@.RFparams$has.variance),
            select.variables, # = 1:vdim,
            zlim,
            legend=TRUE,
            MARGIN.movie = NULL,
            ...)
          plotRFspatialDataFrame(x=x, y=y, MARGIN=MARGIN,
                                 MARGIN.slices=MARGIN.slices,
                                 n.slices=n.slices, nmax=nmax,
                                 plot.variance = plot.variance,
                                 select=select.variables,
                                 zlim=zlim,
                                 legend=legend,
                                 MARGIN.movie = MARGIN.movie,
                                 ...))


setMethod(f="persp",
          signature(x="RFspatialGridDataFrame"),
	  definition=function(
            x, y, MARGIN = c(1, 2),
            MARGIN.slices = NULL,
            n.slices= if (is.null(MARGIN.slices)) 1 else 10,
            nmax = 6,
            plot.variance = (!is.null(x@.RFparams$has.variance) &&
                             x@.RFparams$has.variance),
            select.variables, # = 1:vdim,
            zlim,
            legend=TRUE, MARGIN.movie = NULL, ...)
          plotRFspatialDataFrame(x=x, y=y, MARGIN=MARGIN,
                                 MARGIN.slices=MARGIN.slices,
                                 n.slices=n.slices, nmax=nmax,
                                 plot.variance = plot.variance,
                                 select=select.variables,
                                 zlim=zlim,
                                 legend=legend,
                                 MARGIN.movie = MARGIN.movie,
                                 ..., plotmethod="persp"))

contour.RFspatialGridDataFrame <-
  function( x, y, zlim,
           MARGIN = c(1, 2),
           MARGIN.slices = NULL,
           n.slices = if (is.null(MARGIN.slices)) 1 else 10,
           nmax = 6,
           plot.variance = (!is.null(x@.RFparams$has.variance) &&
                            x@.RFparams$has.variance),
           select.variables, # = 1:vdim,
            legend=TRUE,  MARGIN.movie = NULL, ...)
  plotRFspatialDataFrame(x=x, y=y, MARGIN=MARGIN,
                         MARGIN.slices=MARGIN.slices,
                         n.slices=n.slices, nmax=nmax,
                         plot.variance = plot.variance,
                         select=select.variables,
                         zlim=zlim,
                         legend=legend,MARGIN.movie = MARGIN.movie,
                         ..., plotmethod="contour")


errMsgNoPlotAvailable <- function(x, y)
  warning(paste("no plot method available for signature c(",
                class(x), ",", class(y), ")"))

setMethod(f="plot", signature(x="RFspatialPointsDataFrame",
            y="RFspatialGridDataFrame"),
	  definition=function(x, y) {
            errMsgNoPlotAvailable(x, y)
            return(invisible(NULL))
          })
 
# plotRFgridDataFrame <- function(x, y, nmax, plot.variance, ...)
# siehe nicht.nachladbar.R
          
plotRFdataFrame <-  function(x, y, nmax=6, plot.variance, legend, ...) {
  ## grid   : sorted = TRUE
  ## points : sorted = FALSE
#  Print(close.screen(), dev.cur()); print(dev.list())

  stopifnot(!missing(x))
  x <- trafo_pointsdata(x)
  nc <- ncol(x$data)

  if (!missing(y)) {
    y <- trafo_pointsdata(y)
    y$data <- rep(y$data, length.out=nrow(y$data) * nc)
    dim(y$data) <- c(length(y$coords), nc)
  }
  has.variance <- !is.null(x$RFparams$has.variance) && x$RFparams$has.variance
  if (!has.variance) plot.variance <- FALSE
  n <- min(x$RFparams$n, nmax) + plot.variance
  vdim <- x$RFparams$vdim

  if (nc < n*vdim) {
    if (n==1) vdim <- nc else if (vdim==1) n <- nc else {
      stop("ncol(x@data) does not match 'x@.RFparams'; change 'x@.RFparams'")
    }
  }

  
  graphics <- RFoptions()$graphics
#  Print(graphics, close.screen(), dev.cur()); print(dev.list())
  ArrangeDevice(graphics, c(1, n)) ## NIE par vor ArrangeDevice !!!!

#  Print(close.screen(), dev.cur()); print(dev.list())

  always.close <- n > 1 || graphics$always_close_screen
  if (any(par()$mfcol != c(1,1))) par(mfcol=c(1,1))
  dots <- list(...)
  dotnames <- names(dots)
  if ("bg" %in% dotnames) {
    par(bg=dots$bg)
    dots$bg <- NULL
  }
 
  if (!("xlab" %in% dotnames)) dots$xlab <- x$lab$x
  if (!("type" %in% dotnames)) dots$type <- "l"

  make.small.mar <- ("xlab" %in% dotnames &&
                     is.null(dots$xlab) && is.null(dots$ylab))

  ## variable names

##  Print(x); lll
  
  if (!is.null(x$labdata) && all(nchar(x$labdata)>0))
    names.vdim <- unlist(lapply(strsplit(x$labdata[1:vdim], ".n"),
                                FUN=function(li) li[[1]]))
  else {
    names.vdim <- paste("variable", 1:vdim)
    x$labdata <- names.vdim
  }

  if (n>1){
    ylab.vec <- c(paste("realization ", 1:(n-plot.variance), sep=""),
                  if (plot.variance) "kriging variance")
  } else {
    ylab.vec <- if (vdim==1) x$colnames else ""
  }

  if ("ylab" %in% dotnames) {
    if (!is.null(dots$ylab))
      ylab.vec[1:length(ylab.vec)] <- dots$ylab
    dots$ylab <- NULL
  }

  col <- 1:vdim
  if ("col" %in% dotnames) {
    if (!is.null(dots$col))
      col[1:length(col)] <- dots$col
    dots$col <- NULL
  }

  split.screen(c(n,1))
  
#  if (always.close) {
#    close.screen(all.screens=TRUE)
#    par(mfrow=c(1,1))
#    split.screen(c(n,1))
#  }
                
  for (i in 1:n){
    screen(i)
    if (make.small.mar)
      par(oma=c(3,0,1,1)+.1, mar=c(0,3,0,0))
    else
      par(oma=c(4,0,1,1)+.1, mar=c(0,4,0,0))
    ylab <- ylab.vec[i]
    
    if (tmp.idx <- (plot.variance && i==n)){
      i <- x$RFparams$n + plot.variance
    }

    do.call(graphics::plot,
            args=c(dots, list(
              x=x$coords, y=x$data[ , vdim*(i-1)+1],
              xaxt="n", yaxt="n", ylab=ylab, col=col[1]))
            )

    if (!missing(y)) {
      points(x=y$coords, y=y$data[ , vdim*(i-1)+1], pch=22, col="red")
    }
    axis(2)
    if (tmp.idx) i <- n
    
    if(i==n){
      axis(1, outer=always.close)
      title(xlab=dots$xlab, outer=TRUE) # always.close) 
    }
    else axis(1, labels=FALSE)
    for (j in 1:vdim){
      if (j==1) next
      do.call(graphics::points, quote=TRUE,
              args=c(dots, list(
                x=x$coords, y=x$data[ , vdim*(i-1)+j], col=col[j]))
              )
      if (!missing(y)) {
        points(x=y$coords, y=y$data[ , vdim*(i-1)+j], pch=22, col="red")
      }
      
      if (i==1) {
        if ( (!TRUE || vdim > 1) && legend) {
          legend("topright", col=col, lty=1, legend = c(names.vdim))
        }
      }
    }
  }
  if (always.close) close.screen(all.screens=TRUE)
}

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