Merge pull request #15 from dramanica/sf

Sf

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: geoGraph
 Type: Package
 Title: Walking through the geographic space using graphs
-Version: 1.1.1.9002
+Version: 1.1.1.9003
 Authors@R: c(
     person("Thibaut", "Jombart", role = "aut"),
     person("Andrea", "Manica", email = "[email protected]", role = c("aut", "cre")))
 Maintainer: Andrea Manica <[email protected]>
 Description: Classes and methods for spatial graphs interfaced with support for GIS shapefiles.
 License: GPL (>=2)
-Language: en-GB
+Language: en-US
 URL: https://github.com/EvolEcolGroup/geograph,
     https://evolecolgroup.github.io/geograph/
 BugReports: https://github.com/EvolEcolGroup/geograph/issues
@@ -23,17 +23,16 @@ Depends:
   methods,
   graph
 Imports:
-    fields,
-    RBGL,
-    rnaturalearth,
-    rnaturalearthdata,
-    sp,
-    sf,
-    magrittr
+ fields,
+ RBGL,
+ rnaturalearth,
+ sf,
+ magrittr
 Suggests: 
   testthat, 
   knitr, 
-  rmarkdown
+  rmarkdown,
+  rnaturalearthdata
 RoxygenNote: 7.2.3
 Collate: 
     'classes.R'

NAMESPACE

@@ -74,8 +74,9 @@ exportMethods(setDistCosts)
 exportMethods(setEdges)
 import(graph)
 import(methods)
-import(sp)
+import(sf)
 importFrom(graphics,identify)
 importFrom(graphics,locator)
 importFrom(graphics,segments)
 importFrom(magrittr,"%>%")
+importFrom(rnaturalearth,ne_countries)

NEWS.md

@@ -1,6 +1,7 @@
 # geoGraph (development version)
 
-* 
+* remove all use of deprecated packages (`sp` and `maptools`), and move to
+  `sf` objects
 
 # geoGraph v1.1
 

R/buffer.R

@@ -12,7 +12,7 @@
 #' @aliases buffer buffer-methods buffer,gGraph-method buffer,gData-method
 #' @param x a valid \linkS4class{gGraph} or \linkS4class{gData} object.
 #' @param \dots further arguments passed to specific methods.
-#' @param nodes a character vector identifying the nodes aournd which buffers
+#' @param nodes a character vector identifying the nodes around which buffers
 #' should be computed.
 #' @param d the radius of the buffer, in km.
 #' @param res.type the type of result that should be returned (see section

R/combineCosts.R

@@ -1,7 +1,7 @@
 #' Combine the costs of two gGraph objects
 #'
 #' The function \code{combineCosts} combines the edge costs of two
-#' \linkS4class{gGraph} objects. The first object is used as a temlate to generate
+#' \linkS4class{gGraph} objects. The first object is used as a template to generate
 #' the objects with the combined costs. Two two \linkS4class{gGraph} objects must
 #' have the same edges.
 #'
@@ -20,7 +20,7 @@
 #' the product or a custom function (defined in \code{FUN}) of the costs of its nodes.
 #' @param FUN a function used to compute the cost between two nodes (needed if \code{method="function"}).
 #' @param \dots additional parameters to be passed to \code{FUN}.
-#' @return A \linkS4class{gGraph} object with the newly defined costs, basedd on the combination of the
+#' @return A \linkS4class{gGraph} object with the newly defined costs, based on the combination of the
 #' two gGraph objects, used as weightings of edges.
 #' @export
 #' @examples

R/connectivity.R

@@ -50,7 +50,7 @@
 #'
 #' - \code{isConnected}: a single logical value, being TRUE if nodes of the
 #' object form a connected set.\cr
-
+#' @include classes.R
 #' @keywords utilities methods
 #' @name connectivity
 #' @examples

R/datasets.R

@@ -17,7 +17,7 @@
 #' @docType data
 #' @format \code{hgdp} is a \linkS4class{gGraph} object with the following
 #' data: % \describe{ % \item{@nodes.attr$habitat}{habitat corresponding to
-#' each % vertice; currently 'land' or 'sea'.} % \item{@meta$color}{a matrix
+#' each % vertex; currently 'land' or 'sea'.} % \item{@meta$color}{a matrix
 #' assigning a color for plotting % vertices (second column) to different
 #' values of habitat (first % column).} % }
 #' @references Authors \emph{Journal}, YEAR, \bold{nb}: pp-pp.
@@ -70,24 +70,20 @@ NULL
 #' connectivity between edges at some places. The most noticeable change is that
 #' all edges involving sea vertices have been removed.\cr
 #'
-#' 'worldshape' is a shapefile of countries of the world (snapshot from 1994).
-#'
-#'
 #' @name worldgraph
 #' @aliases worldgraph rawgraph.10k rawgraph.40k worldgraph.10k worldgraph.40k
-#' worldshape
 #' @docType data
 #' @format \code{worldgraph.10k} and \code{worldgraph.40k} are
 #' \linkS4class{gGraph} objects with the following specificities: \describe{
-#' \item{@nodes.attr\$habitat}{habitat corresponding to each vertice; currently
-#' 'land' or 'sea'.} \item{@meta\$color}{a matrix assigning a color for
+#' \item{@nodes.attr$habitat}{habitat corresponding to each vertex; currently
+#' 'land' or 'sea'.} \item{@meta$color}{a matrix assigning a color for
 #' plotting vertices (second column) to different values of habitat (first
 #' column).} }
 #' @references === On the construction of the graph ===\cr Randall, D. A.;
 #' Ringler, T. D.; Heikes, R. P.; Jones, P. & Baumgardner, J. Climate Modeling
 #' with Spherical Geodesic Grids \emph{Computing in science & engineering},
 #' 2002, \bold{4}: 32-41.
-#' @source Graph reconstructed by Andrea Manica.
+#' @source Graph constructed by Andrea Manica.
 #' @keywords datasets
 #' @examples
 #'

R/dijkstra.R

@@ -364,7 +364,7 @@ plot.gPath <- function(x, col = "rainbow", lwd = 3, ...) {
     N <- length(vecNodes)
     if (N < 2) {
       return()
-    } # escape if a path is a single vertice
+    } # escape if a path is a single vertex
     from <- vecNodes[1:(N - 1)]
     to <- vecNodes[2:N]
     ## segments(xy[from,1], xy[from,2], xy[to,1], xy[to,2], col=col, lwd=lwd, ...)

R/extractFromLayer.R

@@ -18,15 +18,13 @@
 #' two columns giving longitudes and latitudes of locations being considered.
 #' For list, input must have two components being vectors giving longitudes and
 #' latitudes of locations.
-#' @param layer a shapefile of the class \code{SpatialPolygonsDataFrame} (see
-#' \code{readShapePoly} in maptools package to import such data from a GIS
+#' @param layer a shapefile of the class [`sf`] (see
+#' [sf::st_read()] to import a GIS
 #' shapefile). Alternatively, a character string indicating one shapefile
-#' released with geoGraph; currently, only 'world' is available (see
-#' \code{?data(worldshape)}).
+#' released with geoGraph; currently, only 'world' is available.
 #' @param attr a character vector giving names of the variables to be extracted
 #' from the layer. If 'all', all available variables are extracted. In case of
-#' problem, available names are displayed with the error message. Available
-#' data are also stored in \code{layer@data}.
+#' problem, available names are displayed with the error message.
 #' @param \dots further arguments to be passed to other methds. Currently not
 #' used.
 #' @return The output depends on the nature of the input:\cr - \code{matrix,
@@ -51,13 +49,13 @@
 #'
 #' ## retrieve continent info for all nodes
 #' ## (might take a few seconds)
-#' x <- extractFromLayer(worldgraph.10k, layer = "world", attr = "CONTINENT")
+#' x <- extractFromLayer(worldgraph.10k, layer = "world", attr = "continent")
 #' x
-#' table(getNodesAttr(x, attr.name = "CONTINENT"))
+#' table(getNodesAttr(x, attr.name = "continent"))
 #'
 #'
 #' ## subset Africa
-#' temp <- getNodesAttr(x, attr.name = "CONTINENT") == "Africa"
+#' temp <- getNodesAttr(x, attr.name = "continent") == "Africa"
 #' temp[is.na(temp)] <- FALSE
 #' x <- x[temp]
 #' plot(x, reset = TRUE)
@@ -84,17 +82,13 @@ setGeneric("extractFromLayer", function(x, ...) {
 #' @rdname extractFromLayer
 #' @export
 setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all", ...) {
-
-
-  ## This functions automatically assigns to land all points overlapping the country polygons
-  # if(!require(maptools)) stop("maptools package is required.")
 
   ## Load default shapefile ##
   if (is.character(layer) && layer[1] == "world") {
     # use rnaturalearth instead of the inbuilt dataset
-    # layer <- rnaturalearth::ne_countries(scale="medium", returnclass = "sf")
-    # sf::sf_use_s2(FALSE)
-    layer <- sf::st_read(system.file("files/shapefiles/world-countries.shp", package = "geoGraph"))
+    layer <- rnaturalearth::ne_countries(scale="medium", returnclass = "sf")
+    sf::sf_use_s2(FALSE)
+    #layer <- sf::st_read(system.file("files/shapefiles/world-countries.shp", package = "geoGraph"))
   }
 
   ## TODO if the layer is null, we should throw an error!!!

R/findLand.R

@@ -13,11 +13,10 @@
 #' @param x a matrix, a data.frame, or a valid \linkS4class{gGraph} object. For
 #' matrix and data.frame, input must have two columns giving longitudes and
 #' latitudes of locations being considered.
-#' @param shape a shapefile of the class \code{SpatialPolygonsDataFrame} (see
-#' \code{readShapePoly} in maptools package to import such data from a GIS
+#' @param shape a shapefile of the class [`sf`] (see
+#' [sf::st_read()] to import a GIS
 #' shapefile). Alternatively, a character string indicating one shapefile
-#' released with geoGraph; currently, only 'world' is available (see
-#' \code{?data(worldshape)}).
+#' released with geoGraph; currently, only 'world' is available.
 #' @param \dots further arguments to be passed to other methods. Currently not
 #' used.
 #' @param attr.name a character string giving the name of the node attribute in
@@ -49,7 +48,7 @@
 #' ## define rules for colors
 #' temp <- data.frame(habitat = c("land", "sea"), color = c("green", "blue"))
 #' temp
-#' obj@meta$color <- temp
+#' obj@meta$colors <- temp
 #'
 #' ## plot object with new colors
 #' plot(obj)
@@ -77,43 +76,42 @@ setGeneric("findLand", function(x, ...) {
 #' @rdname findLand
 #' @export
 setMethod("findLand", "matrix", function(x, shape = "world", ...) {
-  ## This functions automatically assigns to land all points overlapping the country polygons
-  #    if(!require(maptools)) stop("maptools package is required.")
 
-  ## Load country shapefile
+  ## Load default shapefile ##
   if (is.character(shape) && shape[1] == "world") {
-    shape <- worldshape
+    # use rnaturalearth 
+    shape <- rnaturalearth::ne_countries(scale="medium", returnclass = "sf")
+    sf::sf_use_s2(FALSE)
   }
 
-  if (!is.null(shape)) { # with background
-    if (!inherits(shape, "SpatialPolygonsDataFrame")) {
-      stop("Layer must be a SpatialPolygonsDataFrame object \n(see st_read and as_Spatial in sf to import such data from a GIS shapefile).")
+
+  ## TODO if the shape is null, we should throw an error!!!
+  if (!is.null(shape)) {
+    if (!inherits(shape, "sf")) {
+      if (inherits(shape, "SpatialPolygonsDataFrame")){
+        shape <- sf::st_as_sf(shape)
+      } else {
+        stop("shape must be a sf object \n(see st_read in sf to import such data from a GIS shapefile).")
+      }
     }
   }
-
+
+
   if (any(is.na(x))) {
     stop("Matrix contains NA values.")
   }
-
-  long <- x[, 1]
-  lat <- x[, 2]
-  n.country <- length(shape@polygons)
-
-  ## create land vector to score land
-  land <- rep(0, length(lat))
-
-  for (i in 1:n.country) {
-    this.country <- shape@polygons[i][[1]]
-    n.polys <- length(this.country@Polygons)
-
-    for (p in 1:n.polys) {
-      this.poly <- this.country@Polygons[p][[1]]
-      land <- land + point.in.polygon(long, lat, this.poly@coords[, 1], this.poly@coords[, 2])
-    }
-  }
-  land[land > 1] <- 1
-  land[land == 0] <- "sea"
-  land[land == 1] <- "land"
+
+  # create an sf point object from the coordinates
+  locations_st <- x %>% as.data.frame %>% 
+    sf::st_as_sf(coords=c(1,2)) %>%
+    sf::st_set_crs(sf::st_crs(shape))
+  # now find points in polygons
+  points_within <- sf::st_intersects(shape, locations_st)
+  points_within <- data.frame(x = unlist(points_within), 
+                              polygon = rep(seq_along(lengths(points_within)), lengths(points_within)))
+
+  land<-rep("sea",nrow(x))
+  land[points_within$x]<-"land"
 
   return(factor(land))
 })

R/geograph.R

@@ -45,7 +45,7 @@
 #'
 #' - \code{\link{findLand}}: checks which nodes are on land.\cr
 #'
-#' - \code{\link{setCosts}}: define edges weights accoring to rules specified
+#' - \code{\link{setCosts}}: define edges weights according to rules specified
 #' in the @meta slot.\cr
 #'
 #' - \code{\link{geo.add.edges}}, \code{\link{geo.remove.edges}}: graphical
@@ -83,14 +83,11 @@
 #' since they provide the spatial models used in later operations.
 #'
 #' Two main datasets are proposed, each being a \linkS4class{gGraph} resulting
-#' from the spliting of the earth into cells of (allmost perfectly) equal
+#' from the spliting of the earth into cells of (almost perfectly) equal
 #' sizes. Two different resolutions are provided:\cr -
 #' \code{\link{worldgraph.10k}}: coverage using about 10,000 nodes\cr -
 #' \code{\link{worldgraph.40k}}: coverage using about 40,000 nodes\cr
 #'
-#' Other datasets are:\cr - \code{\link{worldshape}}: shapefile containing
-#' world countries.\cr
-#'
 #' To cite geoGraph, please use the reference given by
 #' \code{citation("geoGraph")}.
 #'

R/globals.R

@@ -1 +1 @@
-utils::globalVariables(c("rawgraph.10k", "rawgraph.40k", "worldshape"))
+utils::globalVariables(c("rawgraph.10k", "rawgraph.40k"))

R/isInArea.R

@@ -23,7 +23,7 @@
 #' so \code{locator(1)} is a valid value for \code{reg}.
 #' @param res.type a character string indicating what kind of output should be
 #' produced. See value.
-#' @param buffer a numeric value giving a buffer adding extra space aroung the
+#' @param buffer a numeric value giving a buffer adding extra space around the
 #' area, as a proportion of current area's dimensions.
 #' @return The output depends on the value of the argument \code{res.type}:\cr
 #' - \code{logical}: a vector of logicals having one value for each node of the

R/plot.R

@@ -23,10 +23,10 @@
 #' points,gGraph-method points.gGraph plotEdges
 #' @docType methods
 #' @param x a \linkS4class{gGraph} object.
-#' @param shape a shapefile used as background to the object. Must be of the
-#' class \code{SpatialPolygonsDataFrame} (see \code{readShapePoly} in maptools
-#' package to import such data from a GIS shapefile). Alternatively, a
-#' character string indicating one shapefile released with geoGraph.
+#' @param shape a shapefile of the class [`sf`] (see
+#' [sf::st_read()] to import a GIS
+#' shapefile). Alternatively, a character string indicating one shapefile
+#' released with geoGraph; currently, only 'world' is available.
 #' @param psize a numeric giving the size of points.
 #' @param pch a numeric or a character indicating the type of point.
 #' @param col a character string indicating the color to be used.
@@ -64,6 +64,7 @@
 #'
 #' - \code{\link{isInArea}}, to retain a set of visible data.\cr
 #' @keywords methods hplot spatial
+#' @importFrom rnaturalearth ne_countries
 #' @examples
 #'
 #'
@@ -103,7 +104,7 @@ NULL
 ## plot for gGraph
 ###################
 #' @export
-#' @import sp
+#' @import sf
 setMethod("plot", signature(x = "gGraph", y = "missing"), function(x, y, shape = "world", psize = NULL, pch = 19, col = NULL,
                                                                    edges = FALSE, reset = FALSE, bg.col = "gray", border.col = "dark gray",
                                                                    lwd = 1, useCosts = NULL, maxLwd = 3, col.rules = NULL, ...) {
@@ -191,16 +192,23 @@ setMethod("plot", signature(x = "gGraph", y = "missing"), function(x, y, shape =
 
   ## handle shape
   if (!is.null(shape) && is.character(shape) && shape == "world") {
-    shape <- worldshape
-  }
-
-  if (!is.null(shape)) { ## plot with background ##
-    if (!inherits(shape, "SpatialPolygonsDataFrame")) {
-      stop("Layer must be a SpatialPolygonsDataFrame object \n(see st_read and as_Spatial in sf to import such data from a GIS shapefile).")
+    #shape <- sf::st_read(system.file("files/shapefiles/world-countries.shp", package = "geoGraph"))
+    shape <- rnaturalearth::ne_countries(scale="medium", returnclass = "sf")
+    sf::sf_use_s2(FALSE)
+  }
+
+  ## TODO if the shape is null, we should throw an error!!!
+  if (!is.null(shape)) {
+    if (!inherits(shape, "sf")) {
+      if (inherits(shape, "SpatialPolygonsDataFrame")){
+        shape <- sf::st_as_sf(shape)
+      } else {
+        stop("shape must be a sf object \n(see st_read in sf to import such data from a GIS shapefile).")
+      }
     }
 
     ## plot background
-    plot(shape, col = bg.col, border = border.col, xlim = xlim, ylim = ylim)
+    plot(sf::st_geometry(shape), col = bg.col, border = border.col, xlim = xlim, ylim = ylim)
 
     ## subset of points in area
     toKeep <- isInArea(x, reg = "current", res.type = "character")