Merge branch 'adopt-geonetwork'

DESCRIPTION

 Package: mapMCDA
 Title: Produce an epidemiological risk map by weighting multiple risk factors
-Version: 0.3.2.9000
+Version: 0.3.3
 Date: 2018-06-27
 Authors@R: c(
   person("Elena", "Arsevska", email = "elena.arsevska@cirad.fr", role = c("ctb")),
@@ -22,6 +22,7 @@ Imports:
   deldir,
   geojsonio,
   geojsonlint,
+  geonetwork,
   igraph,
   methods,
   maps,

NAMESPACE

@@ -39,6 +39,7 @@ importFrom(igraph,edge_attr_names)
 importFrom(igraph,gorder)
 importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,is.weighted)
+importFrom(igraph,vertex.attributes)
 importFrom(raster,intersect)
 importFrom(rgeos,gUnaryUnion)
 importFrom(stats,setNames)

NEWS.md

 # mapMCDA 0.3.0.9000
 
+* Plot geographic networks (#13)
+
 * Export CSV with units and risk categories (#10)
 
 * Animal mobility data as a specific input type (#9)

R/network.R

@@ -113,7 +113,7 @@ must be respected:",
     stop("Node(s) ", idx.nodes, " have inconsistent coordinates in the dataset.")
   }
   
-  ans <- igraph::graph_from_data_frame(e_list, vertices = v_coord, directed = TRUE)
+  ans <- geonetwork::geonetwork(e_list, v_coord, directed = TRUE)
   
   ## If there are edge attributes, it must be only one, and must be
   ## the weight.
@@ -125,8 +125,8 @@ must be respected:",
   return(ans)
 }
 
-# ' @import igraph
-setOldClass("igraph")
+# ' @import geonetwork
+setOldClass("geonetwork")
 
 
 #' Rasterize a geographic network
@@ -140,7 +140,7 @@ setOldClass("igraph")
 #' If you want the unweighted importance, remove the weight attribute
 #' from the graph with \code{igraph::delete_edge_attr(x, "weight")}.
 #' 
-#' @param x a geographic network (a igraph object with node attributes
+#' @param x a geographic network (a geonetwork object with node attributes
 #'   "Lon" and "Lat" in the WGS84 reference system)
 #' @param y a Raster* or a SpatialPolygons* object.
 #' @param field character. The attribute of the network nodes to be
@@ -152,13 +152,14 @@ setOldClass("igraph")
 #' @param ... Other arguments passed on to
 #'   \code{\link[raster]{rasterize}}.
 #' @importMethodsFrom raster rasterize
+#' @importFrom igraph vertex.attributes
 #' @importFrom stats setNames
 #' @export
 #' @name rasterize_geonetwork
 #' @rdname rasterize_geonetwork
-#' @aliases rasterize,igraph,Raster-method
+#' @aliases rasterize,geonetwork,Raster-method
 setMethod(
-  rasterize, c("igraph", "Raster"),
+  rasterize, c("geonetwork", "Raster"),
   {
     function(
       x, y, field = "importance", ...) {
@@ -177,7 +178,13 @@ setMethod(
         c("name", "importance")
       )
       
-      nodes <- as.data.frame(igraph::vertex.attributes(x))
+      nodes <- cbind(
+        as.data.frame(igraph::vertex.attributes(x)),
+        setNames(
+          data.frame(sf::st_coordinates(attr(x, "geom_node"))),
+          c("Lon", "Lat")
+        )
+      )
       
       nodes <- merge(nodes, node_importance, by = "name", all.y=FALSE)
       
@@ -198,10 +205,10 @@ setMethod(
 #' @param res numeric vector of length 2. Resolution in Lon/Lat of
 #'   rasterisation.
 #' @rdname rasterize_geonetwork
-#' @aliases rasterize,igraph,SpatialPolygons-method
+#' @aliases rasterize,geonetwork,SpatialPolygons-method
 #' @export
 setMethod(
-  rasterize, c("igraph", "SpatialPolygons"),
+  rasterize, c("geonetwork", "SpatialPolygons"),
   {
     function (x, y, res = resolution(y, min_ncells = 100), ...) {
       

inst/interface/server.R

@@ -447,8 +447,17 @@ server <- function(input, output, session) {
       
     }
     
-    plot(finalLayer[[indRawLay]])
-
+    ## Plot the epidemiological units lightly in the background
+    epidUnitLayer <- isolate(curEpidUnitLayer())
+    
+    if(is.null(epidUnitLayer)) {
+      addsetting = FALSE
+    } else {
+      plot(epidUnitLayer[[indRawLay]], border = "lightgray")
+      addsetting = TRUE
+    }
+    
+    plot(finalLayer[[indRawLay]], add = addsetting)
 
   })
   
@@ -715,7 +724,7 @@ server <- function(input, output, session) {
   })
   
   
-  ##### Render for display of final unit raster ####
+  ##### Render for display of final unit vector ####
   
   output$resultUnitDisplay <- renderPlot({
     

man/rasterize_geonetwork.Rd

@@ -3,17 +3,17 @@
 \docType{methods}
 \name{rasterize_geonetwork}
 \alias{rasterize_geonetwork}
-\alias{rasterize,igraph,Raster-method}
-\alias{rasterize,igraph,SpatialPolygons-method}
+\alias{rasterize,geonetwork,Raster-method}
+\alias{rasterize,geonetwork,SpatialPolygons-method}
 \title{Rasterize a geographic network}
 \usage{
-\S4method{rasterize}{igraph,Raster}(x, y, field = "importance", ...)
+\S4method{rasterize}{geonetwork,Raster}(x, y, field = "importance", ...)
 
-\S4method{rasterize}{igraph,SpatialPolygons}(x, y, res = resolution(y,
-  min_ncells = 100), ...)
+\S4method{rasterize}{geonetwork,SpatialPolygons}(x, y,
+  res = resolution(y, min_ncells = 100), ...)
 }
 \arguments{
-\item{x}{a geographic network (a igraph object with node attributes
+\item{x}{a geographic network (a geonetwork object with node attributes
 "Lon" and "Lat" in the WGS84 reference system)}
 
 \item{y}{a Raster* or a SpatialPolygons* object.}

tests/testthat/test-load.R

@@ -35,17 +35,12 @@ test_that("load_dir() skips unknnown file formats", {
   res <- load_dir(testdata)
   
   test_files <- c("mobility", "points", "points", "raster")
+  exp_classes <- c("geonetwork",  "SpatialPointsDataFrame", "SpatialPointsDataFrame", "RasterLayer")
   
   expect_is(res, "list")
   expect_identical(names(res), test_files)
   
-  expect_identical(
-    vapply(res, class, "char")[test_files],
-    setNames(
-      c("igraph",  "SpatialPointsDataFrame", "SpatialPointsDataFrame", "RasterLayer"),
-      test_files
-    )
-  )
+  expect_true(all(mapply(inherits, res, exp_classes)))
   
 })