- removed remain dependencies of sp package

- removed suggest packages: osmar,RCurl,rgdal
atmoschem · Mar 24, 2023 · 5730129 · 5730129
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: EmissV
 Title: Tools for Create Emissions for Air Quality Models
-Date: 2022-05-31
-Version: 0.665.6.3
+Date: 2023-03-24
+Version: 0.665.6.6
 Authors@R: c(
   person(given = "Daniel",
          family = "Schuch",
@@ -25,14 +25,11 @@ Description: Processing tools to create emissions for use in numerical air
   such as satellite images (Martins et al, 2012) <doi:10.3389/fenvs.2015.00009> 
   or openstreetmap data (Andrade et al, 2015) <doi:10.3389/fenvs.2015.00009>.
 Depends: R (>= 3.4)
-Imports: ncdf4, units(>= 0.5-1), raster, sp, sf, methods, data.table
+Imports: ncdf4, units(>= 0.5-1), raster, sf, methods, data.table
 Suggests: 
     testthat (>= 2.1.0),
     covr,
-    osmar,
-    RCurl,
-    lwgeom,
-    rgdal
+    lwgeom
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

diff --git a/NAMESPACE b/NAMESPACE
@@ -15,7 +15,6 @@ export(vehicles)
 import(ncdf4)
 import(raster)
 import(sf)
-import(sp)
 import(units)
 importFrom(data.table,.SD)
 importFrom(data.table,data.table)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+## Version: 0.665.6.6 (2023-03-24)
+- removed remain dependencies of sp package
+- removed suggest packages: osmar,RCurl,rgdal
+- updated on examples, documentation and site
+
 ## Version: 0.665.6.2 (2022-02-19)
 - update in gridInfo cen_lon
 

diff --git a/R/areaSouce.R b/R/areaSouce.R
@@ -13,7 +13,7 @@
 #'
 #' @export
 #'
-#' @import raster sp sf
+#' @import raster sf
 #'
 #' @examples
 #' shape  <- raster::shapefile(paste(system.file("extdata", package = "EmissV"),
@@ -24,12 +24,8 @@
 #' grid   <- gridInfo(paste(system.file("extdata", package = "EmissV"),"/wrfinput_d02",sep=""))
 #' SP     <- areaSource(shape,raster,grid,name = "SPMA")
 #' \donttest{
-#' sp::spplot(SP,scales = list(draw=TRUE),ylab="Lat",xlab="Lon",
-#'            main=list(label="Spatial Distribution by Lights for Sao Paulo - Brazil"),
-#'            col.regions = c("#031638","#001E48","#002756","#003062",
-#'                            "#003A6E","#004579","#005084","#005C8E",
-#'                            "#006897","#0074A1","#0081AA","#008FB3",
-#'                            "#009EBD","#00AFC8","#00C2D6","#00E3F0"))
+#' raster::plot(SP,ylab="Lat",xlab="Lon",
+#'              main ="Spatial Distribution by Lights for Sao Paulo - Brazil")
 #'}
 #'
 #'@source Data avaliable \url{https://www.ospo.noaa.gov/Operations/DMSP/index.html}
@@ -41,7 +37,8 @@ areaSource <- function(s,r,grid = NA,name = "",as_frac=FALSE,verbose = TRUE){
     cat(paste("processing ",name,"area ... \n",sep = ""))
   }
 
-  sp <- suppressWarnings( raster::mask(r,sp::spTransform(s,sp::CRS(sp::proj4string(r)))) )
+  # sp <- suppressWarnings( raster::mask(r,sp::spTransform(s,sp::CRS(sp::proj4string(r)))) )
+  sp <- suppressWarnings( raster::mask(r,sf::st_transform(sf::st_as_sf(s),crs = raster::crs(r,asText=TRUE))))
 
   if(!is.na(grid[1])){
     if(grid$map_proj == 1){

diff --git a/R/emission.R b/R/emission.R
@@ -29,7 +29,7 @@
 #'
 #' @export
 #'
-#' @import units raster sp
+#' @import units raster
 #'
 #' @examples
 #' fleet  <- vehicles(example = TRUE)
@@ -107,14 +107,20 @@ emission <- function(inventory = NULL,grid,mm = 1, aerosol = FALSE,check = TRUE,
         legenda <- paste("Emissions of", pol ,"[",units::deparse_unit(VAR_e),"]")
       }
 
-      a <- sp::spplot(r,scales = list(draw=TRUE),ylab="Lat",xlab="Lon",
-                      main=list(label=legenda),
-                      col.regions = c("#031638","#001E48","#002756","#003062",
-                                      "#003A6E","#004579","#005084","#005C8E",
-                                      "#006897","#0074A1","#0081AA","#008FB3",
-                                      "#009EBD","#00AFC8","#00C2D6","#00E3F0"))
+      # a <- sp::spplot(r,scales = list(draw=TRUE),ylab="Lat",xlab="Lon",
+      #                 main=list(label=legenda),
+      #                 col.regions = c("#031638","#001E48","#002756","#003062",
+      #                                 "#003A6E","#004579","#005084","#005C8E",
+      #                                 "#006897","#0074A1","#0081AA","#008FB3",
+      #                                 "#009EBD","#00AFC8","#00C2D6","#00E3F0"))
+      #
+      # print(a)
 
-      print(a)
+      plot(r,main = legenda,
+           col = c("#031638","#001E48","#002756","#003062",
+                   "#003A6E","#004579","#005084","#005C8E",
+                   "#006897","#0074A1","#0081AA","#008FB3",
+                   "#009EBD","#00AFC8","#00C2D6","#00E3F0"))
     }
     if(check){
       VAR_e <- check_positive(VAR_e,pol)
@@ -153,7 +159,8 @@ emission <- function(inventory = NULL,grid,mm = 1, aerosol = FALSE,check = TRUE,
     area <- unname(area)
 
     if(length(area) > 1){
-      VAR_e  <- do.call(sp::merge,area)
+      # VAR_e  <- do.call(sp::merge,area)
+      VAR_e  <- Reduce(raster::merge, area)
     }else{
       VAR_e  <- area[[1]]
     }
@@ -204,14 +211,20 @@ emission <- function(inventory = NULL,grid,mm = 1, aerosol = FALSE,check = TRUE,
     raster::values(r) <- as.matrix(as.numeric(VAR_e),ncol = col,nrow = row,byrow = TRUE)
     r                 <- raster::flip(r,2)
 
-    a <- sp::spplot(r,scales = list(draw=TRUE),ylab="Lat",xlab="Lon",
-                    main=list(label=paste("Emisions of", pol ,"[",deparse_unit(VAR_e),"]")),
-                    col.regions = c("#031638","#001E48","#002756","#003062",
-                                    "#003A6E","#004579","#005084","#005C8E",
-                                    "#006897","#0074A1","#0081AA","#008FB3",
-                                    "#009EBD","#00AFC8","#00C2D6","#00E3F0"))
+    # a <- sp::spplot(r,scales = list(draw=TRUE),ylab="Lat",xlab="Lon",
+    #                 main=list(label=paste("Emisions of", pol ,"[",deparse_unit(VAR_e),"]")),
+    #                 col.regions = c("#031638","#001E48","#002756","#003062",
+    #                                 "#003A6E","#004579","#005084","#005C8E",
+    #                                 "#006897","#0074A1","#0081AA","#008FB3",
+    #                                 "#009EBD","#00AFC8","#00C2D6","#00E3F0"))
+    # print(a)
+
+    plot(r,#main = legenda,
+         col = c("#031638","#001E48","#002756","#003062",
+                 "#003A6E","#004579","#005084","#005C8E",
+                 "#006897","#0074A1","#0081AA","#008FB3",
+                 "#009EBD","#00AFC8","#00C2D6","#00E3F0"))
 
-    print(a)
   }
   if(check){
     VAR_e <- check_positive(VAR_e,pol)

diff --git a/R/gridinfo.R b/R/gridinfo.R
@@ -10,7 +10,7 @@
 #'
 #' @note just WRF-Chem is suported by now
 #'
-#' @import ncdf4 sp
+#' @import ncdf4
 #'
 #' @export
 #'
@@ -23,16 +23,15 @@
 #'                                       "/wrfinput_d03",sep=""))
 #' names(grid_d1)
 #' # for plot the shapes
-#' library(sp)
 #' shape   <- raster::shapefile(paste0(system.file("extdata", package = "EmissV"),
 #'                                                 "/BR.shp"))
-#' plot(shape,xlim = c(-55,-40),ylim = c(-30,-15), main="3 nested domains")
+#' raster::plot(shape,xlim = c(-55,-40),ylim = c(-30,-15), main="3 nested domains")
 #' axis(1); axis(2); box(); grid()
-#' lines(grid_d1$Box, col = "red")
+#' lines(grid_d1$boundary, col = "red")
 #' text(grid_d1$xlim[2],grid_d1$Ylim[1],"d1",pos=4, offset = 0.5)
-#' lines(grid_d2$Box, col = "red")
+#' lines(grid_d2$boundary, col = "red")
 #' text(grid_d2$xlim[2],grid_d2$Ylim[1],"d2",pos=4, offset = 0.5)
-#' lines(grid_d3$Box, col = "red")
+#' lines(grid_d3$boundary, col = "red")
 #' text(grid_d3$xlim[1],grid_d3$Ylim[2],"d3",pos=2, offset = 0.0)
 #'}
 
@@ -155,9 +154,12 @@ gridInfo <- function(file = file.choose(),z = FALSE,verbose = TRUE){
                             y = c(ly[2],ly[2],ly[1],ly[1],ly[2])),
                  boundary = list(x = c(lon[1,],lon[,nxj],rev(lon[nxi,]),rev(lon[,1])),
                                  y = c(lat[1,],lat[,nxj],rev(lat[nxi,]),rev(lat[,1]))),
-                 poligon = sp::Polygon(matrix(c( c(lon[1,],lon[,nxj],rev(lon[nxi,]),rev(lon[,1])),
-                                                 c(lat[1,],lat[,nxj],rev(lat[nxi,]),rev(lat[,1]))),
-                                              ncol = 2)),
+                 # polygon = sp::Polygon(matrix(c( c(lon[1,],lon[,nxj],rev(lon[nxi,]),rev(lon[,1])),
+                 #                                 c(lat[1,],lat[,nxj],rev(lat[nxi,]),rev(lat[,1]))),
+                 #                              ncol = 2)),
+                 polygon  = sf::st_polygon(x = list(matrix(c( c(lon[1,],lon[,nxj],rev(lon[nxi,]),rev(lon[,1])),
+                                                              c(lat[1,],lat[,nxj],rev(lat[nxi,]),rev(lat[,1]))),
+                                                           ncol = 2))),
                  map_proj    = map_proj,
                  coords      = coords,
                  geogrd.proj = geogrd.proj)

diff --git a/R/lineSource.R b/R/lineSource.R
@@ -34,25 +34,17 @@
 #'
 #' @seealso \code{\link{gridInfo}} and \code{\link{rasterSource}}
 #'
-#'
 #' @examples \donttest{
-#' roads <- osmar::get_osm(osmar::complete_file(),
-#'                         source = osmar::osmsource_file(paste(system.file("extdata",
-#'                         package="EmissV"),"/streets.osm.xz",sep="")))
-#' road_lines <- osmar::as_sp(roads,what = "lines")
-#'
-#' # selecting only 2 roads
-#' road_lines <- road_lines[1:2,]
-#'
-#' roads <- sf::st_as_sf(road_lines)
-#'
+#' # loading a shapefile with osm data for sao paulo metropolitan area
+#' roads <- sf::st_read(paste0(system.file("extdata",package="EmissV"),"/streets.shp"))
 #' d3    <- gridInfo(paste0(system.file("extdata", package = "EmissV"),"/wrfinput_d03"))
 #'
-#' roadLength <- lineSource(roads,d3,as_raster=TRUE)
-#' sp::spplot(roadLength,
-#'            scales = list(draw=TRUE),
-#'            ylab="Lat", xlab="Lon",main="Length of roads",
-#'            sp.layout=list("sp.lines", road_lines))
+#' # calculating only for 2 streets
+#' roadLength <- lineSource(roads[1:2,],d3,as_raster=TRUE)
+#'
+#' # to generate a quick plot
+#' raster::plot(roadLength,ylab="Lat", xlab="Lon",main="Length of roads")
+#' # lines(road_lines)
 #' }
 #'
 #'

diff --git a/R/pointSource.R b/R/pointSource.R
@@ -8,7 +8,7 @@
 #'
 #' @return a raster
 #'
-#' @import sp raster
+#' @import raster
 #'
 #' @export
 #'
@@ -22,8 +22,8 @@
 #'
 #' p_emissions <- pointSource(emissions = p, grid = d1)
 #' \donttest{
-#' sp::spplot(p_emissions,scales = list(draw=TRUE), ylab="Lat", xlab="Lon",
-#'            main = "3 point sources for domain d1")
+#' raster::plot(p_emissions,ylab="Lat", xlab="Lon",
+#'              main = "3 point sources for domain d1")
 #'}
 #'
 #' @seealso \code{\link{gridInfo}} and \code{\link{rasterSource}}
@@ -40,8 +40,9 @@ pointSource <- function(emissions, grid, verbose = TRUE){
     values(emis) <- rep(0,ncell(emis))
 
     for(i in 1:length(emissions[[1]])){
-      id.cell <- extract(emis,SpatialPoints(cbind(emissions$lon[i],emissions$lat[i])),
-                         cellnumbers=TRUE)[1]
+      id.cell <- raster::extract(emis,
+                                 cbind(emissions$lon[i],emissions$lat[i]),
+                                 cellnumbers=TRUE)[1]
       if(verbose){
         xy <- xyFromCell(emis,id.cell)
         lon <- xy[1]
@@ -66,7 +67,8 @@ pointSource <- function(emissions, grid, verbose = TRUE){
     values(emis) <- rep(0,ncell(emis))
 
     for(i in 1:length(emissions[[1]])){
-      id.cell <- extract(emis,SpatialPoints(cbind(emissions$lon[i],emissions$lat[i])),
+      id.cell <- extract(emis,
+                         cbind(emissions$lon[i],emissions$lat[i]),
                          cellnumbers=TRUE)[1]
       altura  <- z[rowFromCell(emis, id.cell),rowFromCell(emis, id.cell),]
       if(verbose){

diff --git a/R/rasterSource.R b/R/rasterSource.R
@@ -16,7 +16,7 @@
 #'
 #' @export
 #'
-#' @import raster sp sf
+#' @import raster sf
 #'
 #' @examples
 #' grid  <- gridInfo(paste(system.file("extdata", package = "EmissV"),"/wrfinput_d01",sep=""))

diff --git a/R/read.R b/R/read.R
@@ -82,10 +82,13 @@
 #'              spec    = c(E_NO  = 0.9 ,   # 90% of NOx is NO
 #'                          E_NO2 = 0.1 ))  # 10% of NOx is NO2
 #' setwd(folder)
-#'
-#' sp::spplot(nox$E_NO, scales = list(draw=TRUE),
-#'            xlab="Lat", ylab="Lon",
-#'            main="NO emissions from EDGAR (in g / m2 s)")
+#' # creating a color scale
+#' cor <- colorRampPalette(colors = c(c("#031057", "#0522FC",
+#'                                      "#7E0AFA", "#EF0AFF",
+#'                                      "#FFA530", "#FFF957")))
+#' raster::plot(nox$E_NO,xlab="Lat", ylab="Lon",
+#'              col = cor(12),zlim = c(-6.5e-7,1.4e-5),
+#'              main="NO emissions from EDGAR (in g / m2 s)")
 #'
 #' d1  <- gridInfo(paste(system.file("extdata", package = "EmissV"),"/wrfinput_d01",sep=""))
 #' NO  <- emission(grid = d1, inventory = nox$E_NO, pol = "NO", mm = 30.01, plot = TRUE)