added 'MACCITY' to read

R/read.R

@@ -1,14 +1,16 @@
 #' Read NetCDF data from global inventaries
 #'
-#' @description Read data from global inventories, can read several files and merge into one emission
-#' and/or split into several species (speciation process)
+#' @description Read data from global inventories, can read several files and merge into one
+#' emission and/or split into several species (speciation process)
 #'
 #' @return Matrix or raster
 #'
 #' @param file file name or names (variables are summed)
 #' @param coef coef to merge different sources into one emission
 #' @param spec numeric speciation vector to split emission into different species
-#' @param version inventory name and verion
+#' @param version inventory name 'EDGAR' or 'MACCITY'
+#' @param month the desired month of the inventary (MACCITY)
+#' @param categories considered categories (MACCITY variable names), empty for all
 #' @param as_raster return a raster (defoult) or matrix (with units)
 #' @param verbose display additional information
 #'
@@ -22,7 +24,21 @@
 #'
 #' @seealso \code{\link{species}}
 #'
-#' @source Read abbout EDGAR at http://edgar.jrc.ec.europa.eu
+#' @source Read abbout EDGAR at http://edgar.jrc.ec.europa.eu and MACCITY at
+#' http://accent.aero.jussieu.fr/MACC_metadata.php
+#'
+#' @references
+#' Janssens-Maenhout, G., Dentener, F., Van Aardenne, J., Monni, S., Pagliari, V., Orlandini,
+#' L., ... & Wankmüller, R. (2012). EDGAR-HTAP: a harmonized gridded air pollution emission dataset
+#' based on national inventories. European Commission Joint Research Centre Institute for
+#' Environment and Sustainability. JRC 68434 UR 25229 EUR 25229, ISBN 978-92-79-23123-0.
+#'
+#' Lamarque, J.-F., Bond, T. C., Eyring, V., Granier, C., Heil, A., Klimont, Z., Lee, D., Liousse,
+#' C., Mieville, A., Owen, B., Schultz, M. G., Shindell, D., Smith, S. J., Stehfest, E.,
+#' Van Aardenne, J., Cooper, O. R., Kainuma, M., Mahowald, N., McConnell, J. R., Naik, V.,
+#' Riahi, K., and van Vuuren, D. P.: Historical (1850-2000) gridded anthropogenic and biomass
+#' burning emissions of reactive gases and aerosols: methodology and application,
+#' Atmos. Chem. Phys., 10, 7017-7039, doi:10.5194/acp-10-7017-2010, 2010.
 #'
 #' @examples \donttest{
 #' d1     <- gridInfo(paste(system.file("extdata", package = "EmissV"),"/wrfinput_d01",sep=""))
@@ -38,37 +54,82 @@
 #'}
 
 read <- function(file = file.choose(), coef = rep(1,length(file)), spec = NULL,
-                 version = "EDGAR 4.3.1 v2", as_raster = T, verbose = T){
+                 version = "EDGAR", month = 1, categories, as_raster = T, verbose = T){
 
   if(is.list(coef))
     coef <- as.numeric(as.character(unlist(coef))) #nocov
   if(is.list(spec))
     spec <- as.numeric(as.character(unlist(spec))) #nocov
 
 
-  if(version == "EDGAR 4.3.1 v2"){
+  if(version == "MACCITY"){                        # nocov start
     ed   <- ncdf4::nc_open(file[1])
     name <- names(ed$var)
+    if(verbose)
+      cat(paste0("reading",
+                 " (",version,")",
+                 " emissions for ",
+                 format(ISOdate(1996,month,1),"%B"),
+                 ", output unit is g m-2 s-1 ...\n"))
     var  <- ncdf4::ncvar_get(ed,name[1])
+    var  <- var[,,month]
     varall <- units::as_units(0.0 * var,"g m-2 s-1")
     var  <- apply(var,1,rev)
     if(as_raster){
-      # r  <- raster::raster(x = 1000 * var,xmn=-180,xmx=180,ymn=-90,ymx=90)
-      # rz <- raster::raster(0.0 * var,xmn=-180,xmx=180,ymn=-90,ymx=90)
       r  <- raster::raster(x = 1000 * var,xmn=0,xmx=360,ymn=-90,ymx=90)
       rz <- raster::raster(0.0 * var,xmn=0,xmx=360,ymn=-90,ymx=90)
       values(rz) <- rep(0,ncell(rz))
       raster::crs(rz) <- "+proj=longlat +ellps=GRS80 +no_defs"
     }
 
+    for(i in 1:length(file)){
+      cat(paste0("from ",file[i]),"x",sprintf("%02.2f",coef[i]),"\n")
+      ed   <- ncdf4::nc_open(file[i])
+      if(missing(categories)){
+        name <- names(ed$var)
+      }else{
+        name <- categories
+      }
+      for(j in 1:length(name)){
+        cat(paste0("using ",name[j]),"\n")
+        var_a  <- ncdf4::ncvar_get(ed,name[j])[,,month]
+        var_a  <- units::as_units(var_a,"g m-2 s-1")
+        var_a  <- apply(var_a,1,rev)
+        var    <- var + var_a
+      }
+      if(as_raster){
+        r   <- raster::raster(x = 1000 * var,xmn=0,xmx=360,ymn=-90,ymx=90)
+        raster::crs(r) <- "+proj=longlat +ellps=GRS80 +no_defs"
+        names(r) <- name[1]
+        rz       <- rz + r * coef[i]
+      }else{
+        var    <- units::set_units(1000 * var,"g m-2 s-1")
+        return(varall)
+        varall <- varall + var * coef[i]
+      }
+    }
+  }                                                # nocov end
+
+  if(version == "EDGAR"){
+    ed   <- ncdf4::nc_open(file[1])
+    name <- names(ed$var)
     if(verbose)
-      cat(paste0("reading ",name," (",version,") units are g m-2 s-1 ...\n"))
+      cat(paste0("reading ",name," (",version,") output unit is g m-2 s-1 ...\n"))
+    var  <- ncdf4::ncvar_get(ed,name)
+    varall <- units::as_units(0.0 * var,"g m-2 s-1")
+    var  <- apply(var,1,rev)
+    if(as_raster){
+      r  <- raster::raster(x = 1000 * var,xmn=0,xmx=360,ymn=-90,ymx=90)
+      rz <- raster::raster(0.0 * var,xmn=0,xmx=360,ymn=-90,ymx=90)
+      values(rz) <- rep(0,ncell(rz))
+      raster::crs(rz) <- "+proj=longlat +ellps=GRS80 +no_defs"
+    }
 
     for(i in 1:length(file)){
       cat(paste0("from ",file[i]),"x",sprintf("%02.2f",coef[i]),"\n")
       ed   <- ncdf4::nc_open(file[i])
       name <- names(ed$var)
-      var  <- ncdf4::ncvar_get(ed,name[1])
+      var  <- ncdf4::ncvar_get(ed,name)
       if(as_raster){
         var <- apply(var,1,rev)
         r   <- raster::raster(x = 1000 * var,xmn=0,xmx=360,ymn=-90,ymx=90)
@@ -80,40 +141,33 @@ read <- function(file = file.choose(), coef = rep(1,length(file)), spec = NULL,
         varall <- varall + var * coef[i]
       }
     }
-    if(as_raster){
+  }
 
-      if(is.null(spec)){
-        return(raster::rotate(rz))
-      }else{
-        if(verbose)  cat("using the following speciation:\n") # nocov start
-        rz_spec <- list()
-        for(i in 1:length(spec)){
-          if(verbose) cat(paste0(names(spec)[i]," = ",spec[i],"\n"))
-          rz_spec[[i]] <- raster::rotate(rz * spec[i])
-        }
-        names(rz_spec) <- names(spec)
-        return(rz_spec)                                      # nocov end
+  if(as_raster){
+    if(is.null(spec)){
+      return(raster::rotate(rz))
+    }else{
+      if(verbose)  cat("using the following speciation:\n") # nocov start
+      rz_spec <- list()
+      for(i in 1:length(spec)){
+        if(verbose) cat(paste0(names(spec)[i]," = ",spec[i],"\n"))
+        rz_spec[[i]] <- raster::rotate(rz * spec[i])
       }
+      names(rz_spec) <- names(spec)
+      return(rz_spec)                                      # nocov end
+    }
+  }else{
+    if(is.null(spec)){
+      return(varall)
     }else{
-      if(is.null(spec)){
-        return(varall)
-      }else{
-        if(verbose)  cat("using the following speciation:\n") # nocov start
-        var_spec <- list()
-        for(i in 1:length(spec)){
-          if(verbose) cat(paste0(names(spec)[i]," = ",spec[i],"\n"))
-          var_spec[[i]] <- varall * spec[i]
-        }
-        names(var_spec) <- names(spec)
-        return(var_spec)                                     # nocov end
+      if(verbose)  cat("using the following speciation:\n") # nocov start
+      var_spec <- list()
+      for(i in 1:length(spec)){
+        if(verbose) cat(paste0(names(spec)[i]," = ",spec[i],"\n"))
+        var_spec[[i]] <- varall * spec[i]
       }
+      names(var_spec) <- names(spec)
+      return(var_spec)                                     # nocov end
     }
   }
-  # if(version == "osm"){
-  #   cat(paste("reading osm data from",file,"\n"))
-  #   roads <- osmar::get_osm(osmar::complete_file(),source = osmar::osmsource_file(file))
-  #   road_lines <- osmar::as_sp(roads,what = "lines")
-  #   roads <- sf::st_as_sf(road_lines)
-  #   return(roads)
-  # }
 }