Merge pull request PecanProject#3228 from istfer/rgdal_data_atmosphere

Remove rgdal and maptools from data.atmosphere

docker/depends/pecan.depends.R

@@ -9,6 +9,7 @@ Sys.setenv(RLIB = rlib)
 
 # install remotes first in case packages are references in dependencies
 remotes::install_github(c(
+'adokter/suntools',
 'araiho/linkages_package',
 'chuhousen/amerifluxr',
 'ebimodeling/[email protected]',
@@ -76,7 +77,6 @@ wanted <- c(
 'magic',
 'magrittr',
 'maps',
-'maptools',
 'markdown',
 'MASS',
 'Matrix',
@@ -113,7 +113,6 @@ wanted <- c(
 'reshape',
 'reshape2',
 'reticulate',
-'rgdal',
 'rjags',
 'rjson',
 'rlang',
@@ -130,6 +129,7 @@ wanted <- c(
 'stats',
 'stringi',
 'stringr',
+'suntools',
 'swfscMisc',
 'terra',
 'testthat',

modules/data.atmosphere/DESCRIPTION

@@ -36,7 +36,6 @@ Imports:
     jsonlite,
     lubridate (>= 1.6.0),
     magrittr,
-    maptools,
     MASS,
     mgcv,
     ncdf4 (>= 1.15),
@@ -49,10 +48,12 @@ Imports:
     raster,
     REddyProc,
     reshape2,
-    rgdal,
     rlang (>= 0.2.0),
+    sf,
     sp,
     stringr (>= 1.1.0),
+    suntools,
+    terra,
     testthat (>= 2.0.0),
     tibble,
     tidyr,
@@ -69,6 +70,7 @@ Suggests:
     progress,
     reticulate
 Remotes:
+    github::adokter/suntools,
     github::chuhousen/amerifluxr,
     github::ropensci/geonames,
     github::ropensci/nneo

modules/data.atmosphere/NAMESPACE

@@ -113,5 +113,5 @@ export(write_noaa_gefs_netcdf)
 import(dplyr)
 import(tidyselect)
 importFrom(magrittr,"%>%")
-importFrom(rgdal,checkCRSArgs)
 importFrom(rlang,.data)
+importFrom(sf,st_crs)

modules/data.atmosphere/R/GEFS_helper_functions.R

@@ -243,25 +243,30 @@ process_gridded_noaa_download <- function(lat_list,
 
     for(hr in 1:length(curr_hours)){
       file_name <- paste0(base_filename2, curr_hours[hr])
+      grib_file_name <- paste0(working_directory,"/", file_name,".grib")
 
-      if(file.exists(paste0(working_directory,"/", file_name,".grib"))){
-        grib <- rgdal::readGDAL(paste0(working_directory,"/", file_name,".grib"), silent = TRUE)
-        lat_lon <- sp::coordinates(grib)
+      if(file.exists(grib_file_name)){
+        grib_data <- terra::rast(grib_file_name)
+
+        ## Convert to data frame
+        grib_data_df <- terra::as.data.frame(grib_data, xy=TRUE)
+        lat_lon <- grib_data_df[, c("x", "y")]
+
         for(s in 1:length(site_id)){
 
           index <- which(lat_lon[,2] == lats[s] & lat_lon[,1] == lons[s])
 
-          pressfc[s, hr]  <- grib$band1[index]
-          tmp2m[s, hr] <- grib$band2[index]
-          rh2m[s, hr]  <- grib$band3[index]
-          ugrd10m[s, hr]  <- grib$band4[index]
-          vgrd10m[s, hr]  <- grib$band5[index]
+          pressfc[s, hr]  <- grib_data_df$`SFC=Ground or water surface; Pressure [Pa]`[index]
+          tmp2m[s, hr]    <- grib_data_df$`2[m] HTGL=Specified height level above ground; Temperature [C]`[index]
+          rh2m[s, hr]     <- grib_data_df$`2[m] HTGL=Specified height level above ground; Relative humidity [%]`[index]
+          ugrd10m[s, hr]  <- grib_data_df$`10[m] HTGL=Specified height level above ground; u-component of wind [m/s]`[index]
+          vgrd10m[s, hr]  <- grib_data_df$`10[m] HTGL=Specified height level above ground; v-component of wind [m/s]`[index]
 
           if(curr_hours[hr] != "000"){
-            apcpsfc[s, hr]  <- grib$band6[index]
-            tcdcclm[s, hr]  <-  grib$band7[index]
-            dswrfsfc[s, hr]  <- grib$band8[index]
-            dlwrfsfc[s, hr]  <- grib$band9[index]
+            apcpsfc[s, hr]  <- grib_data_df$`SFC=Ground or water surface; 03 hr Total precipitation [kg/(m^2)]`[index]
+            tcdcclm[s, hr]  <- grib_data_df$`RESERVED(10) (Reserved); Total cloud cover [%]`[index]
+            dswrfsfc[s, hr] <- grib_data_df$`SFC=Ground or water surface; Downward Short-Wave Rad. Flux [W/(m^2)]`[index]
+            dlwrfsfc[s, hr] <- grib_data_df$`SFC=Ground or water surface; Downward Long-Wave Rad. Flux [W/(m^2)]`[index]
           }
         }
       }

modules/data.atmosphere/R/download.NARR_site.R

@@ -465,9 +465,9 @@ latlon2narr <- function(nc, lat.in, lon.in) {
 #' @inheritParams get_NARR_thredds
 #' @return `sp::SpatialPoints` object containing transformed x and y
 #' coordinates, in km, which should match NARR coordinates
-#' @importFrom rgdal checkCRSArgs
+#' @importFrom sf st_crs
   # ^not used directly here, but needed by sp::CRS.
-  # sp lists rgdal in Suggests rather than Imports,
+  # sp lists sf in Suggests rather than Imports,
   # so importing it here to ensure it's available at run time
 #' @author Alexey Shiklomanov
 #' @export

modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R

@@ -216,11 +216,11 @@ met_temporal_downscale.Gaussian_ensemble <- function(in.path, in.prefix, outfold
       day <- as.POSIXct(sprintf("%s 12:00:00", date), tz = tz)
       sequence <- seq(from = day, length.out = span, by = "days")
 
-      sunrise <- maptools::sunriset(lon.lat, sequence, direction = "sunrise", 
+      sunrise <- suntools::sunriset(lon.lat, sequence, direction = "sunrise", 
                                     POSIXct.out = TRUE)
-      sunset <- maptools::sunriset(lon.lat, sequence, direction = "sunset", 
+      sunset <- suntools::sunriset(lon.lat, sequence, direction = "sunset", 
                                    POSIXct.out = TRUE)
-      solar_noon <- maptools::solarnoon(lon.lat, sequence, POSIXct.out = TRUE)
+      solar_noon <- suntools::solarnoon(lon.lat, sequence, POSIXct.out = TRUE)
 
       data.frame(date = as.Date(sunrise$time), sunrise = as.numeric(format(sunrise$time, "%H%M")), 
                  solarnoon = as.numeric(format(solar_noon$time, "%H%M")), 

modules/data.atmosphere/tests/Rcheck_reference.log

@@ -76,13 +76,13 @@ Found the following (possibly) invalid URLs:
 The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... WARNING
-Imports includes 39 non-default packages.
+Imports includes 40 non-default packages.
 Importing from so many packages makes the package vulnerable to any of
 them becoming unavailable.  Move as many as possible to Suggests and
 use conditionally.
 
 * checking package dependencies ... NOTE
-Imports includes 39 non-default packages.
+Imports includes 40 non-default packages.
 Importing from so many packages makes the package vulnerable to any of
 them becoming unavailable.  Move as many as possible to Suggests and
 use conditionally.