Merge pull request #3229 from istfer/rgdal_data_land

removed rgdal from data.land and data.remote

modules/data.land/DESCRIPTION

@@ -61,7 +61,6 @@ Suggests:
     PEcAn.settings,
     redland,
     raster,
-    rgdal,
     RPostgreSQL,
     testthat (>= 1.0.2)
 License: BSD_3_clause + file LICENSE

modules/data.land/R/gis.functions.R

@@ -68,14 +68,13 @@ shp2kml <- function(dir, ext, kmz = FALSE, proj4 = NULL, color = NULL, NameField
     # Read in shapefile(s) & get coordinates/projection info shp.file <-
     # readShapeSpatial(file.path(dir,i),verbose=TRUE) coordinates(test) <- ~X+Y
 
-    layers <- rgdal::ogrListLayers(file.path(dir, i))
-    info   <- rgdal::ogrInfo(file.path(dir, i), layers)
+    layers <- sf::st_layers(file.path(dir, i))
     # shp.file <- readOGR(file.path(dir,i),layer=layers) # no need to read in file
 
     # Display vector info to the console
     print("")
-    print(paste0("Input layers: ", layers))
-    print(paste0("Input projection info: ", info$p4s))
+    print(paste0("Input layers: ", layers$name))
+    print(paste0("Input projection info: ", layers$crs[[1]]$input))
     print("")
 
     # Write out kml/kmz using plotKML package if (is.null(color)){ color <- 'grey70' }
@@ -133,6 +132,7 @@ get.attributes <- function(file, coords) {
 
   #library(fields)
   #require(rgdal)
+  # note that OGR support is now provided by the sf and terra packages among others 
 
   # print('NOT IMPLEMENTED YET') subset_layer(file,coords)
 } # get.attributes

modules/data.remote/DESCRIPTION

@@ -20,14 +20,14 @@ Imports:
     PEcAn.utils,
     purrr,
     XML,
-    raster,
     sp,
     MODISTools (>= 1.1.0),
     reticulate,
     PEcAn.logger,
     magrittr,
     PEcAn.remote,
     stringr (>= 1.1.0),
+    terra,
     doParallel,
     parallel,
     foreach
@@ -36,7 +36,7 @@ Suggests:
     dplyr,
     ggplot2,
     lubridate,
-    rgdal,
+    raster,
     reshape,
     testthat (>= 1.0.2),
     tibble

modules/data.remote/R/NLCD.R

@@ -23,7 +23,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
 
     ## before downloading, check if the file already exists on this host
     if (!is.null(con)) {
-        library(PEcAn.DB)
+
         chk <- dbfile.check(type = "Input", id = input.id, con = con)
         if (nrow(chk) > 0) {
             machines <- db.query(paste("SELECT * from machines where id in (", 
@@ -68,11 +68,9 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
 ##' 
 ##' @description Based on codes from Christy Rollinson and from Max Joseph (http://mbjoseph.github.io/2014/11/08/nlcd.html)
 extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 2011) {
-    library(raster)
-    require(rgdal)
-
+
     if (!is.null(con)) {
-        library(PEcAn.DB)
+
         if (year == 2001) {
             input.id <- 1000000482
         } else if (year == 2011) {
@@ -104,21 +102,24 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         print(paste("File not found:", filename))
         return(NULL)
     }
-    nlcd <- raster(filename)
+
+    # WARNING: the following extraction previously used raster and sp package functions
+    # this new implementation with terra functions has not been thoroughly tested
+    nlcd <- terra::rast(filename)
 
     # transform points
-    sites <- SpatialPoints(coords = coords, proj4string = CRS("+proj=longlat +datum=WGS84"))
-    sites <- spTransform(sites, crs(nlcd))
+    sites <- terra::vect(coords, geom=c("long", "lat"), crs="+proj=longlat +datum=WGS84")
+    sites <- terra::buffer(sites, width=buffer)
 
     # extract
-    sum.raw <- table(extract(nlcd, sites, buffer = buffer))
+    sum.raw <- table(terra::extract(nlcd, sites))
     summ <- prop.table(sum.raw)
-    mydf <- data.frame(cover = names(summ), percent = as.vector(summ), count = as.vector(sum.raw))
+    mydf <- data.frame(cover.name = colnames(summ), percent = as.vector(summ), count = as.vector(sum.raw))
+    mydf <- mydf[mydf$count!=0,]
 
-    # land cover number to name conversions
-    cover.table <- nlcd@data@attributes[[1]]
-    cover.names <- cover.table[as.numeric(as.character(mydf$cover)) + 1, grep("Land", names(cover.table))]
-    mydf$cover.name <- cover.names
+    # land cover name to number conversions
+    nlcd_levels <- terra::levels(nlcd)[[1]]
+    mydf$cover  <- nlcd_levels$value[nlcd_levels$`Land Cover Class` %in% mydf$cover.name]
 
     return(mydf)
 } # extract_NLCD

modules/data.remote/R/download.thredds.R

@@ -82,7 +82,7 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE,
     } else {
       ncores <- parallel::detectCores() -1
     }
-    require(doParallel)
+
     PEcAn.logger::logger.info(paste0("Running in parallel with: ", ncores))
     cl = parallel::makeCluster(ncores)
     doParallel::registerDoParallel(cl)

modules/data.remote/tests/Rcheck_reference.log

@@ -82,8 +82,6 @@ Author field differs from that derived from Authors@R
 * checking loading without being on the library search path ... OK
 * checking use of S3 registration ... OK
 * checking dependencies in R code ... WARNING
-'library' or 'require' calls not declared from:
-  ‘PEcAn.DB’ ‘doParallel’ ‘raster’
 'library' or 'require' calls in package code:
   ‘PEcAn.DB’ ‘doParallel’ ‘raster’ ‘rgdal’
   Please use :: or requireNamespace() instead.