From b24df9751dbcfb57bb349cd65734a1be21ed9a09 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 14:05:05 +0200
Subject: [PATCH 1/8] rgdal to sf in gis.functions

---
 modules/data.land/DESCRIPTION       | 1 -
 modules/data.land/R/gis.functions.R | 8 ++++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/modules/data.land/DESCRIPTION b/modules/data.land/DESCRIPTION
index 5ec23616b0f..eb187ac1667 100644
--- a/modules/data.land/DESCRIPTION
+++ b/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
diff --git a/modules/data.land/R/gis.functions.R b/modules/data.land/R/gis.functions.R
index 8f9434aea3f..0fa83941f88 100644
--- a/modules/data.land/R/gis.functions.R
+++ b/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

From 87559d7c6130b629ca45cfe8fe68db02126515f4 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 14:25:19 +0200
Subject: [PATCH 2/8] removed rgdal call from data.remote as well

---
 modules/data.remote/DESCRIPTION | 1 -
 modules/data.remote/R/NLCD.R    | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/modules/data.remote/DESCRIPTION b/modules/data.remote/DESCRIPTION
index 68e3ee22e89..c994d1cd476 100644
--- a/modules/data.remote/DESCRIPTION
+++ b/modules/data.remote/DESCRIPTION
@@ -36,7 +36,6 @@ Suggests:
     dplyr,
     ggplot2,
     lubridate,
-    rgdal,
     reshape,
     testthat (>= 1.0.2),
     tibble
diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index dfc712f2e09..98fc995fa1a 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -69,8 +69,7 @@ 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) {

From c97edb155c0465a2666afd0f95df9590b26427fd Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:34:00 +0200
Subject: [PATCH 3/8] attempt to change raster with terra

---
 modules/data.remote/R/NLCD.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 98fc995fa1a..6c7e1ff71cb 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -103,21 +103,21 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         print(paste("File not found:", filename))
         return(NULL)
     }
-    nlcd <- raster(filename)
+    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(x, 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

From 1114f56796a157b55a12d4cfa4b5afb31fa5e9fb Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:39:38 +0200
Subject: [PATCH 4/8] add warning

---
 modules/data.remote/R/NLCD.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 6c7e1ff71cb..01005ddc479 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -103,6 +103,9 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         print(paste("File not found:", filename))
         return(NULL)
     }
+    
+    # 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

From bfb03a83141bf131b23bc490c416f6e9962f838e Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:50:46 +0200
Subject: [PATCH 5/8] remove library call to raster

---
 modules/data.remote/R/NLCD.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 01005ddc479..a0416cdebbb 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -68,7 +68,6 @@ 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)
 
     if (!is.null(con)) {
         library(PEcAn.DB)

From 20315900ada53664babefe13f957899f45fd7cc8 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:51:45 +0200
Subject: [PATCH 6/8] fix typo

---
 modules/data.remote/R/NLCD.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index a0416cdebbb..0e891aec2eb 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -109,7 +109,7 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
     
     # transform points
     sites <- terra::vect(coords, geom=c("long", "lat"), crs="+proj=longlat +datum=WGS84")
-    sites <- terra::buffer(x, width=buffer)
+    sites <- terra::buffer(sites, width=buffer)
     
     # extract
     sum.raw <- table(terra::extract(nlcd, sites))

From 8263c71e923cac88e92431b4be36c72d96d0a898 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Thu, 2 Nov 2023 17:09:10 +0200
Subject: [PATCH 7/8] remove library and require calls from data.remote

---
 modules/data.remote/R/NLCD.R             | 4 ++--
 modules/data.remote/R/download.thredds.R | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 0e891aec2eb..32517eff2ae 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/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 (", 
@@ -70,7 +70,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
 extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 2011) {
 
     if (!is.null(con)) {
-        library(PEcAn.DB)
+
         if (year == 2001) {
             input.id <- 1000000482
         } else if (year == 2011) {
diff --git a/modules/data.remote/R/download.thredds.R b/modules/data.remote/R/download.thredds.R
index 09d44ac1337..04fc4b99923 100755
--- a/modules/data.remote/R/download.thredds.R
+++ b/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)

From 9137628fa99dd82ab1d1e98b059092d879fbdbcb Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Thu, 2 Nov 2023 18:56:38 +0200
Subject: [PATCH 8/8] CI updates

---
 modules/data.remote/DESCRIPTION                | 3 ++-
 modules/data.remote/tests/Rcheck_reference.log | 2 --
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/data.remote/DESCRIPTION b/modules/data.remote/DESCRIPTION
index c994d1cd476..617f49b1338 100644
--- a/modules/data.remote/DESCRIPTION
+++ b/modules/data.remote/DESCRIPTION
@@ -20,7 +20,6 @@ Imports:
     PEcAn.utils,
     purrr,
     XML,
-    raster,
     sp,
     MODISTools (>= 1.1.0),
     reticulate,
@@ -28,6 +27,7 @@ Imports:
     magrittr,
     PEcAn.remote,
     stringr (>= 1.1.0),
+    terra,
     doParallel,
     parallel,
     foreach
@@ -36,6 +36,7 @@ Suggests:
     dplyr,
     ggplot2,
     lubridate,
+    raster,
     reshape,
     testthat (>= 1.0.2),
     tibble
diff --git a/modules/data.remote/tests/Rcheck_reference.log b/modules/data.remote/tests/Rcheck_reference.log
index 822a9411303..182f76f6d12 100644
--- a/modules/data.remote/tests/Rcheck_reference.log
+++ b/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.