From 0e1cce1c848b3e171b0ea012670135e23cd27fec Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Mon, 20 Jun 2022 21:49:10 +0200
Subject: [PATCH 01/17] update gh actions

---
 .github/workflows/R-CMD-check.yaml | 85 +++++-------------------------
 1 file changed, 14 insertions(+), 71 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 7fb79c3..271d466 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,18 +1,10 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -28,76 +20,27 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.1.0 (ubuntu-18.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
+      - uses: r-lib/actions/setup-pandoc@v1
+
       - uses: r-lib/actions/setup-r@v1
-        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
+          extra-packages: rcmdcheck
 
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
+      - uses: r-lib/actions/check-r-package@v1

From b749c9a2edcdf0faef31b78d75101d4b5f5c0ff1 Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Mon, 20 Jun 2022 22:14:59 +0200
Subject: [PATCH 02/17] update gh actions to r-lib v2

---
 .github/workflows/R-CMD-check.yaml   | 15 ++++---
 .github/workflows/lint.yaml          | 41 ++++++--------------
 .github/workflows/pkgdown.yaml       | 58 ++++++++++++++--------------
 .github/workflows/test-coverage.yaml | 43 +++++++--------------
 4 files changed, 61 insertions(+), 96 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 271d466..52c2b27 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -31,16 +31,19 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 82704a1..342d4bd 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -1,48 +1,29 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: lint
 
 jobs:
   lint:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("lintr")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr
+          needs: lint
 
       - name: Lint
         run: lintr::lint_package()
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 3c908d3..0b26021 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -1,48 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@4.1.4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 5910c1a..4b65418 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -1,48 +1,31 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}

From 1777e16e9268a56f0eae8f6fa4c84d7d0d3258da Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Tue, 14 Jun 2022 11:19:15 +0200
Subject: [PATCH 03/17] minor error in vignette

---
 vignettes/hddtools_vignette.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/hddtools_vignette.Rmd b/vignettes/hddtools_vignette.Rmd
index e07f4cd..f00fb8a 100644
--- a/vignettes/hddtools_vignette.Rmd
+++ b/vignettes/hddtools_vignette.Rmd
@@ -115,7 +115,7 @@ The GRDC catalogue (or a subset) can be used to create a map.
 ```{r catalogueGRDC7, eval = FALSE}
 # Visualise outlets on an interactive map
 library(leaflet)
-leaflet(data = GRDC_catalogue %>% filter(river == "PO, FIUME")) %>%
+leaflet(data = GRDC_catalogue %>% dplyr::filter(river == "PO, FIUME")) %>%
   addTiles() %>%  # Add default OpenStreetMap map tiles
   addMarkers(~long, ~lat, popup = ~station)
 ```

From 3a984093927672025d7768530ecd248c70de356a Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Tue, 14 Jun 2022 15:50:52 +0200
Subject: [PATCH 04/17] remove dependency from sp and raster for the
 bboxSpatialPolygon function

---
 R/bboxSpatialPolygon.R                   | 60 +++++++++++++++++-------
 tests/testthat/test-bboxSpatialPolygon.R |  4 +-
 2 files changed, 44 insertions(+), 20 deletions(-)

diff --git a/R/bboxSpatialPolygon.R b/R/bboxSpatialPolygon.R
index 524d78a..cd2979f 100644
--- a/R/bboxSpatialPolygon.R
+++ b/R/bboxSpatialPolygon.R
@@ -15,43 +15,67 @@
 #'
 #' @examples
 #' \dontrun{
-#'   boundingbox <- raster::extent(-180, +180, -50, +50)
-#'   bbSP <- bboxSpatialPolygon(boundingbox = boundingbox)
+#' boundingbox <- raster::extent(-180, +180, -50, +50)
+#' bbSP <- bboxSpatialPolygon(boundingbox = boundingbox)
 #' }
 #'
-
 bboxSpatialPolygon <- function(boundingbox,
                                proj4stringFrom = NULL,
                                proj4stringTo = NULL) {
+  if (!is.null(proj4stringFrom)) {
+    stopifnot(class(proj4stringFrom) == "crs")
+  }
 
   if (is.null(proj4stringFrom)) {
+    proj4stringFrom <- sf::st_crs("+proj=longlat +datum=WGS84")
+  }
 
-    proj4stringFrom <- sp::CRS("+proj=longlat +datum=WGS84")
+  if(is.matrix(boundingbox)) if(dim(boundingbox)==c(2,2)) bb <- boundingbox
+
+  #For compatibility with raster input bounding box objects
+  if(class(boundingbox) == "Extent"){
+  bb <- matrix(as.numeric(c(
+    boundingbox@xmin, boundingbox@ymin,
+    boundingbox@xmax, boundingbox@ymax
+  )),
+  nrow = 2
+  )}
 
-  }
 
-  bb <- matrix(as.numeric(c(boundingbox@xmin, boundingbox@ymin,
-                            boundingbox@xmax, boundingbox@ymax)),
-               nrow = 2)
+  if(class(boundingbox) == "SpatExtent"){
+    bb <- matrix(as.numeric(c(
+      boundingbox$xmin, boundingbox$ymin,
+      boundingbox$xmax, boundingbox$ymax
+    )),
+    nrow = 2
+    )}
+
+  if(!exists("bb")) stop("No valid bounding box provided")
+
   rownames(bb) <- c("lon", "lat")
   colnames(bb) <- c("min", "max")
 
   # Create unprojected boundingbox as spatial object
   # clockwise, 5 points to close it
-  bboxMat <- rbind(c(bb["lon", "min"], bb["lat", "min"]),
-                   c(bb["lon", "min"], bb["lat", "max"]),
-                   c(bb["lon", "max"], bb["lat", "max"]),
-                   c(bb["lon", "max"], bb["lat", "min"]),
-                   c(bb["lon", "min"], bb["lat", "min"]))
+  bboxMat <- rbind(
+    c(bb["lon", "min"], bb["lat", "min"]),
+    c(bb["lon", "min"], bb["lat", "max"]),
+    c(bb["lon", "max"], bb["lat", "max"]),
+    c(bb["lon", "max"], bb["lat", "min"]),
+    c(bb["lon", "min"], bb["lat", "min"])
+  )
+
+  bboxSP <- bboxMat %>%
+    list() %>%
+    sf::st_polygon() %>%
+    sf::st_sfc(., crs = proj4stringFrom)
+
 
-  bboxSP <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(bboxMat)),
-                                                  "bbox")),
-                                proj4string = proj4stringFrom)
 
   if (!is.null(proj4stringTo)) {
-    bboxSP <- sp::spTransform(bboxSP, proj4stringTo)
+    stopifnot(class(proj4stringTo) == "crs")
+    bboxSP <- sf::sf_project(bboxSP, proj4stringTo)
   }
 
   return(bboxSP)
-
 }
diff --git a/tests/testthat/test-bboxSpatialPolygon.R b/tests/testthat/test-bboxSpatialPolygon.R
index 32d2ae6..e9c6f23 100644
--- a/tests/testthat/test-bboxSpatialPolygon.R
+++ b/tests/testthat/test-bboxSpatialPolygon.R
@@ -2,9 +2,9 @@ context("bboxSpatialPolygon")
 
 test_that("Test bboxSpatialPolygon function", {
 
-  boundingbox <- raster::extent(c(-180, +180, -50, +50))
+  boundingbox <- terra::ext(c(-180, +180, -50, +50))
   bbSP <- bboxSpatialPolygon(boundingbox = boundingbox)
 
-  expect_that("SpatialPolygons" %in% class(bbSP), equals(TRUE))
+  expect_that("sfc_POLYGON" %in% class(bbSP), equals(TRUE))
 
 })

From e0f06fb9accabf6644e78e64461624b2418fd12e Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Wed, 15 Jun 2022 11:47:26 +0200
Subject: [PATCH 05/17] fix new terra syntax

---
 R/KGClimateClass.R        | 12 ++++++------
 R/bboxSpatialPolygon.R    | 10 +++-------
 man/KGClimateClass.Rd     |  2 +-
 man/bboxSpatialPolygon.Rd |  4 ++--
 4 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/R/KGClimateClass.R b/R/KGClimateClass.R
index 856dcea..fc674d3 100644
--- a/R/KGClimateClass.R
+++ b/R/KGClimateClass.R
@@ -17,7 +17,7 @@
 #' @examples
 #' \dontrun{
 #'   # Define a bounding box
-#'   areaBox <- raster::extent(-3.82, -3.63, 52.41, 52.52)
+#'   areaBox <- terra::ext(-3.82, -3.63, 52.41, 52.52)
 #'   # Get climate classes
 #'   KGClimateClass(areaBox = areaBox)
 #' }
@@ -28,7 +28,7 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
   # crop to bounding box
 
   if (is.null(areaBox)){
-    areaBox <- raster::extent(c(-180, +180, -90, +90))
+    areaBox <- terra::ext(c(-180, +180, -90, +90))
   }
   bbSP <- bboxSpatialPolygon(areaBox)
 
@@ -50,10 +50,10 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
     utils::untar(system.file(file.path("extdata", "KOTTEK_KG.tar.gz"),
                              package = "hddtools"), exdir = td)
 
-    kgRaster <- raster::raster(paste0(td, "/KOTTEK_koeppen-geiger.tiff",
+    kgRaster <- terra::rast(paste0(td, "/KOTTEK_koeppen-geiger.tiff",
                                       sep = ""))
 
-    temp <- data.frame(table(raster::extract(kgRaster, bbSP)))
+    temp <- data.frame(table(terra::extract(kgRaster, bbSP)))
     temp$Class <- NA
     for (i in 1:dim(temp)[1]){
       class1 <- which(kgLegend[,1] == temp[i,1])
@@ -89,9 +89,9 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
     utils::untar(system.file(file.path("extdata", "PEEL_KG.tar.gz"),
                              package = "hddtools"), exdir = td)
 
-    kgRaster <- raster::raster(paste0(td, "/PEEL_koppen_ascii.txt", sep = ""))
+    kgRaster <- terra::rast(paste0(td, "/PEEL_koppen_ascii.txt", sep = ""))
 
-    temp <- data.frame(table(raster::extract(kgRaster, bbSP)))
+    temp <- data.frame(table(terra::extract(kgRaster, bbSP)))
     temp$Class <- NA
     for (i in 1:dim(temp)[1]){
       class1 <- which(kgLegend[,1] == temp[i,1])
diff --git a/R/bboxSpatialPolygon.R b/R/bboxSpatialPolygon.R
index cd2979f..2b27773 100644
--- a/R/bboxSpatialPolygon.R
+++ b/R/bboxSpatialPolygon.R
@@ -15,7 +15,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' boundingbox <- raster::extent(-180, +180, -50, +50)
+#' boundingbox <- terra::ext(-180, +180, -50, +50)
 #' bbSP <- bboxSpatialPolygon(boundingbox = boundingbox)
 #' }
 #'
@@ -27,7 +27,7 @@ bboxSpatialPolygon <- function(boundingbox,
   }
 
   if (is.null(proj4stringFrom)) {
-    proj4stringFrom <- sf::st_crs("+proj=longlat +datum=WGS84")
+    proj4stringFrom <- "+proj=longlat +datum=WGS84"
   }
 
   if(is.matrix(boundingbox)) if(dim(boundingbox)==c(2,2)) bb <- boundingbox
@@ -65,12 +65,8 @@ bboxSpatialPolygon <- function(boundingbox,
     c(bb["lon", "min"], bb["lat", "min"])
   )
 
-  bboxSP <- bboxMat %>%
-    list() %>%
-    sf::st_polygon() %>%
-    sf::st_sfc(., crs = proj4stringFrom)
-
 
+  bboxSP <- terra::vect(bboxMat, "polygon", crs = proj4stringFrom)
 
   if (!is.null(proj4stringTo)) {
     stopifnot(class(proj4stringTo) == "crs")
diff --git a/man/KGClimateClass.Rd b/man/KGClimateClass.Rd
index 96b0816..d5b9996 100644
--- a/man/KGClimateClass.Rd
+++ b/man/KGClimateClass.Rd
@@ -22,7 +22,7 @@ Given a bounding box, the function identifies the overlapping climate zones.
 \examples{
 \dontrun{
   # Define a bounding box
-  areaBox <- raster::extent(-3.82, -3.63, 52.41, 52.52)
+  areaBox <- terra::ext(-3.82, -3.63, 52.41, 52.52)
   # Get climate classes
   KGClimateClass(areaBox = areaBox)
 }
diff --git a/man/bboxSpatialPolygon.Rd b/man/bboxSpatialPolygon.Rd
index b28cb11..b870906 100644
--- a/man/bboxSpatialPolygon.Rd
+++ b/man/bboxSpatialPolygon.Rd
@@ -25,8 +25,8 @@ Bounding box is first created (in lat/lon) then projected if specified
 }
 \examples{
 \dontrun{
-  boundingbox <- raster::extent(-180, +180, -50, +50)
-  bbSP <- bboxSpatialPolygon(boundingbox = boundingbox)
+boundingbox <- terra::ext(-180, +180, -50, +50)
+bbSP <- bboxSpatialPolygon(boundingbox = boundingbox)
 }
 
 }

From 66e742025baa4804d81ab5f37f3bfe1839d04a4f Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Wed, 15 Jun 2022 12:39:32 +0200
Subject: [PATCH 06/17] fix new syntax

---
 R/Data60UK.R                         | 14 +++++++-------
 R/KGClimateClass.R                   | 18 ++++++++++--------
 R/bboxSpatialPolygon.R               |  6 +++---
 man/catalogueData60UK.Rd             |  2 +-
 tests/testthat/test-KGClimateClass.R |  2 +-
 vignettes/hddtools_vignette.Rmd      |  2 +-
 6 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/R/Data60UK.R b/R/Data60UK.R
index e3cdd96..5a0d277 100644
--- a/R/Data60UK.R
+++ b/R/Data60UK.R
@@ -18,7 +18,7 @@
 #'   \item{\code{Latitude}}{}
 #'   \item{\code{Longitude}}{}
 #' }
-#' 
+#'
 #' @source \url{http://nrfaapps.ceh.ac.uk/datauk60/data.html}
 #'
 #' @export
@@ -29,7 +29,7 @@
 #'   Data60UK_catalogue_all <- catalogueData60UK()
 #'
 #'   # Filter the catalogue based on a bounding box
-#'   areaBox <- raster::extent(-4, -2, +52, +53)
+#'   areaBox <- terra::ext(-4, -2, +52, +53)
 #'   Data60UK_catalogue_bbox <- catalogueData60UK(areaBox)
 #' }
 #'
@@ -43,13 +43,13 @@ catalogueData60UK <- function(areaBox = NULL){
   Data60UKcatalogue <- tables[[which.max(n.rows)]]
   names(Data60UKcatalogue) <- c("id", "River", "Location")
   Data60UKcatalogue[] <- lapply(Data60UKcatalogue, as.character)
-  
+
   # Find grid reference browsing the NRFA catalogue
   # This was temp <- rnrfa::catalogue() but the catalogue has been saved as
   # external data here so that the dependency from rnrfa could be removed.
   temp <- readRDS(system.file("extdata", "rnrfa_cat.rds", package = "hddtools"))
   temp <- temp[which(temp$id %in% Data60UKcatalogue$id), ]
-  
+
   Data60UKcatalogue$gridReference <- temp$`grid-reference`$ngr
   Data60UKcatalogue$Latitude <- temp$latitude
   Data60UKcatalogue$Longitude <- temp$longitude
@@ -103,16 +103,16 @@ tsData60UK <- function(id){
 
   temp <- utils::read.table(file_url)
   names(temp) <- c("P", "Q", "DayNumber", "Year", "nStations")
-  
+
   # Combine the first four columns into a character vector
   date_info <- with(temp, paste(Year, DayNumber))
   # Parse that character vector
   datetime <- strptime(date_info, "%Y %j")
   P <- zoo::zoo(temp$P, order.by = datetime) # measured in mm
   Q <- zoo::zoo(temp$Q, order.by = datetime) # measured in m3/s
-  
+
   myTS <- zoo::merge.zoo(P,Q)
-  
+
   return(myTS)
 
 }
diff --git a/R/KGClimateClass.R b/R/KGClimateClass.R
index fc674d3..a7c6c9f 100644
--- a/R/KGClimateClass.R
+++ b/R/KGClimateClass.R
@@ -38,7 +38,7 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
     kgLegend <- utils::read.table(system.file(file.path("extdata",
                                                         "KOTTEK_Legend.txt"),
                                               package = "hddtools"))
-
+    kgLegend$V1 <- as.character(kgLegend$V1)
     # message("OFFLINE results")
 
     # create a temporary directory
@@ -53,10 +53,11 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
     kgRaster <- terra::rast(paste0(td, "/KOTTEK_koeppen-geiger.tiff",
                                       sep = ""))
 
-    temp <- data.frame(table(terra::extract(kgRaster, bbSP)))
+    temp <- data.frame(table(terra::extract(kgRaster, bbSP)))[,2:3]
+    colnames(temp)[1] <- "ID"
     temp$Class <- NA
     for (i in 1:dim(temp)[1]){
-      class1 <- which(kgLegend[,1] == temp[i,1])
+      class1 <- which(kgLegend[,1] == as.character(temp[i,1]))
       if (length(class1) > 0){
         temp$Class[i] <- as.character(kgLegend[class1,3])
       }
@@ -64,7 +65,7 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
 
     temp <- temp[which(!is.na(temp$Class)),]
 
-    df <- data.frame(ID = temp$Var1,
+    df <- data.frame(ID = temp$ID,
                      Class = temp$Class,
                      Frequency = temp$Freq)
 
@@ -77,7 +78,7 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
                                                         "PEEL_Legend.txt"),
                                               package = "hddtools"),
                                   header = TRUE)
-
+    kgLegend$ID <- as.character(kgLegend$ID)
     # message("OFFLINE results")
 
     # create a temporary directory
@@ -91,10 +92,11 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
 
     kgRaster <- terra::rast(paste0(td, "/PEEL_koppen_ascii.txt", sep = ""))
 
-    temp <- data.frame(table(terra::extract(kgRaster, bbSP)))
+    temp <- data.frame(table(terra::extract(kgRaster, bbSP)))[,2:3]
+    colnames(temp)[1] <- "ID"
     temp$Class <- NA
     for (i in 1:dim(temp)[1]){
-      class1 <- which(kgLegend[,1] == temp[i,1])
+      class1 <- which(kgLegend[,1] == as.character(temp[i,1]))
       if (length(class1) > 0){
         temp$Class[i] <- as.character(kgLegend[class1,2])
       }
@@ -102,7 +104,7 @@ KGClimateClass <- function(areaBox = NULL, updatedBy = "Peel", verbose = FALSE){
 
     temp <- temp[which(!is.na(temp$Class)),]
 
-    df <- data.frame(ID = temp$Var1,
+    df <- data.frame(ID = temp$ID,
                      Class = temp$Class,
                      Frequency = temp$Freq)
 
diff --git a/R/bboxSpatialPolygon.R b/R/bboxSpatialPolygon.R
index 2b27773..8c124df 100644
--- a/R/bboxSpatialPolygon.R
+++ b/R/bboxSpatialPolygon.R
@@ -23,7 +23,7 @@ bboxSpatialPolygon <- function(boundingbox,
                                proj4stringFrom = NULL,
                                proj4stringTo = NULL) {
   if (!is.null(proj4stringFrom)) {
-    stopifnot(class(proj4stringFrom) == "crs")
+    stopifnot(class(sf::st_crs(proj4stringFrom)) == "crs")
   }
 
   if (is.null(proj4stringFrom)) {
@@ -69,8 +69,8 @@ bboxSpatialPolygon <- function(boundingbox,
   bboxSP <- terra::vect(bboxMat, "polygon", crs = proj4stringFrom)
 
   if (!is.null(proj4stringTo)) {
-    stopifnot(class(proj4stringTo) == "crs")
-    bboxSP <- sf::sf_project(bboxSP, proj4stringTo)
+    stopifnot(class(sf::st_crs(proj4stringTo)) == "crs")
+    bboxSP <- terra::project(bboxSP, proj4stringTo)
   }
 
   return(bboxSP)
diff --git a/man/catalogueData60UK.Rd b/man/catalogueData60UK.Rd
index 6c01a89..18741cb 100644
--- a/man/catalogueData60UK.Rd
+++ b/man/catalogueData60UK.Rd
@@ -35,7 +35,7 @@ listing 61 gauging stations.
   Data60UK_catalogue_all <- catalogueData60UK()
 
   # Filter the catalogue based on a bounding box
-  areaBox <- raster::extent(-4, -2, +52, +53)
+  areaBox <- terra::ext(-4, -2, +52, +53)
   Data60UK_catalogue_bbox <- catalogueData60UK(areaBox)
 }
 
diff --git a/tests/testthat/test-KGClimateClass.R b/tests/testthat/test-KGClimateClass.R
index c1e5d95..c08a82c 100644
--- a/tests/testthat/test-KGClimateClass.R
+++ b/tests/testthat/test-KGClimateClass.R
@@ -3,7 +3,7 @@ context("KGClimateClass")
 test_that("Test KGClimateClass function", {
 
   # Define a bounding box
-  areaBox <- raster::extent(-3.82, -3.63, 52.41, 52.52)
+  areaBox <- terra::ext(-3.82, -3.63, 52.41, 52.52)
   # Get climate classes
   x <- try(KGClimateClass(areaBox = areaBox), silent = TRUE)
 
diff --git a/vignettes/hddtools_vignette.Rmd b/vignettes/hddtools_vignette.Rmd
index f00fb8a..734a875 100644
--- a/vignettes/hddtools_vignette.Rmd
+++ b/vignettes/hddtools_vignette.Rmd
@@ -63,7 +63,7 @@ The package hddtools contains a function to identify the updated Koppen-Greiger
 
 ```{r KGClimateClass1, eval = TRUE}
 # Define a bounding box
-areaBox <- raster::extent(-10, 5, 48, 62)
+areaBox <- terra::ext(-10, 5, 48, 62)
 
 # Extract climate zones from Peel's map:
 KGClimateClass(areaBox = areaBox, updatedBy = "Peel")

From 516a43892a3f2147c4872f1fd7ca34c0b24c87d3 Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Wed, 15 Jun 2022 14:37:52 +0200
Subject: [PATCH 07/17] remove further {raster} dependencies

---
 DESCRIPTION                              |  4 +-
 NAMESPACE                                |  8 ---
 R/Data60UK.R                             | 10 ++--
 R/hddtools-package.R                     |  3 -
 inst/experimental/moreGRDC.R             | 76 ++++++++++++------------
 man/catalogueData60UK.Rd                 |  2 +-
 tests/testthat/test-Data60UK.R           |  8 +--
 tests/testthat/test-bboxSpatialPolygon.R |  2 +-
 vignettes/hddtools_vignette.Rmd          |  2 +-
 9 files changed, 52 insertions(+), 63 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 00e9ed4..3f2b9b4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,8 +15,8 @@ Maintainer: Dorothea Hug Peter <dorothea.hug@wsl.ch>
 URL: https://docs.ropensci.org/hddtools/, https://github.com/ropensci/hddtools
 BugReports: https://github.com/ropensci/hddtools/issues
 Description: Tools to discover hydrological data, accessing catalogues and databases from various data providers. The package is described in Vitolo (2017) "hddtools: Hydrological Data Discovery Tools" <doi:10.21105/joss.00056>.
-Depends: R (>= 3.5.0), rgdal
-Imports: zoo, sp, curl, XML, raster, readxl, tidyr
+Depends: R (>= 3.5.0)
+Imports: zoo, curl, XML, terra, readxl, tidyr
 Suggests: testthat, leaflet, rmarkdown, knitr, dplyr
 VignetteBuilder: knitr
 License: GPL-3
diff --git a/NAMESPACE b/NAMESPACE
index c492d42..0c74fcc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,17 +9,9 @@ export(catalogueSEPA)
 export(tsData60UK)
 export(tsMOPEX)
 export(tsSEPA)
-import(rgdal)
 importFrom(XML,readHTMLTable)
 importFrom(curl,curl_download)
-importFrom(raster,extent)
-importFrom(raster,extract)
-importFrom(raster,raster)
 importFrom(readxl,read_xlsx)
-importFrom(sp,CRS)
-importFrom(sp,Polygon)
-importFrom(sp,Polygons)
-importFrom(sp,SpatialPolygons)
 importFrom(tidyr,pivot_longer)
 importFrom(utils,download.file)
 importFrom(utils,read.csv)
diff --git a/R/Data60UK.R b/R/Data60UK.R
index 5a0d277..f2671cd 100644
--- a/R/Data60UK.R
+++ b/R/Data60UK.R
@@ -7,7 +7,7 @@
 #'
 #' @param areaBox bounding box, a list made of 4 elements: minimum longitude
 #' (lonMin), minimum latitude (latMin), maximum longitude (lonMax), maximum
-#' latitude (latMax)
+#' latitude (latMax) or an object of type "SpatExtent"
 #'
 #' @return This function returns a data frame containing the following columns:
 #' \describe{
@@ -56,10 +56,10 @@ catalogueData60UK <- function(areaBox = NULL){
 
   # Latitude is the Y axis, longitude is the X axis.
   if (!is.null(areaBox)){
-    lonMin <- areaBox@xmin
-    lonMax <- areaBox@xmax
-    latMin <- areaBox@ymin
-    latMax <- areaBox@ymax
+    lonMin <- areaBox$xmin
+    lonMax <- areaBox$xmax
+    latMin <- areaBox$ymin
+    latMax <- areaBox$ymax
   }else{
     lonMin <- -180
     lonMax <- +180
diff --git a/R/hddtools-package.R b/R/hddtools-package.R
index a9dfd56..36b4468 100644
--- a/R/hddtools-package.R
+++ b/R/hddtools-package.R
@@ -18,11 +18,8 @@
 #' Vitolo C, Buytaert W, 2014, HDDTOOLS: an R package serving Hydrological Data
 #' Discovery Tools, AGU Fall Meeting, 15-19 December 2014, San Francisco, USA.
 #'
-#' @import rgdal
 #' @importFrom curl curl_download
-#' @importFrom raster raster extract extent
 #' @importFrom readxl read_xlsx
-#' @importFrom sp CRS SpatialPolygons Polygon Polygons
 #' @importFrom tidyr pivot_longer
 #' @importFrom utils download.file read.csv read.fwf read.table untar unzip
 #' @importFrom XML readHTMLTable
diff --git a/inst/experimental/moreGRDC.R b/inst/experimental/moreGRDC.R
index 325dcd3..e2a6d51 100644
--- a/inst/experimental/moreGRDC.R
+++ b/inst/experimental/moreGRDC.R
@@ -46,7 +46,7 @@
 #'   GRDC_catalogue_all <- catalogueGRDC()
 #'
 #'   # Define a bounding box
-#'   areaBox <- raster::extent(-3.82, -3.63, 52.41, 52.52)
+#'   areaBox <- terra::ext(-3.82, -3.63, 52.41, 52.52)
 #'   # Filter the catalogue based on bounding box
 #'   GRDC_catalogue_bbox <- catalogueGRDC(areaBox = areaBox)
 #'
@@ -61,39 +61,39 @@
 #'
 
 test_catalogueGRDC <- function() {
-  
+
   the_url <- "ftp://ftp.bafg.de/pub/REFERATE/GRDC/catalogue/"
-  
+
   # Retrieve the catalogue
   result <- RCurl::getURL(the_url, ftp.use.epsv=TRUE, dirlistonly = TRUE)
   list_of_files <- strsplit(result, "\r*\n")[[1]]
   yesterday <- gsub(pattern = "-", replacement = "_", Sys.Date() - 1)
   today <- gsub(pattern = "-", replacement = "_", Sys.Date())
-  latest_file <- 
+  latest_file <-
     ifelse(test = length(list_of_files[grep(pattern = today,
                                             x = list_of_files)]),
            yes = list_of_files[grep(pattern = today, x = list_of_files)],
            no = list_of_files[grep(pattern = yesterday, x = list_of_files)])
   latest_file <- paste0(the_url, latest_file)
-  
+
   my_tmp_file <- tempfile()
   x <- RCurl::getBinaryURL(latest_file, ftp.use.epsv = FALSE,crlf = TRUE)
   writeBin(object = x, con = my_tmp_file)
   GRDCcatalogue <- readxl::read_xlsx(my_tmp_file, sheet = "Catalogue")
-  
+
   # Cleanup non
   GRDCcatalogue <- data.frame(lapply(GRDCcatalogue,
                                      function(x) {gsub("n.a.|-999|-", NA, x)}),
                               stringsAsFactors = FALSE)
-  
+
   # Convert to numeric some of the columns
   colx <- which(!(names(GRDCcatalogue) %in% c("grdc_no", "wmo_reg", "sub_reg",
                                               "nat_id", "river", "station",
                                               "country", "provider_id")))
   GRDCcatalogue[, colx] <- lapply(GRDCcatalogue[, colx], as.numeric)
-  
+
   return(GRDCcatalogue)
-  
+
 }
 
 #' Interface for the Global Runoff Data Centre database of Monthly Time Series.
@@ -233,58 +233,58 @@ test_catalogueGRDC <- function() {
 #'
 
 test_tsGRDC <- function(id) {
-  
+
   options(warn = -1)
-  
+
   catalogueTmp <- catalogueGRDC()
   catalogueTmp <- catalogueTmp[which(catalogueTmp$grdc_no == id), ]
-  
+
   # Retrieve look-up table
   grdcLTMMD <- NULL
   load(system.file(file.path("data", "grdcLTMMD.rda"), package = "hddtools"))
-  
+
   # Retrieve WMO region from catalogue
   wmoRegion <- catalogueTmp$wmo_reg
-  
+
   # Retrieve ftp server location
   zipFile <- as.character(grdcLTMMD[which(grdcLTMMD$WMO_Region == wmoRegion),
                                     "Archive"])
-  
+
   # create a temporary directory
   td <- tempdir()
-  
+
   # create the placeholder file
   tf <- tempfile(tmpdir = td, fileext = ".zip")
-  
+
   # download into the placeholder file
   # Switched from downloader::download to utils::download.file
   # to ensure it works cross-platform
   downloader::download(url = zipFile, destfile = tf, mode = "wb")
-  
+
   # Type of tables
   tablenames <- c("LTVD", "LTVM", "PVD", "PVM", "YVD", "YVM")
-  
+
   # get the name of the file to unzip
   fname <- paste0(id, "_Q_", tablenames, ".csv")
-  
+
   # unzip the file to the temporary directory
   utils::unzip(tf, files = fname, exdir = td, overwrite = TRUE)
-  
+
   # fpath is the full path to the extracted file
   fpath <- file.path(td, fname)
-  
+
   if (!all(file.exists(fpath))) {
-    
+
     stop("Data are not available at this station")
-    
+
   }
-  
+
   # Initialise empty list of tables
   ltables <- list()
-  
+
   # Populate tables
   for (j in seq_along(fpath)) {
-    
+
     TS <- readLines(fpath[j])
     # find dataset content
     row_data <- grep(pattern = "# Data Set Content:", x = TS)
@@ -295,7 +295,7 @@ test_tsGRDC <- function(id) {
     data_names <- gsub(pattern = ")", replacement = "", x = data_names)
     data_names <- gsub(pattern = "\\(", replacement = "_", x = data_names)
     data_names <- gsub(pattern = "\\.", replacement = "_", x = data_names)
-    
+
     ## find data lines
     row_data_lines <- grep(pattern = "# Data lines:", x = TS)[1]
     chr_positions <- gregexpr(pattern = "[0-9]",
@@ -304,14 +304,14 @@ test_tsGRDC <- function(id) {
     rows_to_read <- as.numeric(substr(x = TS[row_data_lines],
                                       start = chr_positions[1],
                                       stop = chr_positions[lchr_positions]))
-    
+
     if (rows_to_read > 0) {
-      
+
       # find tables
       row_data <- grep(pattern = "DATA", x = TS, ignore.case = FALSE)
       row_start <- row_data + 2
       row_end <- row_start + rows_to_read - 1
-      
+
       # Read columns and assign names
       column_names <- c()
       for (k in seq_along(data_names)) {
@@ -322,7 +322,7 @@ test_tsGRDC <- function(id) {
         column_names <- c(column_names, paste0(data_names[k], "__",
                                                tempcolnames))
       }
-      
+
       for (w in seq_along(row_start)) {
         # Assemble data frame
         row_split <- unlist(strsplit(TS[row_start[w]:row_end[w]], ";"))
@@ -334,20 +334,20 @@ test_tsGRDC <- function(id) {
                                    byrow = TRUE))
         }
       }
-      
+
       df <- data.frame(tmp, stringsAsFactors = FALSE)
       names(df) <- column_names
-      
+
       ltables[[j]] <- df
     }else{
       message(paste(tablenames[j], "data are not available at this station"))
       ltables[[j]] <- NULL
     }
-    
+
   }
-  
+
   names(ltables) <- tablenames
-  
+
   return(ltables)
-  
+
 }
diff --git a/man/catalogueData60UK.Rd b/man/catalogueData60UK.Rd
index 18741cb..46ac9a0 100644
--- a/man/catalogueData60UK.Rd
+++ b/man/catalogueData60UK.Rd
@@ -12,7 +12,7 @@ catalogueData60UK(areaBox = NULL)
 \arguments{
 \item{areaBox}{bounding box, a list made of 4 elements: minimum longitude
 (lonMin), minimum latitude (latMin), maximum longitude (lonMax), maximum
-latitude (latMax)}
+latitude (latMax) or an object of type "SpatExtent"}
 }
 \value{
 This function returns a data frame containing the following columns:
diff --git a/tests/testthat/test-Data60UK.R b/tests/testthat/test-Data60UK.R
index 85b661b..6555f74 100644
--- a/tests/testthat/test-Data60UK.R
+++ b/tests/testthat/test-Data60UK.R
@@ -13,7 +13,7 @@ test_that("Test catalogueData60UK", {
 test_that("Test catalogueData60UK bounding box", {
 
   # Define a bounding box
-  areaBox <- raster::extent(c(-4, -2, +52, +53))
+  areaBox <- terra::ext(c(-4, -2, +52, +53))
   # Filter the catalogue based on a bounding box
   x2 <- catalogueData60UK(areaBox)
 
@@ -22,11 +22,11 @@ test_that("Test catalogueData60UK bounding box", {
 })
 
 test_that("Test tsData60UK function", {
-  
+
   # Retrieve sample data
   x <- tsData60UK(id = 39015)
-  
+
   expect_that(class(x) == "zoo", equals(TRUE))
   expect_that(all(names(x) == c("P", "Q")), equals(TRUE))
-  
+
 })
diff --git a/tests/testthat/test-bboxSpatialPolygon.R b/tests/testthat/test-bboxSpatialPolygon.R
index e9c6f23..823cb7b 100644
--- a/tests/testthat/test-bboxSpatialPolygon.R
+++ b/tests/testthat/test-bboxSpatialPolygon.R
@@ -5,6 +5,6 @@ test_that("Test bboxSpatialPolygon function", {
   boundingbox <- terra::ext(c(-180, +180, -50, +50))
   bbSP <- bboxSpatialPolygon(boundingbox = boundingbox)
 
-  expect_that("sfc_POLYGON" %in% class(bbSP), equals(TRUE))
+  expect_that("SpatVector" %in% class(bbSP), equals(TRUE))
 
 })
diff --git a/vignettes/hddtools_vignette.Rmd b/vignettes/hddtools_vignette.Rmd
index 734a875..53e27bc 100644
--- a/vignettes/hddtools_vignette.Rmd
+++ b/vignettes/hddtools_vignette.Rmd
@@ -134,7 +134,7 @@ The hddtools contain two functions to interact with this database: one to retrei
 Data60UK_catalogue_all <- catalogueData60UK()
 
 # Filter Data60UK catalogue based on bounding box
-areaBox <- raster::extent(-4, -3, 51, 53)
+areaBox <- terra::ext(-4, -3, 51, 53)
 Data60UK_catalogue_bbox <- catalogueData60UK(areaBox = areaBox)
 ```
 

From d1671afda19991b676f9e321de9922a203d4164c Mon Sep 17 00:00:00 2001
From: dhugpeter <dorothea.hug@gmail.com>
Date: Wed, 15 Jun 2022 22:38:24 +0200
Subject: [PATCH 08/17] import sf

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3f2b9b4..75a4358 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,7 +16,7 @@ URL: https://docs.ropensci.org/hddtools/, https://github.com/ropensci/hddtools
 BugReports: https://github.com/ropensci/hddtools/issues
 Description: Tools to discover hydrological data, accessing catalogues and databases from various data providers. The package is described in Vitolo (2017) "hddtools: Hydrological Data Discovery Tools" <doi:10.21105/joss.00056>.
 Depends: R (>= 3.5.0)
-Imports: zoo, curl, XML, terra, readxl, tidyr
+Imports: zoo, curl, XML, terra, readxl, tidyr, sf
 Suggests: testthat, leaflet, rmarkdown, knitr, dplyr
 VignetteBuilder: knitr
 License: GPL-3

From 22aa07c7e1aa711aa875e72a7efe075fd9b5d995 Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Mon, 27 Jun 2022 23:05:08 +0200
Subject: [PATCH 09/17] remove tsMOPEX test on CI for now

---
 tests/testthat/test-MOPEX.R | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/tests/testthat/test-MOPEX.R b/tests/testthat/test-MOPEX.R
index 778e332..08ef6fa 100644
--- a/tests/testthat/test-MOPEX.R
+++ b/tests/testthat/test-MOPEX.R
@@ -6,7 +6,7 @@ test_that("Test catalogueMOPEX - MAP = FALSE", {
 
   # Retrieve the MOPEX catalogue
   x1 <- catalogueMOPEX(MAP = FALSE)
-  
+
   expect_true("data.frame" %in% class(x1))
   expect_true(all(dim(x1) == c(1861, 12)))
   expect_true(is.na(x1$State[x1$USGS_ID == "08167000"]))
@@ -16,38 +16,40 @@ test_that("Test catalogueMOPEX - MAP = FALSE", {
 test_that("Test catalogueMOPEX - MAP = TRUE", {
 
   testthat::skip_on_cran()
+  testthat::ski_on_ci()
+
 
   # Retrieve the MOPEX catalogue
   x2 <- catalogueMOPEX(MAP = TRUE)
-  
+
   expect_true("data.frame" %in% class(x2))
   expect_true(all(dim(x2) == c(438, 12)))
   expect_true(x2$State[x2$USGS_ID == "01048000"] == "ME")
-  
+
 })
 
 test_that("Test tsMOPEX - MAP = FALSE", {
 
   testthat::skip_on_cran()
-
+  testthat::ski_on_ci()
   # Retrieve data
   x3 <- tsMOPEX(id = "01010000", MAP = FALSE)
-  
+
   expect_true("zoo" %in% class(x3))
   expect_true(all(names(x3) == "Q"))
   expect_true(as.numeric(x3$Q[1]) == 13.45)
-  
+
 })
 
 test_that("Test tsMOPEX - MAP = TRUE", {
 
   testthat::skip_on_cran()
-
+  testthat::ski_on_ci()
   # Retrieve data
   x4 <- tsMOPEX(id = "01048000", MAP = TRUE)
-  
+
   expect_true("zoo" %in% class(x4))
   expect_true(all(names(x4) == c("P", "E", "Q", "T_max", "T_min")))
   expect_true(as.numeric(x4$T_min[1]) == -10.8444)
-  
+
 })

From d4fa74876639013b84b5e09816a590c97aa6d1a1 Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Mon, 27 Jun 2022 23:14:47 +0200
Subject: [PATCH 10/17] fix gh-actions

---
 .github/workflows/R-CMD-check.yaml   | 2 +-
 .github/workflows/lint.yaml          | 2 +-
 .github/workflows/pkgdown.yaml       | 2 +-
 .github/workflows/test-coverage.yaml | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 52c2b27..67b00c6 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -41,7 +41,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck any::XML
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 342d4bd..e7b89bb 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -22,7 +22,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::lintr
+          extra-packages: any::lintr any::XML
           needs: lint
 
       - name: Lint
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 0b26021..89b145a 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -30,7 +30,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, local::. any::XML
           needs: website
 
       - name: Build site
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 4b65418..335d954 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -23,7 +23,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr any::XML
           needs: coverage
 
       - name: Test coverage

From d9aa58d06a106d8f048ba420d5402553de5678e4 Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Mon, 27 Jun 2022 23:53:45 +0200
Subject: [PATCH 11/17] fix typo

---
 tests/testthat/test-MOPEX.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-MOPEX.R b/tests/testthat/test-MOPEX.R
index 08ef6fa..2b6c84f 100644
--- a/tests/testthat/test-MOPEX.R
+++ b/tests/testthat/test-MOPEX.R
@@ -16,7 +16,7 @@ test_that("Test catalogueMOPEX - MAP = FALSE", {
 test_that("Test catalogueMOPEX - MAP = TRUE", {
 
   testthat::skip_on_cran()
-  testthat::ski_on_ci()
+  testthat::skip_on_ci()
 
 
   # Retrieve the MOPEX catalogue
@@ -31,7 +31,7 @@ test_that("Test catalogueMOPEX - MAP = TRUE", {
 test_that("Test tsMOPEX - MAP = FALSE", {
 
   testthat::skip_on_cran()
-  testthat::ski_on_ci()
+  testthat::skip_on_ci()
   # Retrieve data
   x3 <- tsMOPEX(id = "01010000", MAP = FALSE)
 
@@ -44,7 +44,7 @@ test_that("Test tsMOPEX - MAP = FALSE", {
 test_that("Test tsMOPEX - MAP = TRUE", {
 
   testthat::skip_on_cran()
-  testthat::ski_on_ci()
+  testthat::skip_on_ci()
   # Retrieve data
   x4 <- tsMOPEX(id = "01048000", MAP = TRUE)
 

From 43f6100aabb80344f86384ac7c017369d87d24be Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Tue, 28 Jun 2022 11:09:22 +0200
Subject: [PATCH 12/17] skip Mopex test on ci

---
 tests/testthat/test-MOPEX.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-MOPEX.R b/tests/testthat/test-MOPEX.R
index 2b6c84f..327965d 100644
--- a/tests/testthat/test-MOPEX.R
+++ b/tests/testthat/test-MOPEX.R
@@ -3,6 +3,7 @@ context("MOPEX")
 test_that("Test catalogueMOPEX - MAP = FALSE", {
 
   testthat::skip_on_cran()
+  testthat::skip_on_ci()
 
   # Retrieve the MOPEX catalogue
   x1 <- catalogueMOPEX(MAP = FALSE)

From f287ddccb8cbcd71dabd30cf0a5e2b0b2ee613ca Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Tue, 28 Jun 2022 13:38:13 +0200
Subject: [PATCH 13/17] remove tsGRDC doc

---
 _pkgdown.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index eb5bae5..bfb32d3 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -34,7 +34,6 @@ reference:
     Get data from various providers
   contents:
   - tsData60UK
-  - tsGRDC
   - tsMOPEX
   - tsSEPA
   - grdcLTMMD

From c92f0ea2e410c7add44876ed84b15ef688ea381a Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Tue, 28 Jun 2022 15:10:34 +0200
Subject: [PATCH 14/17] fix pkgdown

---
 _pkgdown.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index bfb32d3..d1ebfa9 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -44,7 +44,6 @@ reference:
     Utility functions, mainly used internally
   contents:
   - bboxSpatialPolygon
-  - getContent
 
 - title: Cached catalogues
   desc: >

From 3d9956eb54156da1ac337cdb45ba6657b39c1ed5 Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Tue, 28 Jun 2022 15:19:49 +0200
Subject: [PATCH 15/17] simplify website

---
 _pkgdown.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index d1ebfa9..2922219 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -45,14 +45,6 @@ reference:
   contents:
   - bboxSpatialPolygon
 
-- title: Cached catalogues
-  desc: >
-    Cached version of the output of the catalogue*() functions
-  contents:
-  - Data60UKcatalogue
-  - GRDCcatalogue
-  - MOPEXcatalogue
-  - SEPAcatalogue
 
 articles:
 - title: All articles

From 767c002e10e1ccceecf2f2039ff920abd81dcfa4 Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Mon, 18 Jul 2022 11:34:11 +0200
Subject: [PATCH 16/17] remove if(class=) statement

---
 R/bboxSpatialPolygon.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/bboxSpatialPolygon.R b/R/bboxSpatialPolygon.R
index 8c124df..fa0d92b 100644
--- a/R/bboxSpatialPolygon.R
+++ b/R/bboxSpatialPolygon.R
@@ -23,7 +23,7 @@ bboxSpatialPolygon <- function(boundingbox,
                                proj4stringFrom = NULL,
                                proj4stringTo = NULL) {
   if (!is.null(proj4stringFrom)) {
-    stopifnot(class(sf::st_crs(proj4stringFrom)) == "crs")
+    stopifnot(inherits(sf::st_crs(proj4stringFrom),"crs"))
   }
 
   if (is.null(proj4stringFrom)) {
@@ -33,7 +33,7 @@ bboxSpatialPolygon <- function(boundingbox,
   if(is.matrix(boundingbox)) if(dim(boundingbox)==c(2,2)) bb <- boundingbox
 
   #For compatibility with raster input bounding box objects
-  if(class(boundingbox) == "Extent"){
+  if(inherits(boundingbox, "Extent")){
   bb <- matrix(as.numeric(c(
     boundingbox@xmin, boundingbox@ymin,
     boundingbox@xmax, boundingbox@ymax
@@ -42,7 +42,7 @@ bboxSpatialPolygon <- function(boundingbox,
   )}
 
 
-  if(class(boundingbox) == "SpatExtent"){
+  if(inherits(boundingbox, "SpatExtent")){
     bb <- matrix(as.numeric(c(
       boundingbox$xmin, boundingbox$ymin,
       boundingbox$xmax, boundingbox$ymax

From a8f4cf4d9643990da53680b2a34bb197cd5ee58e Mon Sep 17 00:00:00 2001
From: Dorothea Hug Peter <12996416+dhugpeter@users.noreply.github.com>
Date: Mon, 18 Jul 2022 11:34:36 +0200
Subject: [PATCH 17/17] add news about removed dependency from rgdal and raster

---
 DESCRIPTION | 2 +-
 NEWS.md     | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 75a4358..ad59f26 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hddtools
 Title: Hydrological Data Discovery Tools
-Version: 0.9.4
+Version: 0.9.5
 Authors@R: c(person(given = "Claudia", family = "Vitolo",
                     role = c("aut"), email = "cvitolodev@gmail.com",
                     comment = c(ORCID = "0000-0002-4252-1176")),
diff --git a/NEWS.md b/NEWS.md
index dc45292..d995632 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# hddtools 0.9.5
+
+*Removed dependency fom rgdal and raster packages
+
 # hddtools 0.9.4
 
 * Removed dependency from the rnrfa package