Merge pull request #50 from EvolEcolGroup/master

Update to v2.1.0

.Rbuildignore

@@ -12,3 +12,4 @@ ci_dependencies
 ^CRAN-SUBMISSION$
 ^codecov.yml
 ^data-raw$
+.covrignore

.covrignore

@@ -4,3 +4,4 @@ R/download_worldclim_future.R
 R/download_etopo.R
 R/load_etopo.R
 R/download_chelsa.R
+R/download_chelsa_trace21k.R

.github/workflows/recheck.yml

@@ -0,0 +1,18 @@
+on:
+  workflow_dispatch:
+    inputs:
+      which:
+        type: choice
+        description: Which dependents to check
+        options:
+        - strong
+        - most
+
+name: Reverse dependency check
+
+jobs:
+  revdep_check:
+    name: Reverse check ${{ inputs.which }} dependents
+    uses: r-devel/recheck/.github/workflows/recheck.yml@v1
+    with:
+      which: ${{ inputs.which }}

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.0.0
-Date: 2023-11-01 17:32:06 UTC
-SHA: dc93c5c9f92f52ac7b178eac2b7095536868867d
+Version: 2.1.0
+Date: 2024-06-19 15:11:32 UTC
+SHA: 632c24b70ad487380186aaad24532545b4ffda56

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: pastclim
 Type: Package
 Title: Manipulate Time Series of Palaeoclimate Reconstructions 
-Version: 2.0.0.9003
+Version: 2.1.0
 Authors@R: c(
        person("Michela", "Leonardi", role = "aut"),
        person(c("Emily","Y."), "Hallet", role = "ctb"),
        person("Robert", "Beyer", role = "ctb"),
        person("Mario", "Krapp", role = "ctb"),
+       person(c("Andrea", "V."), "Pozzi", role = "ctb"),
        person("Andrea", "Manica", role = c("aut","cre"),
          email = "[email protected]")
      )
@@ -22,7 +23,7 @@ BugReports: https://github.com/EvolEcolGroup/pastclim/issues
 Encoding: UTF-8
 LazyData: true
 LazyDataCompression: xz
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Depends: 
   R (>= 4.0.0),

NEWS.md

@@ -1,4 +1,4 @@
-# development version
+# pastclim 2.1.0
 * Add all CHELSA present and future datasets (including the use of virtual rasters to avoid downloading all data)
 * Add paleoclim at multiple resolutions
 * Add CHELSA-TraCE21k (including the use of virtual rasters to avoid downloading all data)

R/datasets_docs.R

@@ -198,14 +198,14 @@ NULL
 #' in `pastclim`
 #'
 #' More details on the dataset are available on its 
-#' dedicated \href{https://hyde-portal.geo.uu.nl/}{website}.
+#' dedicated \href{https://landuse.sites.uu.nl/hyde-project/}{website}.
 #' 
 #' IMPORTANT: If you use this dataset, make sure to cite the original publication
 #' for the HYDE 3.2 (there is no current publication for 3.3):
 #'
 #' Klein Goldewijk, K., Beusen, A., Doelman, J., and Stehfest, E.:
 #' Anthropogenic land-use estimates for the Holocene; HYDE 3.2,
-#' Earth Syst. Sci. Data, 9, 927-953, 2017. \doi{10.5194/essd-9-1-2017}
+#' Earth Syst. Sci. Data, 9, 927-953, 2017. \doi{10.5194/essd-9-927-2017}
 #'
 #' @name HYDE_3.3_baseline
 NULL
@@ -319,7 +319,7 @@ NULL
 #'    using the CHELSA V1.2 algorithm.
 #' 
 #' More details on the dataset are available on its dedicated
-#'  \href{https://chelsa-climate.org/chelsa-trace21k//}{website}.
+#'  \href{https://chelsa-climate.org/chelsa-trace21k/}{website}.
 #'  
 #'  An alternative to
 #' downloading very large files is to use virtual rasters. Simply append

R/get_data_path.R

@@ -37,10 +37,11 @@ get_data_path <- function(silent = FALSE) {
       "pastclim_data.txt"
     ))[1, 1]
     if (!dir.exists(path_to_nc)) {
-      stop(
+      warning(
         "The path ", path_to_nc, " from the config file does not exist!\n",
         "You can reset the path with `set_data_path`."
       )
+      return(NULL)
     }
     return(path_to_nc)
   }

R/location_slice_from_region_series.R

@@ -19,7 +19,7 @@
 #' coordinates, as found in `data`. If left to NULL, the function will
 #' try to guess the columns based on standard names `c("x", "y")`, `c("X","Y")`,
 #'  `c("longitude", "latitude")`, or `c("lon", "lat")`
-#' @param region_series a [`SpatRasterDataset`] obtained with [region_series()]
+#' @param region_series a [`terra::SpatRasterDataset`] obtained with [region_series()]
 #' @param nn_interpol boolean determining whether nearest neighbour
 #' interpolation is used to estimate climate for cells that lack such
 #' information (i.e. they are under water or ice). By default, interpolation is only

R/slice_region_series.R

@@ -11,7 +11,7 @@
 #' can use `time_bp(x)`.
 #' @param time_ce time slice in years CE. Only one of `time_bp` or `time_ce` should
 #' be used.
-#' @returns a [SpatRaster] of the relevant slice.
+#' @returns a [`terra::SpatRaster`] of the relevant slice.
 #'
 #' @export
 

R/url_is_valid.R

@@ -10,7 +10,7 @@ url_is_valid <- function(url, verbose = FALSE) {
   if (requireNamespace("httr", quietly = TRUE)) {
     HTTP_STATUS_OK <- 200
     HTTP_STATUS_REDIRECT_SUCCESS <- 302
-    hd <- httr::HEAD(url)
+    hd <- httr::HEAD(url, httr::timeout(30))
     status <- hd$all_headers[[1]]$status
     if (verbose){
       message("status is ",status)

README.md

@@ -30,16 +30,15 @@ install.packages("pastclim")
 The version on CRAN is recommended for every day use. New features and
 bug fixes appear first on the `dev` branch on GitHub, before they make
 their way to CRAN. If you need to have early access to these new
-features, you can install `pastclim` directly from GitHub. To install
-from GitHub, you will need to use `devtools`; if you haven't done so
-already, get it from CRAN with `install.packages("devtools")`. Also,
+features, you can install the development version of `pastclim` directly 
+from GitHub, using `devtools`, or more simply get a compiled version
+from r-universe. Also,
 note that the `dev` version of `pastclim` tracks changes in the `dev`
 version of `terra`, so you will need to upgrade both libraries with:
 
 ```         
 install.packages('terra', repos='https://rspatial.r-universe.dev')
-
-devtools::install_github("EvolEcolGroup/pastclim", ref="dev")
+install.packages("pastclim", repos = c("https://evolecolgroup.r-universe.dev")
 ```
 
 ## Overview of functionality
@@ -55,32 +54,21 @@ updated for the `dev` branch of `pastclim` (on the top left of the dev
 website, the version number is in red and in the format x.x.x.9xxx,
 indicating it is a development version).
 
-Pastclim currently includes data from Beyer et al 2020 (a reconstruction
+`pastclim` currently includes data from Beyer et al 2020 (a reconstruction
 of climate based on the HadCM3 model for the last 120k years), Krapp
 et al 2021 (which covers the last 800k years with a statistical emulator of HadCM3),
-Barreto et al 2023 (covering the last 5M years using the PALEO-PGEM emulator),
-and the WorldClim data (present, and future projections with a number of models and 
+Barreto et al 2023 (covering the last 5M years using the PALEO-PGEM emulator), PaleoClim 
+(providing a few time steps from different palaeoclimate models downscaled to higher 
+resolution), CHELSA-Trace21K (a transient
+reconstruction of the last 21k years, downscaled to 1km resolution), the HYDE3.3 
+database of land use reconstructions for the last 10k years,
+and the WorldClim and CHELSA data (present, and future projections with a number of models and 
 emission scenarios). More details on each of these
 datasets can be found
 [here](https://evolecolgroup.github.io/pastclim/articles/a1_available_datasets.html).
 There are also instructions on how to build and use [custom
 datasets](https://evolecolgroup.github.io/pastclim/articles/a2_custom_datasets.html).
 
-You can also build the vignettes when installing `pastclim` (note that
-you will need to have the necessary tools to build vignettes already
-installed; requirements depend on your OS):
-
-```         
-devtools::install_github("EvolEcolGroup/pastclim", build_vignette = TRUE)
-```
-
-If you built the vignettes, you can read them directly in R. For
-example, the overview can be obtained with:
-
-```         
-vignette("pastclim_overview", package = "pastclim")
-```
-
 ------------------------------------------------------------------------
 
 ## When something does not work

cran-comments.md

@@ -1,24 +1,26 @@
-## This is a re-submission
-DOI incorrectly started with doi.org/; they have all now been fixed and raised
-no issues with any check.
+## This is a resubmission
+The previous submission raised:
+Check: Rd cross-references, Result: NOTE
+   Found the following Rd file(s) with Rd \link{} targets missing package
+   anchors:
+     location_slice_from_region_series.Rd: SpatRasterDataset
+     slice_region_series.Rd: SpatRaster
+   Please provide package anchors for all Rd \link{} targets not in the
+   package itself and the base packages.
+
+Those links have now been fixed with the appropriate package anchors.
 
 ## Test environments
-- R-hub windows-x86_64-devel (r-devel)
-- R-hub ubuntu-gcc-release (r-release)
-- R-hub fedora-clang-devel (r-devel)
+- R-hub linux (r-devel)
+- R-hub macos (r-devel)
+- R-hub macos-arm64 (r-devel)
 - devtools::check_mac_release
+- devtools::check_win_devel
 
 No NOTES on any environment.
 
 ## Checks on CRAN for previous version of pastclim
 As detailed in:
 https://cloud.r-project.org/web/checks/check_results_pastclim.html
 
-there are failures with r-oldrel-macos-arm64 and r-oldrel-macos-x86-64. Old
-versions on mac of `terra`, on which `pastclim` relies, were problematic. This
-affected other packages as well: https://github.com/r-spatial/stars/issues/566
-Pastclim works on r-oldrel-windows-x86-64, as well as on all other release and
-devel versions.
-
-There were notes on a r-devel, which picked up a man page where a parameter
-was named incorrectly. That has been fixed in the current version.
+there are no failures on the previous version (2.0.0)

data-raw/helper_functions/submitting_to_cran.R

@@ -16,7 +16,7 @@ source("./data-raw/helper_functions/check_returns_in_documentation.R")
 # update version number
 # update news
 
-# first check with rhub
+# first check with rhub (TO UPDATE, it now runs on github actions)
 pastclim_checks <- rhub::check_for_cran()
 
 # check on macos and windows via devtools