Merge branch 'dev'

Bump to 1.1.0

.Rbuildignore

@@ -7,3 +7,4 @@ ci_dependencies
 ^docs$
 ^pkgdown$
 ^\.github$
+^cran-comments.md

.github/old/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# 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: [master, dev, gitactions]
+  pull_request:
+    branches: [master, dev, gitactions]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/old/pkgdown_temp.yaml

@@ -0,0 +1,43 @@
+# 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, dev]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+          extra-packages: any::pkgdown
+          needs: website
+
+      - name: Downgrade terra
+        run: |
+          Rscript -e 'pak::pkg_install("devtools")'
+          Rscript -e 'devtools::install_version("terra", version="1.6.7", repos = "https://cloud.r-project.org/")'
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, commit_message =paste0(pkgdown:::construct_commit_message("."),"\n [skip ci]"))'

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# 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:
-    branches: [main, master]
+    branches: [master, dev]
+  pull_request:
+    branches: [master, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,24 +14,38 @@ name: pkgdown
 jobs:
   pkgdown:
     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-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
+      - name: Downgrade terra
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, commit_message =paste0(pkgdown:::construct_commit_message("."),"\n [skip ci]"))'
+          Rscript -e 'pak::pkg_install("devtools")'
+          Rscript -e 'devtools::install_version("terra", version="1.6.7", repos = "https://cloud.r-project.org/")'
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: pastclim
 Type: Package
-Title: This package provides helper functions to interact with timeseries of worldwide climate
-    reconstructions
-Version: 1.0.1
+Title: Manipulate Timeseries of Paleoclimate Reconstructions 
+Version: 1.1.0
 Authors@R: c(
        person("Michela", "Leonardi", role = "aut"),
        person(c("Emily","Y."), "Hallet", role = "ctb"),
@@ -12,32 +11,27 @@ Authors@R: c(
          email = "[email protected]")
      )
 Maintainer: Andrea Manica <[email protected]>
-Description: Currently this package focuses on Beyer et al 2020, a reconstruction
-    of climate based on the HadCM3 model for the last 120k years, and Krapp et al 
-    2021, covering the last 800k years. The reconstructions
-    are bias-corrected and downscaled to 0.5 degree, and this package helps using
-    these data for ecological and archaeological studies.
+Description: This R package is designed to provide an easy way to extract and manipulate paleoclimate
+  reconstructions for ecological and anthropological analyses.
 License: CC BY 4.0
 URL: https://github.com/EvolEcolGroup/pastclim,
     https://evolecolgroup.github.io/pastclim/
 BugReports: https://github.com/EvolEcolGroup/pastclim/issues
 Encoding: UTF-8
 LazyData: true
 LazyDataCompression: xz
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Depends: 
-    R (>= 3.5.0)
+  R (>= 4.0.0)
 Imports:
   curl,
   ncdf4,
-  terra
+  terra,
+  utils
 Suggests: 
-    rmarkdown,
-    knitr,
-    pastclimData,
-    sf,
-    testthat (>= 3.0.0)
-Remotes:
-  EvolEcolGroup/pastclimData  
+  rmarkdown,
+  knitr,
+  sf,
+  testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -1,15 +1,28 @@
 # Generated by roxygen2: do not edit by hand
 
+export(check_dataset_path)
 export(climate_for_locations)
 export(climate_for_time_slice)
+export(df_from_region_series)
+export(df_from_region_slice)
 export(download_dataset)
 export(get_available_datasets)
 export(get_biome_classes)
+export(get_data_path)
 export(get_downloaded_datasets)
 export(get_ice_mask)
 export(get_land_mask)
 export(get_mis_time_steps)
-export(get_pastclimdata_path)
+export(get_time_steps)
 export(get_vars_for_dataset)
+export(is_region_series)
+export(location_series)
+export(location_slice)
+export(region_series)
+export(region_slice)
+export(sample_region_series)
+export(sample_region_slice)
+export(set_data_path)
+export(slice_region_series)
 export(time_series_for_locations)
 import(terra)

NEWS.md

@@ -0,0 +1,18 @@
+# pastclim 1.1.0
+
+* Expand functionality to handle time series for regions; rename functions  to
+  extract data for regions and locations to make them consistent. Old code will
+  still work, but will raise a warning that the functions are deprecated.
+
+* Remove the need for `pastclimData`, we now put any data in the user dir returned
+  by R>=4.0.0. This removes the need of re-downloading the data when upgrading R.
+
+* Add monthly variables to Beyer2020 and Krapp2021.
+
+# pastclim 1.0.1
+
+* Fix bug when information was extracted for just one location.
+
+# pastclim 1.0.0
+
+* Initial public release

R/check_available_datasets.R

@@ -0,0 +1,23 @@
+#' Check if dataset is available.
+#'
+#' Internal getter function
+#'
+#' @param dataset string defining dataset
+#' @param include_custom boolean whether a 'custom' dataset is allowed
+#'
+#' @keywords internal
+
+
+check_available_dataset <- function(dataset, include_custom = FALSE) {
+  available_datasets <- get_available_datasets()
+  if (include_custom) {
+    available_datasets <- c(available_datasets, "custom")
+  }
+  if (!dataset %in% available_datasets) {
+    stop("'dataset' must be one of ", paste(available_datasets,
+      collapse = ", "
+    ))
+  } else {
+    return(TRUE)
+  }
+}

R/check_dataset_path.R

@@ -0,0 +1,30 @@
+#' Check dataset and path_to_nc params.
+#'
+#' Check that the dataset and path_to_nc parameters are valid
+#'
+#' @param dataset string defining the dataset to use. If set to "custom",
+#' then a single nc file is used from "path_to_nc"
+#' @param path_to_nc the path to the custom nc file containing the paleoclimate
+#' reconstructions. All the variables of interest need to be included in
+#' this file.
+#'
+#' @export
+
+
+check_dataset_path <- function(dataset, path_to_nc) {
+  check_available_dataset(dataset = dataset, include_custom = TRUE)
+
+  if (all(dataset == "custom", is.null(path_to_nc))) {
+    stop("you need to set path_to_nc if dataset='custom'")
+  }
+  # check that we are only given path_to_nc if we use a custom dataset
+  if (!is.null(path_to_nc)) {
+    if (dataset != "custom") {
+      stop("path_to_nc can only be set if dataset=='custom'")
+    }
+    if (!file.exists(path_to_nc)) {
+      stop("path_to_nc does not point to a file")
+    }
+  }
+  return(TRUE)
+}

R/check_var_downloaded.R

@@ -0,0 +1,24 @@
+#' Internal functions to check whether we have downloaded a given variable
+#' for a dataset
+#'
+#' @param variable a vector of names of the variables of interest
+#' @param dataset dataset of interest
+#'
+#' @keywords internal
+
+check_var_downloaded <- function(variable, dataset) {
+  # first check the variable exists for that dataset
+  check_available_variable(variable, dataset)
+
+  # test if we have downloaded already
+  if (!all(variable %in% get_downloaded_datasets()
+  [[dataset]])) {
+    missing_vars <- variable[!variable %in%
+      get_downloaded_datasets()[[dataset]]]
+    stop(
+      "variable (", paste(missing_vars, collapse = ", "),
+      ") not yet downloaded, use `download_dataset()`"
+    )
+  }
+  return(TRUE)
+}

R/check_var_in_nc.R

@@ -3,8 +3,8 @@
 #' Internal function to test a custom nc file.
 #'
 #' @param bio_variables vector of names of variables to be extracted
-#' @param path_to_nc the path to the file that contains the downloaded
-#' resonstructions.
+#' @param path_to_nc the path to the custom nc file containing the paleoclimate
+#' reconstructions.
 #'
 #' @keywords internal
 
@@ -25,7 +25,8 @@ check_var_in_nc <- function(bio_variables, path_to_nc) {
   if (!all(bio_variables %in% nc_in_vars)) {
     stop(
       "variable (", paste(bio_variables[!bio_variables %in% nc_in_vars],
-                          collapse = ", "),
+        collapse = ", "
+      ),
       ") not present in the file"
     )
   }