Merge branch 'cran_submission'

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

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master, dev]
+    branches: [master, dev, cran_submission]
   pull_request:
     branches: [master, dev]
 
@@ -43,11 +43,11 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
-      
-      - name: Get dev terra for MacOS
-        if: matrix.config.os == 'macos-latest'
-        run: install.packages('terra', repos='https://rspatial.r-universe.dev')
-        shell: Rscript {0}
+
+#      - name: Get dev terra for dev pastclim
+#        if: matrix.config.os == 'macos-latest' || ${{ github.base_ref == 'dev' }} || ${{ github.ref_name == 'dev' }}
+#        run: install.packages('terra', repos='https://rspatial.r-universe.dev')
+#        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.github/workflows/pkgdown.yaml

@@ -32,6 +32,11 @@ jobs:
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
+
+      - name: Get dev terra for dev pastclim
+        if: ${{ github.base_ref == 'dev' }} || ${{ github.ref_name == 'dev' }}
+        run: install.packages('terra', repos='https://rspatial.r-universe.dev')
+        shell: Rscript {0}
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.2.3
-Date: 2022-12-16 08:38:38 UTC
-SHA: 81c730879176e3ceecabce36f4cadb05d4286291
+Version: 1.2.4
+Date: 2023-04-25 20:01:34 UTC
+SHA: 56d0482f982fd7b991442fd6b8fc62d4168647e3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pastclim
 Type: Package
 Title: Manipulate Time Series of Palaeoclimate Reconstructions 
-Version: 1.2.3
+Version: 1.2.4
 Authors@R: c(
        person("Michela", "Leonardi", role = "aut"),
        person(c("Emily","Y."), "Hallet", role = "ctb"),
@@ -13,7 +13,7 @@ Authors@R: c(
 Maintainer: Andrea Manica <[email protected]>
 Description: Methods to easily extract and manipulate palaeoclimate
   reconstructions for ecological and anthropological analyses, as described
-  in Leonardi et al. (2022) <doi:10.1101/2022.05.18.492456>.
+  in Leonardi et al. (2023) <doi:10.1111/ecog.06481>.
 License: CC BY 4.0
 Language: en-GB
 URL: https://github.com/EvolEcolGroup/pastclim,
@@ -22,19 +22,22 @@ BugReports: https://github.com/EvolEcolGroup/pastclim/issues
 Encoding: UTF-8
 LazyData: true
 LazyDataCompression: xz
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
 Depends: 
   R (>= 4.0.0),
-  terra (>= 1.6.41)
+  methods,
+  terra (>= 1.7.18)
 Imports:
   curl,
   ncdf4,
   utils
 Suggests: 
-  rmarkdown,
-  knitr,
-  sf,
-  ggplot2,
-  testthat (>= 3.0.0)
+    rmarkdown,
+    knitr,
+    sf,
+    ggplot2,
+    testthat (>= 3.0.0),
+    spelling
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -1,10 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+export("time_bp<-")
 export(clean_data_path)
 export(climate_for_locations)
 export(climate_for_time_slice)
 export(df_from_region_series)
 export(df_from_region_slice)
+export(distance_from_sea)
 export(download_dataset)
 export(get_available_datasets)
 export(get_biome_classes)
@@ -17,7 +19,6 @@ export(get_time_steps)
 export(get_vars_for_dataset)
 export(is_region_series)
 export(location_series)
-export(location_series_old)
 export(location_slice)
 export(region_series)
 export(region_slice)
@@ -31,4 +32,7 @@ export(time_series_for_locations)
 export(update_dataset_list)
 export(validate_nc)
 export(var_labels)
+exportMethods("time_bp<-")
+exportMethods(time_bp)
+import(methods)
 import(terra)

NEWS.md

@@ -1,3 +1,6 @@
+# pastclim 1.2.4
+* Updates on how time is handled to stay in sync with changes in `terra`.
+
 # pastclim 1.2.3
 * Added lai to Krapp2021 (the variable is now also present in the original OSF
   repository for that dataset).

R/check_var_downloaded.R

@@ -1,4 +1,4 @@
-#' Internal functions to check whether we have downloaded a given variable
+#' Internal function to check whether we have downloaded a given variable
 #' for a dataset
 #'
 #' @param variable a vector of names of the variables of interest

R/clean_data_path.R

@@ -1,7 +1,7 @@
 #' Clean the data path 
 #'
 #' This function deletes old reconstructions that have been superseded in the
-#' data_path. It assumes that the only files in data_path are part of pastclim
+#' data_path. It assumes that the only files in data_path are part of `pastclim`
 #' (i.e. there are no custom datasets stored in that directory).
 #'
 #' @param ask boolean on whether the user should be asked before deleting

R/data.R

@@ -19,22 +19,22 @@
 
 #' Region outlines.
 #'
-#' An \code{sf} object containing outlines for major regions. Outlines that
+#' An [`sf::sf`] object containing outlines for major regions. Outlines that
 #' span the antimeridian have been split into multiple polygons.
 #'
-#' @format \code{sf} of outlines.
+#' @format [`sf::sf`] of outlines.
 #' \describe{
 #'   \item{name}{names of regions}
 #' }
 "region_outline"
 
 #' Region outlines unioned.
 #'
-#' An \code{sf} object containing outlines for major regions. Each outline is
+#' An [`sf::sf`] object containing outlines for major regions. Each outline is
 #' represented as a single polygon. If you want multiple polygons, use
 #' \link{region_outline}.
 #'
-#' @format \code{sf} of outlines.
+#' @format [`sf::sf`] of outlines.
 #' \describe{
 #'   \item{name}{names of regions}
 #' }

R/df_from_region_series.R

@@ -1,11 +1,11 @@
 #' Extract data frame from a region series
-#'
+#' 
 #' Extract the climatic information from a region series and organise them as
 #' a data frame.
 #' 
-#' To extract a data frame from a region slice, see \code{df_from_region_slice}.
+#' To extract a data frame from a region slice, see [df_from_region_slice()].
 #'
-#' @param x climate time series generated with \code{region_series}
+#' @param x climate time series generated with [region_series()]
 #' @param xy a boolean whether x and y coordinates should be added 
 #' to the dataframe (default to TRUE)
 #' @returns a data.frame where each cell each raster layer (i.e. timestep) is a

R/df_from_region_slice.R

@@ -1,12 +1,12 @@
 #' Extract data frame from a region slice
 #'
 #' Extract the climatic information from a region slice and organise it as
-#' a data frame. This is just a wrapper around \code{terra::as.data.frame}.
+#' a data frame. This is just a wrapper around [terra::as.data.frame()].
 #' 
-#' To extract a data frame from a region series, see \code{df_from_region_series}.
+#' To extract a data frame from a region series, see [df_from_region_series()].
 #'
-#' @param x climate time slice (i.e. a \code{terra::SpatRaster}) 
-#' generated with \code{region_slice}
+#' @param x climate time slice (i.e. a [`terra::SpatRaster`]) 
+#' generated with [region_slice()]
 #' @param xy a boolean whether x and y coordinates should be added 
 #' to the dataframe (default to TRUE)
 #' @returns a data.frame where each cell the raster is a

R/distance_from_sea.R

@@ -0,0 +1,28 @@
+#' Compute a raster of distances from the sea for each land pixel.
+#'
+#' Get the land mask for a dataset at a given time point, and compute distance
+#' from the sea for each land pixel.
+#'
+#' @param time_bp time slice in years before present (negative)
+#' @param dataset string defining the dataset to use (a list of possible
+#' values can be obtained with [get_available_datasets()]). This function
+#' will not work on custom datasets.
+#' @returns a [`terra::SpatRaster`] of distances
+#'
+#' @import terra
+#' @export
+
+distance_from_sea <- function(time_bp, dataset) {
+  this_land_mask <- get_land_mask(time_bp=time_bp,
+                                            dataset=dataset)
+  coastlines_polyline <- terra::as.polygons(this_land_mask) # first get polygon
+  coastlines_polyline <- terra::as.lines(coastlines_polyline) # then extract line
+
+  distances_rast <- terra::distance(this_land_mask$land_mask, 
+                                    coastlines_polyline,
+                                    unit="km")
+  distances_rast <- terra::mask(distances_rast, this_land_mask)
+  names(distances_rast) <- "distance_from_sea"
+
+  return(distances_rast)
+}

R/download_dataset.R

@@ -2,10 +2,10 @@
 #'
 #' This function downloads palaeoclimate reconstructions. Files will be stored
 #' in the data path of `pastclim`, which can be inspected with
-#' \code{get_data_path} and changed with \code{set_data_path}
+#' [get_data_path()] and changed with [set_data_path()]
 #'
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}). This function
+#' values can be obtained with [get_available_datasets()]). This function
 #' will not work on custom datasets.
 #' @param bio_variables one or more variable names to be downloaded. If left
 #' to NULL, all variables available for this dataset will be downloaded

R/get_biome_classes.R

@@ -4,7 +4,7 @@
 #' for a given dataset.
 #'
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}). This function
+#' values can be obtained with [get_available_datasets()]). This function
 #' will not work on custom datasets.
 #' @returns a data.frame with columns id and category.
 #'
@@ -39,5 +39,6 @@ get_biome_classes <- function(dataset) {
       category = biomes_string
     )
   }
+  ncdf4::nc_close(nc_in)
   return(biome_categories)
 }

R/get_data_path.R

@@ -3,7 +3,7 @@
 #' This function returns the path where climate reconstructions are stored.
 #' 
 #' The path is stored in an option for `pastclim` named `data_path`. If
-#' a configuration file was saved when using \code{set_data_path}, the path
+#' a configuration file was saved when using [set_data_path()], the path
 #' is retrieved from a file named "pastclim_data.txt", which
 #' is found in the directory returned by 
 #' `tools::R_user_dir("pastclim","config")` (i.e.

R/get_dataset_info.R

@@ -2,7 +2,7 @@
 #'
 #' This function provides full information about a given dataset. A full
 #' list of datasets available in pastclim can be obtained with
-#' \code{get_available_datasets}
+#' [get_available_datasets()]
 #'
 #' @param dataset A dataset in pastclim
 #' @returns text describing the dataset

R/get_file_for_dataset.R

@@ -4,9 +4,9 @@
 #'
 #' @param variable one or more variable names to be downloaded
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}). This function
+#' values can be obtained with [get_available_datasets()]). This function
 #' will not work on custom datasets.
-#' @returns the filename for taht variable and dataset
+#' @returns the filename for that variable and dataset
 
 get_file_for_dataset <- function(variable, dataset) {
   check_available_variable(variable, dataset)

R/get_ice_mask.R

@@ -4,9 +4,9 @@
 #'
 #' @param time_bp time slice in years before present (negative)
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}). This function
+#' values can be obtained with [get_available_datasets()]). This function
 #' will not work on custom datasets.
-#' @returns a binary \code{terra::SpatRaster} with the ice mask as 1s
+#' @returns a binary [`terra::SpatRaster`] with the ice mask as 1s
 #'
 #' @import terra
 #' @export

R/get_land_mask.R

@@ -4,9 +4,9 @@
 #'
 #' @param time_bp time slice in years before present (negative)
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}). This function
+#' values can be obtained with [get_available_datasets()]). This function
 #' will not work on custom datasets.
-#' @returns a binary \code{terra::SpatRaster} with the land mask as 1s
+#' @returns a binary [`terra::SpatRaster`] with the land mask as 1s
 #'
 #' @import terra
 #' @export

R/get_mis_time_steps.R

@@ -3,9 +3,9 @@
 #' Get the time steps available in a given dataset for a MIS.
 #'
 #' @param mis string giving the mis; it must use the same spelling as used in
-#' /code{mis_boundaries}
+#' [mis_boundaries]
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}). If set to
+#' values can be obtained with [get_available_datasets()]). 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 palaeoclimate
 #' reconstructions. All the variables of interest need to be included in

R/get_time_steps.R

@@ -3,7 +3,7 @@
 #' Get the time steps (in time_bp) available in a given dataset.
 #'
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}). If set to
+#' values can be obtained with [get_available_datasets()]). 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 palaeoclimate
 #' reconstructions. All the variables of interest need to be included in
@@ -24,9 +24,4 @@ get_time_steps <- function(dataset, path_to_nc = NULL) {
 
   climate_nc <- terra::rast(path_to_nc, subds=1)
   return(time_bp(climate_nc))
-
-  # climate_nc <- ncdf4::nc_open(path_to_nc)
-  # time_steps <- (climate_nc$dim$time$vals)
-  # ncdf4::nc_close(climate_nc)
-  # return(time_steps)
 }

R/get_vars_for_dataset.R

@@ -6,7 +6,7 @@
 #' different reconstructions.
 #'
 #' @param dataset string defining dataset to be downloaded (a list of possible
-#' values can be obtained with \code{get_available_datasets}).
+#' values can be obtained with [get_available_datasets()]).
 #' @param path_to_nc the path to the custom nc file containing the palaeoclimate
 #' reconstructions.
 #' @param details boolean determining whether the output should include information

R/is_region_series.R

@@ -1,16 +1,16 @@
 #' Check the object is a valid region series
 #'
-#' A region series is a \code{terra::SpatRasterDataset} for which each
+#' A region series is a [`terra::SpatRasterDataset`] for which each
 #' sub-dataset is a variable, and all variables have the same number of 
 #' time steps.
 #' 
 #' The standard test only checks that each SpatRaster has the same number of
 #' layers. The more thorough test (obtained with strict=TRUE) actually checks
 #' that all time steps are identical by comparing the result of 
-#' \code{terra::time} applied to each variable
+#' [terra::time()] applied to each variable
 #'
-#' @param x a \code{terra::SpatRasterDataset} representing a time series of
-#' regional reconstructions obtained from \code{region_series}.
+#' @param x a [`terra::SpatRasterDataset`] representing a time series of
+#' regional reconstructions obtained from [region_series()].
 #' @param strict a boolean defining whether to preform a thorough test (see
 #' description above for details).
 #' @returns TRUE if the object is a region series

R/load_dataset_list.R

@@ -2,7 +2,7 @@
 #'
 #' This function returns a dataframe with the details for each variable
 #' available in every dataset. It defaults to the copy stored within the
-#' package, but it checks in case there is an udpated version stored as
+#' package, but it checks in case there is an updated version stored as
 #' 'data_list.csv' in 
 #' `tools::R_user_dir("pastclim","config")`. If the latter is present, the last
 #' column, named 'dataset_list_v', provides the version of this table, and the