Add HYDE 3.3. database

NEWS.md

@@ -1,10 +1,12 @@
 # pastclim 2.0.0
 * Add Barreto et al 2023 (based on PALEO-PGEM, covering the last 5 M years)
 * Add all the WorldClim data (present, and future projections with multiple models
-and emission scenarios).
+  and emission scenarios).
+* Add the HYDE 3.3 database providing information on agriculture and population sizes
+  for the last 10k years.
 * Change the units of Krapp et al 2021 to match those of other datasets. Also, fix
-data duplication of some variables which has now also been fixed on the OSF repository
-for that dataset.
+  data duplication of some variables which has now also been fixed on the OSF repository
+  for that dataset.
 * Improve `get_ice_mask()`, `get_land_mask()`, and `distance_from_sea()` to work
   on series rather than just on slices.
 * Speed up `region_*()` functions when subsetting the extent/cropping.

R/datasets_docs.R

@@ -187,3 +187,34 @@ NULL
 #' @name Barreto2023
 NULL
 #> NULL
+
+#' Documentation for HYDE 3.3 dataset
+#'
+#' This database presents an update and expansion of the History Database of 
+#' the Global Environment (HYDE, v 3.3) and replaces former HYDE 3.2 
+#' version from 2017. HYDE is and internally consistent combination of 
+#' updated historical population estimates and land use. Categories 
+#' include cropland, with a new distinction into irrigated and rain fed 
+#' crops (other than rice) and irrigated and rain fed rice. Also grazing 
+#' lands are provided, divided into more intensively used pasture, 
+#' converted rangeland and non-converted natural (less intensively used) 
+#' rangeland. Population is represented by maps of total, urban, rural 
+#' population and population density as well as built-up area. 
+#' 
+#' The period covered is 10 000 BCE to 2023 CE. Spatial resolution is 
+#' 5 arc minutes (approx. 85 km2 at the equator). The full HYDE 3.3 release 
+#' contains: a Baseline estimate scenario, a Lower estimate scenario and an 
+#' Upper estimate scenario. Currently only the baseline scenario is available
+#' in `pastclim`
+#'
+#' 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{doi.org/10.5194/essd-9-1-2017}
+#'
+#' @name HYDE_3.3_baseline
+NULL
+#> NULL
+

R/download_dataset.R

@@ -31,7 +31,7 @@ download_dataset <- function(dataset, bio_variables = NULL, annual = TRUE,
   # check that the variable is available for this dataset
   available_variables <-
     getOption("pastclim.dataset_list")$variable[getOption("pastclim.dataset_list")$dataset == dataset]
-  # if variable is null, donwload all possible variables
+  # if variable is null, download all possible variables
   if (is.null(bio_variables)) {
     bio_variables <- getOption("pastclim.dataset_list")[getOption("pastclim.dataset_list")$dataset == dataset, ]
     if (!monthly) {
@@ -55,13 +55,6 @@ download_dataset <- function(dataset, bio_variables = NULL, annual = TRUE,
     )
   }
 
-  # if (dataset %in% c("Krapp2021", "Beyer2020", "Example")){
-  #   # add biome to list of variables (we need it to generate the landmask)
-  #   if (!"biome" %in% bio_variables) {
-  #     bio_variables <- c(bio_variables, "biome")
-  #   }
-  # }
-
   # add biome to list of variables (we need it to generate the landmask)
   if (all((!"biome" %in% bio_variables), ("biome" %in% available_variables))) {
     bio_variables <- c(bio_variables, "biome")

R/time_bp.R

@@ -24,17 +24,21 @@ setGeneric("time_bp", function(x) {
 setMethod(
   "time_bp", signature(x = "SpatRaster"),
   function(x) {
-    if (timeInfo(x)$step != "years") {
+    if (timeInfo(x)$step == "years") {
+      time_bp <- terra::time(x) - 1950
+    } else if (any(inherits(terra::time(x), "POSIXct"), inherits(terra::time(x), "Date"))) {
+      time_bp <- date2ybp(terra::time(x))
+    } else {
       # as of 1.7.18, the bug in terra setting years to negative has ben fixed
       stop(
-        "The time units of SpatRaster are not 'years'.\n",
+        "The time units of SpatRaster are not 'years' or a 'days'.\n",
         "It might be a problem with the time units not being properly set in the original nc file.\n",
         "Set time units correctly with time_bp(x)<-c(-10000,-400).\n",
         "NOTE do NOT use terra:time, as that terra measures years from 0AD, not BP"
       )
     }
-    time_yr <- terra::time(x)
-    return(time_yr - 1950)
+
+    return(time_bp)
   }
 )
 
@@ -46,17 +50,7 @@ setMethod(
     if (!is_region_series(x)) {
       stop("this is not a valid region series; it should be a SpatRasterDataset where each dataset (i.e. variable) has the same time steps")
     }
-    if (timeInfo(x[[1]])$step != "years") {
-      # as of 1.7.18, the bug in terra setting years to negative has been fixed
-      stop(
-        "The time units of SpatRaster are not 'years'.\n",
-        "It might be a problem with the time units not being properly set in the original nc file.\n",
-        "Set time units correctly with time_bp(x)<-c(-10000,-400).\n",
-        "NOTE do NOT use terra:time, as that terra measures years from 0AD, not BP"
-      )
-    }
-    time_yr <- terra::time(x[[1]])
-    return(time_yr - 1950)
+    time_bp(x[[1]])
   }
 )
 

R/ybp2date.R

@@ -25,8 +25,8 @@ ybp2date <- function(x) {
 #' @rdname ybp2date
 #' @export
 date2ybp <- function(x) {
-  if (!inherits(x, "POSIXct")) {
-    stop("x should be a POSIXct object")
+  if (!any(inherits(x, "POSIXct"), inherits(x, "Date"))) {
+    stop("x should be a POSIXct or Date object")
   }
   lubridate::year(x) - 1950
 }

data-raw/data_files/dataset_list_included.csv

@@ -6528,3 +6528,19 @@ temperature_max_09,temperature_max_09,WorldClim_2.1_UKESM1-0-LL_ssp585_5m,TRUE,W
 temperature_max_10,temperature_max_10,WorldClim_2.1_UKESM1-0-LL_ssp585_5m,TRUE,WorldClim_2.1_UKESM1-0-LL_ssp585_5m_tmax_v1.4.0.nc,,download_worldclim_future,,,1.4.0,maximum temperature Oct,max T Oct,october,degrees Celsius,*degree*C*,
 temperature_max_11,temperature_max_11,WorldClim_2.1_UKESM1-0-LL_ssp585_5m,TRUE,WorldClim_2.1_UKESM1-0-LL_ssp585_5m_tmax_v1.4.0.nc,,download_worldclim_future,,,1.4.0,maximum temperature Nov,max T Nov,november,degrees Celsius,*degree*C*,
 temperature_max_12,temperature_max_12,WorldClim_2.1_UKESM1-0-LL_ssp585_5m,TRUE,WorldClim_2.1_UKESM1-0-LL_ssp585_5m_tmax_v1.4.0.nc,,download_worldclim_future,,,1.4.0,maximum temperature Dec,max T Dec,december,degrees Celsius,*degree*C*,
+cropland,cropland,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_cropland.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/cropland.nc,,,,1.4.0,total cropland area,cropland,annual,km^2 per gridcell,*km^2*,
+grazing_land,grazing_land,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_grazing_land.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/grazing_land.nc,,,,1.4.0,total grazing land,grazing land,annual,km^2 per gridcell,*km^2*,
+irrigated_rice,irrigated_rice,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_irrigated_rice.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/irrigated_rice.nc,,,,1.4.0,irrigated rice,irrigated rice,annual,km^2 per gridcell,*km^2*,
+irrigated_not_rice,irrigated_not_rice,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_irrigated_not_rice.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/irrigated_not_rice.nc,,,,1.4.0,irrigated not rice,irrigated not rice,annual,km^2 per gridcell,*km^2*,
+pasture,pasture,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_pasture.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/pasture.nc,,,,1.4.0,total pasture area,pasture,annual,km^2 per gridcell,*km^2*,
+population_density,population_density,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_population_density.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/population_density.nc,,,,1.4.0,total population_density area,population_density,annual,km^2 per gridcell,*km^2*,
+population,population,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_population.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/population.nc,,,,1.4.0,total population area,population,annual,km^2 per gridcell,*km^2*,
+rainfed_not_rice,rainfed_not_rice,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_rainfed_not_rice.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/rainfed_not_rice.nc,,,,1.4.0,total rainfed_not_rice area,rainfed_not_rice,annual,km^2 per gridcell,*km^2*,
+rainfed_rice,rainfed_rice,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_rainfed_rice.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/rainfed_rice.nc,,,,1.4.0,total rainfed_rice area,rainfed_rice,annual,km^2 per gridcell,*km^2*,
+rangeland,rangeland,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_rangeland.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/rangeland.nc,,,,1.4.0,total rangeland area,rangeland,annual,km^2 per gridcell,*km^2*,
+rural_population,rural_population,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_rural_population.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/rural_population.nc,,,,1.4.0,total rural_population area,rural_population,annual,km^2 per gridcell,*km^2*,
+total_irrigated,total_irrigated,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_total_irrigated.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/total_irrigated.nc,,,,1.4.0,total total_irrigated area,total_irrigated,annual,km^2 per gridcell,*km^2*,
+total_rainfed,total_rainfed,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_total_rainfed.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/total_rainfed.nc,,,,1.4.0,total total_rainfed area,total_rainfed,annual,km^2 per gridcell,*km^2*,
+total_rice,total_rice,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_total_rice.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/total_rice.nc,,,,1.4.0,total total_rice area,total_rice,annual,km^2 per gridcell,*km^2*,
+urban_area,urban_area,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_urban_area.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/urban_area.nc,,,,1.4.0,total urban_area area,urban_area,annual,km^2 per gridcell,*km^2*,
+urban_population,urban_population,HYDE_3.3_baseline,FALSE,HYDE_3.3_baseline_urban_population.nc,https://geo.public.data.uu.nl/vault-hyde-data/HYDE%203.3%5B1696419673%5D/original/Baseline_scenario/NetCDF/urban_population.nc,,,,1.4.0,total urban_population area,urban_population,annual,km^2 per gridcell,*km^2*,