Retrieving data
Use paleoclim() to download paleoclimate data from
PaleoClim, specifying the desired time period (see above) and
resolution. For example, to download data for the Late Holocene
("lh") at 10 min resolution:
paleoclim("lh", "10m")
#> class : SpatRaster
#> dimensions : 1044, 2160, 19 (nrow, ncol, nlyr)
#> resolution : 0.1666667, 0.1666667 (x, y)
#> extent : -180.0001, 179.9999, -90.00014, 83.99986 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> sources : bio_1.tif
#> bio_10.tif
#> bio_11.tif
#> ... and 16 more source(s)
#> names : bio_1, bio_10, bio_11, bio_12, bio_13, bio_14, ...
#> min values : -526, -334, -656, 0, 0, 0, ...
#> max values : 314, 385, 288, 9696, 2399, 651, ...The result is a SpatRaster object with up to 19 layers
containing reconstructed values of the standard “bioclimatic variables”
(see above) for this period. Consult the terra
documentation for information on working with
spatial raster data in R.
By default, paleoclim() loads the entire downloaded
raster into R, i.e. the whole globe. You can conveniently crop it to a
specific (rectangular) region of interest with the region
argument. This can be specified with a SpatExtent object or
anything coercible to one (see ?terra::ext), which includes
most spatial data types, or simply a vector of coordinates (xmin, xmax,
ymin, ymax):
europe <- c(-15, 45, 30, 90)
europe_lh <- paleoclim("lh", "10m", region = europe)
plot(europe_lh[["bio_12"]], main = "Late Holocene annual precipitation, Europe")
If you have already downloaded data from PaleoClim and simply want to
read it into R, you can do so with load_paleoclim(),
passing it the path to the .zip archive:
zipfile <- system.file("testdata", "LH_v1_10m_cropped.zip",
package = "rpaleoclim")
load_paleoclim(zipfile)
#> class : SpatRaster
#> dimensions : 6, 6, 19 (nrow, ncol, nlyr)
#> resolution : 0.1666667, 0.1666667 (x, y)
#> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> sources : bio_1.tif
#> bio_10.tif
#> bio_11.tif
#> ... and 16 more source(s)
#> names : bio_1, bio_10, bio_11, bio_12, bio_13, bio_14, ...
#> min values : -526, -334, -656, 0, 0, 0, ...
#> max values : 314, 385, 288, 9696, 2399, 651, ...Caching
Note that in the examples above, we only downloaded data from the
PaleoClim servers once. Repeated calls to paleoclim() that
ask for the same time period and resolution reuse cached versions of the
previously downloaded file. By default, these files are stored in R’s
temporary directory, so that you only download the files once per
session. The cached files are never modified; subsequent cropping,
warping, etc. is either done in-memory or creates new temporary
files.
The cache_path argument controls the directory that
paleoclim() downloads files to and tries to read cached
data from. It can be useful to change this to somewhere within the
working directory to reuse the same files between sessions and ensure
your analysis can be reproduced in the future, even if the remote
PaleoClim data changes or disappears.
skip_cache = TRUE will force paleoclim() to
download files from PaleoClim even if cached data exists in
cache_path (in which case it will overwrite it).
quiet = TRUE suppresses messages about whether the data
is being downloaded or read from a cached file.
Backwards compatibility with raster
Since version 0.9.1, rpaleoclim has depended on the terra package for reading and
manipulating spatial data. Previous versions used raster and rgdal,
which are
now deprecated. To use the old raster types, you will
need to install the optional dependency raster:
Then pass as = "raster" to paleoclim() or
load_paleoclim() to return the data as a
RasterStack object instead of a
SpatRaster.
paleoclim("lh", "10m", as = "raster")
#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
#> which was just loaded, will retire in October 2023.
#> Please refer to R-spatial evolution reports for details, especially
#> https://r-spatial.org/r/2023/05/15/evolution4.html.
#> It may be desirable to make the sf package available;
#> package maintainers should consider adding sf to Suggests:.
#> The sp package is now running under evolution status 2
#> (status 2 uses the sf package in place of rgdal)
#> Warning: `as = "raster"` is deprecated and will be removed in future versions of rpaleoclim
#> This warning is displayed once per session.
#> class : RasterStack
#> dimensions : 1044, 2160, 2255040, 19 (nrow, ncol, ncell, nlayers)
#> resolution : 0.1666667, 0.1666667 (x, y)
#> extent : -180.0001, 179.9999, -90.00014, 83.99986 (xmin, xmax, ymin, ymax)
#> crs : +proj=longlat +datum=WGS84 +no_defs
#> names : bio_1, bio_10, bio_11, bio_12, bio_13, bio_14, bio_15, bio_16, bio_17, bio_18, bio_19, bio_2, bio_3, bio_4, bio_5, ...
#> min values : -526, -334, -656, 0, 0, 0, 0, 0, 0, 0, 0, 6, 3, 116, -292, ...
#> max values : 314, 385, 288, 9696, 2399, 651, 215, 6321, 2025, 5128, 3860, 169, 90, 24243, 481, ...Please note that raster support will be removed in a
future version of rpaleoclim.