load_raster | R Documentation |
Each of the eBird Status raster products is packaged as a GeoTIFF file
representing predictions on a regular grid. The core products are occurrence,
count, relative abundance, and proportion of population. This function loads
one of the available data products into R as a
SpatRaster object. Note that data must be download using
ebirdst_download_status()
prior to loading it using this function.
load_raster(
species,
product = c("abundance", "count", "occurrence", "proportion-population"),
period = c("weekly", "seasonal", "full-year"),
metric = NULL,
resolution = c("3km", "9km", "27km"),
path = ebirdst_data_dir()
)
species |
character; the species to load data for, given as a scientific
name, common name or six-letter species code (e.g. "woothr"). The full list
of valid species is in the ebirdst_runs data frame included in this
package. To download the example dataset, use |
product |
character; eBird Status raster product to load: occurrence, count, relative abundance, or proportion of population. See Details for a detailed explanation of each of these products. |
period |
character; temporal period of the estimation. The eBird Status models make predictions for each week of the year; however, as a convenience, data are also provided summarized at the seasonal or annual ("full-year") level. |
metric |
character; by default, the weekly products provide estimates of
the median value ( |
resolution |
character; the resolution of the raster data to load. The default is to load the native 3 km resolution data; however, for some applications 9 km or 27 km data may be suitable. |
path |
character; directory to download the data to. All downloaded
files will be placed in a sub-directory of this directory named for the
data version year, e.g. "2020" for the 2020 Status Data Products. Each
species' data package will then appear in a directory named with the eBird
species code. Defaults to a persistent data directory, which can be found
by calling |
The core eBird Status data products provide weekly estimates across a regular spatial grid. They are packaged as rasters with 52 layers, each corresponding to estimates for a week of the year, and we refer to them as "cubes" (e.g. the "relative abundance cube"). All estimates are the median expected value for a standard 2 km, 1 hour eBird Traveling Count by an expert eBird observer at the optimal time of day and for optimal weather conditions to observe the given species. These products are:
occurrence
: the expected probability (0-1) of occurrence of a species.
count
: the expected count of a species, conditional on its occurrence at
the given location.
abundance
: the expected relative abundance of a species, computed as the
product of the probability of occurrence and the count conditional on
occurrence.
proportion-population
: the proportion of the total relative abundance
within each cell. This is a derived product calculated by dividing each cell
value in the relative abundance raster by the total abundance summed across
all cells.
In addition to these weekly data cubes, this function provides access to data
summarized over different periods. Seasonal cubes are produced by taking the
cell-wise mean or max across the weeks within each season. The boundary dates
for each season are species specific and are available in ebirdst_runs
, and
if a season failed review no associated layer will be included in the cube.
In addition, full-year summaries provide the mean or max across all weeks of
the year that fall within a season that passed review. Note that this is not
necessarily all 52 weeks of the year. For example, if the estimates for the
non-breeding season failed expert review for a given species, the full-year
summary for that species will not include the weeks that would fall within
the non-breeding season.
For the weekly cubes, a SpatRaster with 52
layers for the given product, where the layer names are the dates
(YYYY-MM-DD
format) of the midpoint of each week. Seasonal cubes will
have up to four layers named with the corresponding season. The full-year
products will have a single layer.
## Not run:
# download example data if hasn't already been downloaded
ebirdst_download("yebsap-example")
# weekly relative abundance
# note that only 27 km data are available for the example data
abd_weekly <- load_raster("yebsap-example", "abundance", resolution = "27km")
# the weeks for each layer are stored in the layer names
names(abd_weekly)
# they can be converted to date objects with as.Date
as.Date(names(abd_weekly))
# max seasonal abundance
abd_seasonal <- load_raster("yebsap-example", "abundance",
period = "seasonal", metric = "max",
resolution = "27km")
# available seasons in stack
names(abd_seasonal)
# subset to just breeding season abundance
abd_seasonal[["breeding"]]
## End(Not run)
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