ebirdst (version 3.2022.3)

load_raster: Load eBird Status Data Products raster data

Description

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.

Usage

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()
)

Value

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.

Arguments

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 "yebsap-example".

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 (metric = "median") and the summarized products are the cell-wise mean across the weeks within the season (metric = "mean"). However, additional variants exist for some of the products. For the weekly relative abundance, confidence intervals are provided: specify metric = "lower" to get the 10th quantile or metric = "upper" to get the 90th quantile. For the seasonal and annual products, the cell-wise maximum values across weeks can be obtained with metric = "max".

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 ebirdst_data_dir().

Details

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.

Examples

if (FALSE) {
# 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"]]
}