ebirdst (version 0.3.5)

calc_full_extent: Calculate the spatial extent of non-zero data in a raster

Description

eBird Status and Trends data cubes are defined over broad areas, filling in regions where the species doesn't occur with zeros (predicted absences) or NAs (regions where models weren't fit). When producing maps, it's best to only display the spatial extent where the species occurs. To show determine an ideal extent for mapping, this function trims away 0 and NA values. When called on a RasterStack (e.g., a data cube consisting of all 52 weeks), this function returns the extent of occurrence across all layers.To access a pre-calculated extent for the full annual cycle use load_fac_map_parameters().

Usage

calc_full_extent(x, aggregate = TRUE)

Value

The extent of occurrence as a raster

Extent object.

Arguments

x

Raster object; either a full 52-week data cube or a subset.

aggregate

logical; whether data should be aggregated by a factor of 3 in each dimension prior to calculating the extent. When working with the high resolution cubes, data should be aggregated otherwise processing times will be extremely long.

Examples

if (FALSE) {
# simple toy example
r <- raster::raster(nrow = 100, ncol = 100)
r[5025:5075] <- 1
raster::extent(r)
calc_full_extent(r)

# download example data
path <- ebirdst_download("example_data")
# or get the path if you already have the data downloaded
path <- get_species_path("example_data")

# load abundance data
abd <- load_raster(path, "abundance")

# calculate full extent
map_extent <- calc_full_extent(abd)

# plot
raster::plot(abd[[20]], axes = FALSE, ext = map_extent)
}