Function to retrieve background data from occurrence records. The background data is organized as a function of the dated environmental data.
Usage
bg_by_date(
this_species,
buffer_ngbs = NULL,
buffer_distance = 1000,
n_bg = 50000,
process_ngbs_by = 100
)Arguments
- this_species
An object of class sp.temporal.env representing species occurrence data organized by date. See
ex_by_date.- buffer_ngbs
Number of pixel neighbors used to build the buffer around each occurrence point.
- buffer_distance
Distance (in the same units as raster layers) used to create a buffer around occurrence points to sample background data.
- n_bg
Number of background points to sample.
- process_ngbs_by
Numeric parameter to improve memory management. It process neighbor cells by a quantity specified by the user.
Value
An object of class sp.temporal.bg containing background data organized by date. The object is a list with the following components:
"bg_df": A data.frame with columns for longitude, latitude, year, layer_date, layer_path, cell_ids_year, and environmental information.
Other metadata relevant to background sampling.
Details
This function retrieves background data around species occurrence points,
sampled based on the dated environmental data provided in this_species.
Background points are sampled within a buffer around each occurrence point.
The function returns an object of class sp.temporal.bg, which contains
background data organized by date. This object is the input of the function
tenm_selection.
Examples
# \donttest{
library(tenm)
data("abronia")
tempora_layers_dir <- system.file("extdata/bio",package = "tenm")
abt <- tenm::sp_temporal_data(occs = abronia,
longitude = "decimalLongitude",
latitude = "decimalLatitude",
sp_date_var = "year",
occ_date_format="y",
layers_date_format= "y",
layers_by_date_dir = tempora_layers_dir,
layers_ext="*.tif$")
abtc <- tenm::clean_dup_by_date(abt,threshold = 10/60)
#This code is for running in parallel
future::plan("multisession",workers=2)
abex <- tenm::ex_by_date(this_species = abtc,train_prop=0.7)
abbg <- tenm::bg_by_date(this_species = abex,
buffer_ngbs=10,n_bg=50000)
future::plan("sequential")
# }