cells2samp: Helper function to randomly select cell IDs for generating...

In tenm: Temporal Ecological Niche Models

Helper function to randomly select cell IDs for generating environmental background data.

Description

This function returns pixel IDs to be sampled for generating environmental background data around species occurrence points.

Usage

cells2samp(
  data,
  longitude,
  latitude,
  cell_ids = NULL,
  buffer_ngbs = 2,
  raster_mask,
  process_ngbs_by = 10,
  n_bg = 50000,
  progress = TRUE
)

Arguments

data	A data.frame containing longitude and latitude data of occurrence points.
longitude	A character vector specifying the column name of longitude in 'data'.
latitude	A character vector specifying the column name of latitude in 'data'.
cell_ids	A numeric vector indicating the IDs of cells that serve as geographic centers for buffers. Default is NULL.
buffer_ngbs	Number of neighboring pixels around occurrence points used to build the buffer for sampling.
raster_mask	An object of class SpatRaster used to obtain pixel IDs.
process_ngbs_by	Numeric parameter to improve memory management. It process neighbor cells by a quantity specified by the user.
n_bg	Number of background pixels to sample.
progress	Logical. If TRUE, show computation progress.

Value

A numeric vector of cell IDs to be sampled for environmental background data.

Examples

# cells to sample
data(abronia)
temporal_layer <- system.file("extdata/bio/2016/bio_01.tif",package = "tenm")
raster_mask <- terra::rast(temporal_layer)
set.seed(123)
samp_01 <- tenm::cells2samp(data = abronia,
                            longitude = "decimalLongitude",
                            latitude = "decimalLatitude",
                            cell_ids = NULL,
                            buffer_ngbs = 4,
                            raster_mask = raster_mask,
                            process_ngbs_by = 10,
                            n_bg = 50000,
                            progress =TRUE)
# Generete a sample using pixel IDs
samp_02 <- tenm::cells2samp(data = abronia,
                            longitude = NULL,
                            latitude = NULL,
                            cell_ids = c(256,290,326),
                            buffer_ngbs = 4,
                            raster_mask = raster_mask,
                            process_ngbs_by = 10,
                            n_bg = 50000,
                            progress =TRUE)

tenm documentation built on Sept. 11, 2024, 6:34 p.m.