Function to thin occurrence data Cleans up duplicated longitude and latitude data by year using a specified distance threshold. The distance can be specified as a geographic distance or, if a raster_mask is provided, as a pixel distance.

Usage

clean_dup_by_date(
  this_species,
  threshold,
  by_mask = FALSE,
  raster_mask = NULL,
  n_ngbs = 0
)

Arguments

this_species

An object of class sp.temporal.modeling representing species occurrence data organized by date. See sp_temporal_data.

threshold

A numeric value representing the distance threshold between coordinates to be considered duplicates. Units depend on whether by_mask is TRUE or FALSE. If TRUE, the user needs to specify the number of pixels that define the neighborhood of duplicates (see n_ngbs parameter).

by_mask

Logical. If TRUE, the thinning process will use a raster layer as a mask for defining distance in pixel units.

raster_mask

An object of class SpatRaster that serves as a reference to thin the occurrence data. Required if by_mask is TRUE.

n_ngbs

Number of pixels used to define the neighborhood matrix that helps determine which occurrences are duplicates:

0 removes occurrences within the same pixel, keeping one.
1 considers duplicates all occurrences within a distance of one pixel.
n considers duplicates all occurrences within a distance of n pixels.

Value

An object of class sp.temporal.modeling containing a temporal data.frame with cleaned occurrence data, including columns for longitude, latitude, date variable, layers_dates, and layers_path.

Details

This function is based on clean_dup. It cleans up duplicated occurrences based on the specified threshold. If by_mask is TRUE, the distance is interpreted as pixel distance using the provided raster_mask; otherwise, it is interpreted as geographic distance.

Examples

library(tenm)
data("abronia")
tempora_layers_dir <- system.file("extdata/bio",package = "tenm")
tenm_mask <- terra::rast(file.path(tempora_layers_dir,"1939/bio_01.tif"))
# Clean duplicates without raster mask (just by distance threshold)
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$")
abtc1 <- tenm::clean_dup_by_date(abt,threshold = terra::res(tenm_mask)[1])
# Check number of records
print(nrow(abtc1$temporal_df))
#> [1] 40
# Clean duplicates using a raster mask
abtc2 <- tenm::clean_dup_by_date(this_species = abt,
                                by_mask = TRUE,
                                threshold = terra::res(tenm_mask)[1],
                                raster_mask = tenm_mask,
                                n_ngbs = 0)
# Check number of records
print(nrow(abtc2$temporal_df))
#> [1] 50

abtc3 <- tenm::clean_dup_by_date(this_species = abt,
                                by_mask = TRUE,
                                threshold = terra::res(tenm_mask)[1],
                                raster_mask = tenm_mask,
                                n_ngbs = 2)
# Check number of records
print(nrow(abtc3$temporal_df))
#> [1] 38