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Identify records outside natural ranges according to Fauna do Brasil

Source: R/flag_faunabr.R
flag_faunabr.Rd

Flags (validates) occurrence records based on known distribution data from the Catálogo Taxônomico da Fauna do Brasil (faunabr) data. This function checks if an occurrence point for a given species falls within its documented distribution, allowing for user-defined buffers around Brazilian states, or the entire country. Records are flagged as valid (TRUE) if they fall within the specified range for the distribution information available in the faunabr data.

Usage

flag_faunabr(
  data_dir,
  occ,
  species = "species",
  long = "decimalLongitude",
  lat = "decimalLatitude",
  origin = NULL,
  by_state = TRUE,
  buffer_state = 20,
  by_country = TRUE,
  buffer_country = 20,
  keep_columns = TRUE,
  spat_state = NULL,
  spat_country = NULL,
  progress_bar = FALSE,
  verbose = FALSE
)

Arguments

data_dir

(character) Required directory path where the faunabr data is saved.

occ

(data.frame or data.table) a data frame containing the occurrence records to be flagged. Must contain columns for species, longitude, and latitude.

species

(character) the name of the column in occ that contains the species scientific names. Default is "species".

long

(character) the name of the column in occ that contains the longitude values. Default is "decimalLongitude".

lat

(character) the name of the column in occ that contains the latitude values. Default is "decimalLatitude".

origin

(character) filter the faunabr data by origin type before checking ("native", "cryptogenic", or "exotic"). Default is NULL (no filtering).

by_state

(logical) if TRUE, flags records based on their distance to known Brazilian state distributions. Default is TRUE.

buffer_state

(numeric) buffer distance (in kilometers) to be applied around the known state distribution boundaries. Records within this distance are considered valid. Default is 20 km.

by_country

(logical) if TRUE, flags records based on their distance to country distributions. Default is TRUE.

buffer_country

(numeric) buffer distance (in kilometers) to be applied around the country boundaries. Records within this distance are considered valid. Default is 20 km.

keep_columns

(logical) if TRUE, the returned data frame contains all original columns from occ. If FALSE, it returns only the key columns and the flag. Default is TRUE.

spat_state

(SpatVector) a SpatVector of the Brazilian states. By default, it uses the SpatVector provided by geobr::read_state(). It can be another Spatvector, but the structure must be identical to 'faunabr::states', with a column called "abbrev_state" identifying the states codes.

spat_country

(SpatVector) a SpatVector of the world countries. By default, it uses the SpatVector provided by rnaturalearth::ne_countries. It can be another Spatvector, but the structure must be identical to 'faunabr::world_fauna', with a column called "country_code" identifying the country codes.

progress_bar

(logical) whether to display a progress bar during processing. If TRUE, the 'pbapply' package must be installed. Default is FALSE.

verbose

(logical) if TRUE, prints messages about the progress and the number of species being checked. Default is FALSE.

Value

#' A data.frame that is the original occ data frame augmented with a new column named faunabr_flag. This column is logical (TRUE/FALSE) indicating whether the record falls within the expected distribution (plus buffer) based on the faunabr data. Records for species not found in the faunabr data will have NA in the faunabr_flag column.

Examples

# Load example data
data("occurrences", package = "RuHere")
# Get only occurrences from Azure Jay
occ <- occurrences[occurrences$species == "Cyanocorax caeruleus", ]
# Set folder where distributional datasets were saved
# Here, just a sample provided in the package
# You must run 'faunabr_here()' beforehand to download the necessary data files for your species
dataset_dir <- system.file("extdata/datasets", package = "RuHere")
# Flag records using faunabr specialist information
occ_fauna <- flag_faunabr(data_dir = dataset_dir, occ = occ)