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Identify records outside natural ranges according to Flora e Funga do Brasil

Source: R/flag_florabr.R
flag_florabr.Rd

Flags (validates) occurrence records based on known distribution data from the Flora e Funga do Brasil (florabr) 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, biomes, or the entire country. Records are flagged as valid (TRUE) if they fall within the specified range for the distribution information available in the florabr data.

Usage

flag_florabr(
  data_dir,
  occ,
  species = "species",
  long = "decimalLongitude",
  lat = "decimalLatitude",
  origin = NULL,
  by_state = TRUE,
  buffer_state = 20,
  by_biome = TRUE,
  buffer_biome = 20,
  by_endemism = TRUE,
  buffer_brazil = 20,
  state_vect = NULL,
  state_column = NULL,
  biome_vect = NULL,
  biome_column = NULL,
  br_vect = NULL,
  keep_columns = TRUE,
  progress_bar = FALSE,
  verbose = FALSE
)

Arguments

data_dir

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

occ

(data.frame) 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 or NULL) filter the florabr data by origin type before checking ("native", "cultivated", "naturalized", "unknown", or "not_found_in_brazil"). 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_biome

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

buffer_biome

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

by_endemism

(logical) if TRUE, includes a check against the entire Brazilian boundary. Default is TRUE.

buffer_brazil

(numeric) buffer distance (in kilometers) to be applied around the entire Brazilian boundary. Default is 20 km.

state_vect

(SpatVector) qn optional custom simple features (sf) vector representing Brazilian states/regions. If NULL, uses the default data loaded by florabr. Default is NULL.

state_column

(character) the name of the column in state_vect (or the default state vector) used to match distribution information. Default is NULL.

biome_vect

(SpatVector) an optional custom simple features (sf) vector representing Brazilian biomes. If NULL, uses the default data loaded by florabr. Default is NULL.

biome_column

(character) the name of the column in biome_vect (or the default biome vector) used to match distribution information. Default is NULL.

br_vect

(SpatVector) an optional custom simple features (sf) vector representing the entire Brazilian boundary. If NULL, uses the default data loaded by florabr. Default is NULL.

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.

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 florabr_flag. This column is logical (TRUE/FALSE) indicating whether the record falls within the expected distribution (plus buffer) based on the florabr data. Records for species not found in the florabr data will have NA in the florabr_flag column.

Examples

# Load example data
data("occurrences", package = "RuHere")
# Get only occurrences from Araucaria
occ <- occurrences[occurrences$species == "Araucaria angustifolia", ]
# Set folder where distributional datasets were saved
# Here, just a sample provided in the package
# You must run 'florabr_here()' beforehand to download the necessary data files for your species
dataset_dir <- system.file("extdata/datasets", package = "RuHere")

# Flag records using specialist information from Flora do Brasil
occ_flora <- flag_florabr(data_dir = dataset_dir, occ = occ)