faunabr (version 1.0.0)

filter_faunabr: Identify records outside natural ranges according to Fauna do Brasil

Description

This function removes or flags records outside of the species' natural ranges according to information provided by the Fauna do Brasil database

Usage

filter_faunabr(data, occ, species = "species", long = "x", lat = "y",
                      by_state = TRUE, buffer_state = 20, by_country = TRUE,
                      buffer_country = 20, value = "flag&clean",
                      keep_columns = TRUE, spat_state = NULL,
                      spat_country = NULL, verbose = TRUE)

Value

Depending on the 'value' argument. If value = "flag", it returns the same data.frame provided in data with additional columns indicating if the record falls inside the natural range of the specie (TRUE) or outside (FALSE). If value = "clean", it returns a data.frame with only the records that passes all the tests (TRUE for all the filters). If value = "flag&clean" (Default), it returns a list with two data.frames: one with the flagged records and one with the cleaned records.

Arguments

data

(data.frame) the data.frame imported with the load_faunabr function.

occ

(data.frame) a data.frame with the records of the species.

species

(character) column name in occ with species names. Default = "species"

long

(character) column name in occ with longitude data. Default = "x"

lat

(character) column name in occ with latitude data. Default = "y"

by_state

(logical) filter records by state? Default = TRUE

buffer_state

(numeric) buffer (in km) around the polygons of the states of occurrence of the specie. Default = 20.

by_country

(logical) filter records by country? Default = TRUE

buffer_country

(numeric) buffer (in km) around the polygons of the countries of occurrence of the specie. Default = 20.

value

(character) Defines output values. See Value section. Default = "flag&clean".

keep_columns

(logical) if TRUE, keep all the original columns of the input occ. If False, keep only the columns species, long and lat. Default = 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.

verbose

(logical) Whether to display species being filtered during function execution. Set to TRUE to enable display, or FALSE to run silently. Default = TRUE.

Details

If by_state = TRUE and/or by_country = TRUE, the function takes polygons representing the states and/or countrys with confirmed occurrences of the specie, draws a buffer around the polygons, and tests if the records of the species fall inside it.

Examples

data("fauna_data") #Load fauna e Funga do Brasil data
data("occurrences") #Load occurrences
pts <- subset(occurrences, species == "Panthera onca")
fd <- filter_faunabr(data = fauna_data,
                     occ = pts, long = "x", lat = "y", species = "species",
                     by_state = TRUE, buffer_state = 20,
                     by_country = TRUE, buffer_country = 20,
                     value = "flag&clean", keep_columns = TRUE,
                     verbose = FALSE)