R/filter_faunabr.R
filter_faunabr.RdThis function removes or flags records outside of the species' natural ranges according to information provided by the Fauna do Brasil database
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)(data.frame) the data.frame imported with the
load_faunabr function.
(data.frame) a data.frame with the records of the species.
(character) column name in occ with species names. Default = "species"
(character) column name in occ with longitude data. Default = "x"
(character) column name in occ with latitude data. Default = "y"
(logical) filter records by state? Default = TRUE
(numeric) buffer (in km) around the polygons of the states of occurrence of the specie. Default = 20.
(logical) filter records by country? Default = TRUE
(numeric) buffer (in km) around the polygons of the countries of occurrence of the specie. Default = 20.
(character) Defines output values. See Value section. Default = "flag&clean".
(logical) if TRUE, keep all the original columns of the input occ. If False, keep only the columns species, long and lat. Default = TRUE
(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.
(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.
(logical) Whether to display species being filtered during function execution. Set to TRUE to enable display, or FALSE to run silently. Default = TRUE.
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.
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.
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)