R/filter_florabr.R
filter_florabr.RdThis function removes or flags records outside of the species' natural ranges according to information provided by the Flora e Funga do Brasil database.
filter_florabr(data, occ, species = "species", long = "x", lat = "y",
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,
value = "flag&clean", keep_columns = TRUE,
verbose = TRUE)(data.frame) the data.frame imported with the
load_florabr 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 biome? Default = TRUE
(numeric) buffer (in km) around the polygons of the biomes of occurrence of the specie. Default = 20.
(logical) filter records by endemism? Default = TRUE
(numeric) buffer (in km) around the polygons of the brazil. Default = 20.
(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 geobr::read_state().
(character) name of the column in state_vect containing state abbreviations. Only use if biome_vect is not null.
(SpatVector) a SpatVector of the Brazilian biomes. By default, it uses the SpatVector provided by geobr::read_biomes(). It can be another SpatVector, but the structure must be identical to geobr::read_biomes() with biome names in English.
(character) name of the column in biome_vect containing names of brazilian biomes (in English: "Amazon", "Atlantic_Forest", "Caatinga", "Cerrado", "Pampa" and "Pantanal". Only use if biome_vect is not null.
(SpatVector) a SpatVector of brazil. By default, it uses the SpatVector provided by geobr::read_state() after being aggregated/dissolved,
(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
(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_biome = TRUE, the function takes polygons representing the states and/or biomes with confirmed occurrences of the specie, draws a buffer around the polygons, and tests if the records of the species fall inside it. If by_endemism = TRUE, the function checks if the species is endemic to brazil. If it is endemic, the function tests if the records of the specie fall inside a polygon representing the boundaries of brazil (with a buffer).
Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/
data("bf_data") #Load Flora e Funga do Brasil data
data("occurrences") #Load occurrences
pts <- subset(occurrences, species == "Myrcia hatschbachii")
fd <- filter_florabr(data = bf_data, occ = pts,
by_state = TRUE, buffer_state = 20,
by_biome = TRUE, buffer_biome = 20,
by_endemism = TRUE, buffer_brazil = 20,
state_vect = NULL,
biome_vect = NULL, br_vect = NULL,
value = "flag&clean", keep_columns = TRUE,
verbose = FALSE)