| Title: | A Method to Estimate the Accuracy and Biogeographical Status of Georeferenced Biological Data |
| Version: | 2.0.0 |
| Language: | en-GB |
| Description: | Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility https://www.gbif.org/ and from the Global Inventory of Floras and Traits https://gift.uni-goettingen.de/home. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review). |
| Depends: | R (≥ 3.5.0) |
| Imports: | data.table, geojsonio, graphics, grDevices, jsonlite, methods, plotfunctions, raster, rgbif, rnaturalearth, sf, sp, stats |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| URL: | https://github.com/EduardoArle/bRacatus |
| BugReports: | https://github.com/EduardoArle/bRacatus/issues |
| LazyData: | true |
| RoxygenNote: | 7.2.3 |
| Suggests: | knitr, rmarkdown |
| NeedsCompilation: | no |
| Packaged: | 2024-05-03 07:52:01 UTC; carloseduardoaribeiro |
| Author: | Eduardo Arlé [aut, cre], Alexander Zizka [aut], Patrick Weigelt [ctb], Sam Levin [ctb], Carsten Meyer [ths] |
| Maintainer: | Eduardo Arlé <eduardoarle@tauex.tau.ac.il> |
| Repository: | CRAN |
| Date/Publication: | 2024-05-03 13:30:02 UTC |
Hemitriccus mirandae spatialPoints exemplary file
Description
A SpatialPointsDataFrame containing the occurrences of
Hemitriccus mirandae downloaded from GBIF
Examples
data("H_mirandae_sp")
Cell ID raster
Description
A Raster half-degree raster of the world with unique IDs per cell
Examples
data("ID_raster")
Accuracy model
Description
A glm accuracy model
Examples
data("Model_accuracy")
Biogeographical model
Description
A glm biogeographical model
Examples
data("Model_biogeo")
Range Phalanger orientalis
Description
A SpatialPolygonsDataFrame Range Phalanger orientalis
Examples
data("Range_Phalanger_orientalis")
accuracy
Description
Estimates the Accuracy of Each Point Record.
Usage
accuracy(signals)
Arguments
signals |
output of the function "signalCalculation". A data.frame including the original point data and the signals sent by the reference regions. |
Value
The data.frame with the species occurrence information and an extra column indicating the estimated accuracy of each point.
availableCountries
Description
List of countries and entities names for checklists
Usage
availableCountries()
Value
This function provides a list of countries and entities names available with rworldmaps for checklists
Examples
country_list <- availableCountries()
biogeoStatus
Description
Estimates the biogeographic status of each point record.
Usage
biogeoStatus(signals)
Arguments
signals |
output of the function signalCalculation. A dataFrame including the original point data and the signals sent by the reference regions. |
Value
The dataFrame with the species occurrence information and an extra column indicating the estimated biogeographic status of each point.
countryChecklists
Description
Prepares user provided reference regions on a country level
Usage
countryChecklist(countries, biogeo_status)
Arguments
countries |
vector with one or more country names |
biogeo_status |
vector informing the status of each country: alien, native or unknown |
Value
This function provides shapefiles of countries with the correspondent biogeographic status of the species.
Examples
country_checklist <- countryChecklist(
c("Brazil","Argentina","Uruguay","Paraguay"),
c("native","alien","unknown","native"))
getOcc
Description
Downloads GBIF records iterating when necessary to overcome the limitation of 200,000 records
Usage
getOcc(species)
Arguments
species |
character, species binomial name |
Value
This function downloads all records for a species from GBIF that have coordinates info. If necessary it loops several times to overcome the limit of 200,000 occurrences imposed by occ_search function. It returns a data table.
Examples
sps_occurrence <- getOcc("Babiana tubulosa")
giftRegions
Description
Gets regions listed by GIFT for plant species
Usage
giftRegions(species, min_size = 1000, max_size = 1e+11)
Arguments
species |
character, species binomial name |
min_size |
numeric, minimum size of checklists (in km2) to be included in the analysis. |
max_size |
numeric, maximum size of checklists (in km2) to be included in the analysis. |
Value
This function returns a list containing three shapefiles derived by information supplied by GIFT. "regs" includes all the features corresponding to regions where the species has been listed as present. "regs_native" includes all the features corresponding to regions where the species has been listed as native. And "regs_alien" includes all the features corresponding to regions where the species has been listed as alien.
Examples
gift_reference_regions <- giftRegions("Babiana tubulosa")
Input occurrence data
Description
Prepares user provided georeferenced biological data for the models
Usage
giveOcc(
occ_data,
species = "species",
longitude = "longitude",
latitude = "latitude"
)
Arguments
occ_data |
table containing latitude and longitude |
species |
col.name containing the species information |
longitude |
col.name containing the longitude information |
latitude |
col.name containing the latitude information |
Value
This function standardises the user provided georeferenced biological data to be fed into the models.
Examples
# Create a data.frame containing species names and coordinates
test_data <- data.frame(sps=rep("Equus acephalus",10),
lon=c(-43.2,-58.4,-56,-44,-54.5,-57.4,-60.1,-68.5,-71.3,-47.5),
lat=c(-22.9,-34.6,-34.8,-20,-25.5,-25.2,-3,-32.5,-41.1,-15.5),
gender=rep("female",10),head_size=rep("headless individual"))
sps_occurrence <- giveOcc(test_data,"sps","lon","lat")
giveRegions
Description
Input checklist regions
Usage
giveRegions(regs, regs_native, regs_alien)
Arguments
regs |
shapefile containing all regions of occurrence. |
regs_native |
shapefile containing regions where the species is native. |
regs_alien |
shapefile containing regions where the species is alien. |
Value
This function returns a list containing three shapefiles derived by information supplied by GIFT. "regs" includes all the features corresponding to regions where the species has been listed as present. "regs_native" includes all the features corresponding to regions where the species has been listed as native. And "regs_alien" includes all the features corresponding to regions where the species has been listed as alien.
Examples
library(rnaturalearth)
world <- ne_countries(returnclass = "sf")
reg_names <- c("Brazil","Argentina","Uruguay","Paraguay")
reg_native <- c("Brazil","Paraguay")
reg_alien <- c("Argentina")
regs <- world[which(world$name_sort %in% reg_names),]
regs_native <- world[which(world$name_sort %in% reg_native),]
regs_alien <- world[which(world$name_sort %in% reg_alien),]
regs_list <- giveRegions(regs,regs_native,regs_alien)
glonafRegions
Description
Gets regions listed by GloNAF for plant species
Usage
glonafRegions(species, native = "gift", nat_ref_reg = NULL)
Arguments
species |
character, species binomial name |
native |
character, source for the native reference regions. Options are "gift", "range map", or "checklist". If "gift" is chosen, the function will automatically download native regions listed by GIFT for the species. If "range map" or "checklist" is chosen, the user must provide a shapefile with either the species range map, or the features representing regions where it has been listed as native. Default is "gift". |
nat_ref_reg |
shapefile containing either the species native range map or checklist. The user must inform which reference region data type is being provided in the parameter "native". |
Value
This function returns a list containing three shapefiles derived by information supplied by GloNAF for the alien reference regions, and the chosen source for the native reference regions. "regs" includes all the features corresponding to regions where the species has been listed as present. "regs_native" includes all the features corresponding to regions where the species has been listed as native. And "regs_alien" includes all the features corresponding to regions where the species has been listed as alien.
Examples
glonaf_reference_regions <- glonafRegions("Ambrosia grayi")
occSpatialPoints
Description
Downloads gbif records iterating when necessary to overcome the limitation of 200,000 records
Usage
occSpatialPoints(occ)
Arguments
occ |
table |
Value
This function creates spatialPoints from tables containing coordinates.
Examples
# Create a data.frame containing species names and coordinates
test_data <- data.frame(sps=rep("Equus acephalus",10),
lon=c(-43.2,-58.4,-56,-44,-54.5,-57.4,-60.1,-68.5,-71.3,-47.5),
lat=c(-22.9,-34.6,-34.8,-20,-25.5,-25.2,-3,-32.5,-41.1,-15.5),
gender=rep("female",10),head_size=rep("headless individual"))
sps_occurrence <- giveOcc(test_data,"sps","lon","lat")
sps_sp <- occSpatialPoints(sps_occurrence)
plotAccuracy
Description
Plot the species occurrences showing the estimated accuracy of points.
Usage
plotAccuracy(
acc,
regional = TRUE,
reg.by = "country",
borders = TRUE,
col.features = "khaki",
col.bg = "azure2",
plot.range = FALSE,
range = NULL,
box = FALSE
)
Arguments
acc |
dataTable of the species occurrence including a column with the estimated accuracy of points. |
regional |
logical, whether the whole world should be plotted as the background or only the region adjacent to the species countries of occurrence. |
reg.by |
character, by countries where there are points or by area where the points are located. |
borders |
logical, whether country limits should be plotted. |
col.features |
colour for plotting features. |
col.bg |
colour for plotting the background. |
plot.range |
logical, if TRUE, range maps should be provided as a shapefile in argument range. |
range |
shapefile, species range map. |
box |
logical, includes frame with coordinates locations. |
Value
This function plots the species occurrence with estimated accuracy of all points.
plotBiogeoStatus
Description
Plot the species occurrences showing the estimated biogeographical status of points.
Usage
plotBiogeoStatus(
biogeo,
regional = TRUE,
reg.by = "country",
borders = TRUE,
col.features = "khaki",
col.bg = "azure2",
plot.range = FALSE,
range = NULL,
box = FALSE
)
Arguments
biogeo |
dataTable of the species occurrence including a column with the estimated biogeographical status of points. |
regional |
logical, whether the whole world should be plotted as the background or only the region adjacent to the species countries of occurrence. |
reg.by |
character, by countries where there are points or by area where the points are located. |
borders |
logical, whether country limits should be plotted. |
col.features |
colour for plotting features. |
col.bg |
colour for plotting the background. |
plot.range |
logical, if TRUE, range maps should be provided as a shapefile in argument range. |
range |
shapefile, species range map. |
box |
logical, includes frame with coordinates locations. |
Value
This function plots the species occurrence with estimated biogeographical status of all points.
plotOcc
Description
Plot the species occurrences with map background for visualisation
Usage
plotOcc(occ, regional = TRUE)
Arguments
occ |
dataTable of the species occurrence. |
regional |
logical, whether the whole world should be plotted as the background or only the region adjacent to the species countries of occurrence. |
Value
This function plots the species occurrence
Examples
occ <- getOcc("Hemitriccus mirandae")
plotOcc(occ)
test_data <- data.frame(sps=rep("Equus acephalus",10),
lon=c(-43.2,-58.4,-56,-44,-54.5,-57.4,-60.1,-68.5,-71.3,-47.5),
lat=c(-22.9,-34.6,-34.8,-20,-25.5,-25.2,-3,-32.5,-41.1,-15.5),
gender=rep("female",10),head_size=rep("headless individual"))
occ <- giveOcc(test_data,"sps","lon","lat")
plotOcc(occ)
# Plot occurrences with the whole world as background
plotOcc(occ,regional=FALSE)
plotRefRef
Description
Plot the species reference regions with map background for visualisation
Usage
plotRefReg(ref_reg)
Arguments
ref_reg |
list containing three shapefiles derived by information supplied by GIFT. "regs" includes all the features corresponding to regions where the species has been listed as present. "regs_native" includes all the features corresponding to regions where the species has been listed as native. And "regs_alien" includes all the features corresponding to regions where the species has been listed as alien.. |
Value
This function plots three maps of the species occurrence, showing the regions where it is present, native and alien.
pts example 1
Description
A DataFrame pts example 1
Examples
data("pts")
pts example 2
Description
A DataFrame pts example 2
Examples
data("pts2")
rangeMaps
Description
Prepares range maps input by the user to be used as reference regions
Usage
rangeMaps(
range,
biogeo = "legend",
native = "Extant (resident)",
alien = "Introduced"
)
Arguments
range |
SpatialPolygonsDataFrame |
biogeo |
character, name of the column containing information on biogeographic status of features |
native |
character, entries in biogeo column representing the native range of the species |
alien |
character, entries in biogeo column representing the alien range of the species |
Value
This function returns a list containing three shapefiles derived from information supplied by the species range map in a shapefile format. "regs" includes all the features corresponding to regions where the species has been listed as present. "regs_native" includes all the features corresponding to regions where the species has been listed as native. And "regs_alien" includes all the features corresponding to regions where the species has been listed as alien.
Examples
range_map_reference_regions <- rangeMaps(Range_Phalanger_orientalis)
signalCalculation
Description
Calculates signals sent from reference regions to point records.
Usage
signalCalculation(ref_reg, pts, biogeo = TRUE)
Arguments
ref_reg |
a list of shapefiles containing checklist regions as "presence", "native", and "alien" categories. These can be original checklists, or checklists derived from range maps. |
pts |
data.frame containing the point records and their coordinates. |
biogeo |
logical, whether the biogeographical status indices should be calculated or not. Default is true, however at least the native reference regions must be included in the data. |
Value
The data.frame of species occurrences with extra columns containing the location ID and presence signals for each point. If biogeo=TRUE, the data.frame also includes the nativeness and alienness indices.
signals example 1
Description
A SpatialPolygonsDataFrame signals example 1
Examples
data("signals")
signals example 2
Description
A SpatialPolygonsDataFrame signals example 2
Examples
data("signals_2")
signals example 3
Description
A SpatialPolygonsDataFrame signals example 3
Examples
data("signals_3")