, Cory Merow [aut],
Brad Boyle [aut], Xiao Feng [aut], Rethvick Sriram Yugendra
Babu [aut], Brian Enquist [aut]| Title: | Code to Access Open Access Species Range Maps |
|---|---|
| Description: | Allows access to a proof-of-concept database containing Open Access species range models and relevant metadata. Access to the database is via both 'PostgreSQL' connection and API <https://github.com/EnquistLab/Biendata-Frontend>, allowing diverse use-cases. |
| Authors: | Brian Maitner [aut, cre]
, Cory Merow [aut],
Brad Boyle [aut], Xiao Feng [aut], Rethvick Sriram Yugendra
Babu [aut], Brian Enquist [aut] |
| Maintainer: | Brian Maitner <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.0.1 |
| Built: | 2025-01-15 05:25:02 UTC |
| Source: | https://github.com/cran/OpenRange |
OpenRange_api_load_species extracts range maps for the specified species.
OpenRange_api_load_species(species, ...)OpenRange_api_load_species(species, ...)
species |
A single species. |
... |
Additional arguments passed to internal functions. |
Range maps for specified species.
Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/
Other range functions:
OpenRange_api_species(),
OpenRange_get_license(),
OpenRange_get_stats(),
OpenRange_list_scenarios(),
OpenRange_load_species(),
OpenRange_sf(),
OpenRange_species()
library(maps) #a convenient source of maps library(sf) temp_dir <- file.path(tempdir(), "BIEN_temp") #Download ranges Abies_poly <- OpenRange_api_load_species(species = "Abies_amabilis") #Plotting files plot(Abies_poly[,1])#plots the range, but doesn't mean much without any reference map('world', fill = TRUE, col = "grey")#plots a world map (WGS84 projection), in grey plot(Abies_poly,col="forest green",add=TRUE) #adds the range to the map #Getting data from the files Abies_poly |> st_drop_geometry()library(maps) #a convenient source of maps library(sf) temp_dir <- file.path(tempdir(), "BIEN_temp") #Download ranges Abies_poly <- OpenRange_api_load_species(species = "Abies_amabilis") #Plotting files plot(Abies_poly[,1])#plots the range, but doesn't mean much without any reference map('world', fill = TRUE, col = "grey")#plots a world map (WGS84 projection), in grey plot(Abies_poly,col="forest green",add=TRUE) #adds the range to the map #Getting data from the files Abies_poly |> st_drop_geometry()
OpenRange_api_species downloads range maps for the specified species.
OpenRange_api_species(species, directory, include_id = TRUE, ...)OpenRange_api_species(species, directory, include_id = TRUE, ...)
species |
A single species. |
directory |
Directory that range maps should be saved in. |
include_id |
Logical. Should the range_id be appended to the file name? Needed to save multiple maps per species. |
... |
Additional arguments passed to internal functions. |
NULL. Called for its side effect of downloading range maps.
Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/
Other range functions:
OpenRange_api_load_species(),
OpenRange_get_license(),
OpenRange_get_stats(),
OpenRange_list_scenarios(),
OpenRange_load_species(),
OpenRange_sf(),
OpenRange_species()
library(OpenRange) library(maps) #a convenient source of maps library(sf) library(ggplot2) # Create temp directory temp_dir <- file.path(tempdir(), "BIEN_temp") #Download ranges OpenRange_api_species(species = "Abies_amabilis", directory = temp_dir, include_id = TRUE) # saves ranges to a temporary directory #Reading files Abies_poly <- st_read(dsn = temp_dir, layer = "Abies_amabilis_117684") # Get a map to plot on world <- map("world", plot = FALSE, fill = TRUE)|> st_as_sf() #Plotting files ggplot(data = world)+ geom_sf()+ geom_sf(data = Abies_poly, fill="green")+ coord_sf(xlim = st_bbox(Abies_poly)[c(1,3)], ylim = st_bbox(Abies_poly)[c(2,4)]) + theme_bw() #Getting data from the files Abies_poly |> st_drop_geometry()library(OpenRange) library(maps) #a convenient source of maps library(sf) library(ggplot2) # Create temp directory temp_dir <- file.path(tempdir(), "BIEN_temp") #Download ranges OpenRange_api_species(species = "Abies_amabilis", directory = temp_dir, include_id = TRUE) # saves ranges to a temporary directory #Reading files Abies_poly <- st_read(dsn = temp_dir, layer = "Abies_amabilis_117684") # Get a map to plot on world <- map("world", plot = FALSE, fill = TRUE)|> st_as_sf() #Plotting files ggplot(data = world)+ geom_sf()+ geom_sf(data = Abies_poly, fill="green")+ coord_sf(xlim = st_bbox(Abies_poly)[c(1,3)], ylim = st_bbox(Abies_poly)[c(2,4)]) + theme_bw() #Getting data from the files Abies_poly |> st_drop_geometry()
OpenRange_get_license provides information on model licenses.
OpenRange_get_license(...)OpenRange_get_license(...)
... |
Additional arguments passed to internal functions. |
Data.frame containing information on the license associated with the maps.
Other range functions:
OpenRange_api_load_species(),
OpenRange_api_species(),
OpenRange_get_stats(),
OpenRange_list_scenarios(),
OpenRange_load_species(),
OpenRange_sf(),
OpenRange_species()
Other metadata functions:
OpenRange_get_stats(),
OpenRange_list_scenarios()
range_license_info <- OpenRange_get_license()range_license_info <- OpenRange_get_license()
OpenRange_get_stats provides information on model performance.
OpenRange_get_stats(...)OpenRange_get_stats(...)
... |
Additional arguments passed to internal functions. |
List object containing one data.frame for each of the three modeling frameworks.
Other range functions:
OpenRange_api_load_species(),
OpenRange_api_species(),
OpenRange_get_license(),
OpenRange_list_scenarios(),
OpenRange_load_species(),
OpenRange_sf(),
OpenRange_species()
Other metadata functions:
OpenRange_get_license(),
OpenRange_list_scenarios()
range_stats <- OpenRange_get_stats()range_stats <- OpenRange_get_stats()
OpenRange_list_scenarios provides information on climate scenarios with range projections available.
OpenRange_list_scenarios(...)OpenRange_list_scenarios(...)
... |
Additional arguments passed to internal functions. |
Data.frame containing climate change scenarios available in BIEN.
Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/
Other range functions:
OpenRange_api_load_species(),
OpenRange_api_species(),
OpenRange_get_license(),
OpenRange_get_stats(),
OpenRange_load_species(),
OpenRange_sf(),
OpenRange_species()
Other metadata functions:
OpenRange_get_license(),
OpenRange_get_stats()
## Not run: cc_scenarios <- OpenRange_list_scenarios() ## End(Not run)## Not run: cc_scenarios <- OpenRange_list_scenarios() ## End(Not run)
OpenRange_load_species returns spatial data for the specified species.
OpenRange_load_species( species, default_only = TRUE, projection = 4326, scenario = "present", ... )OpenRange_load_species( species, default_only = TRUE, projection = 4326, scenario = "present", ... )
species |
A single species or a vector of species. |
default_only |
Logical. Should only default ranges be included? Default is TRUE. |
projection |
Numeric. What projection should maps be returned in? 4326 (default) or 3857 |
scenario |
Which climate scenario(s) should be represented by maps? See BIEN_ranges_list_scenarios for options. |
... |
Additional arguments passed to internal functions. |
A SpatialPolygonsDataFrame containing range maps for the specified species.
Other range functions:
OpenRange_api_load_species(),
OpenRange_api_species(),
OpenRange_get_license(),
OpenRange_get_stats(),
OpenRange_list_scenarios(),
OpenRange_sf(),
OpenRange_species()
#' library(maps) library(ggplot2) library(sf) species_vector <- c("Abies_lasiocarpa","Abies_amabilis") abies_maps <- OpenRange_load_species(species = species_vector) # To get all maps for a species, use "default = FALSE". # Here, this returns maps with different thresholds from the same model std_all <- OpenRange_load_species(species = "Stellaria debilis", default_only = FALSE) #To just get the default map, use "default = TRUE" std_default <- OpenRange_load_species(species = "Stellaria debilis", default_only = TRUE) #get world map world <- map("world", plot = FALSE, fill = TRUE)|> st_as_sf() #Plotting ranges ggplot(data = world)+ geom_sf()+ geom_sf(data = abies_maps, mapping = aes(fill = species), alpha=0.5)+ coord_sf(xlim = st_bbox(abies_maps)[c(1,3)], ylim = st_bbox(abies_maps)[c(2,4)]) + theme_bw()#' library(maps) library(ggplot2) library(sf) species_vector <- c("Abies_lasiocarpa","Abies_amabilis") abies_maps <- OpenRange_load_species(species = species_vector) # To get all maps for a species, use "default = FALSE". # Here, this returns maps with different thresholds from the same model std_all <- OpenRange_load_species(species = "Stellaria debilis", default_only = FALSE) #To just get the default map, use "default = TRUE" std_default <- OpenRange_load_species(species = "Stellaria debilis", default_only = TRUE) #get world map world <- map("world", plot = FALSE, fill = TRUE)|> st_as_sf() #Plotting ranges ggplot(data = world)+ geom_sf()+ geom_sf(data = abies_maps, mapping = aes(fill = species), alpha=0.5)+ coord_sf(xlim = st_bbox(abies_maps)[c(1,3)], ylim = st_bbox(abies_maps)[c(2,4)]) + theme_bw()
OpenRange_sf extracts range maps that intersect a specified SpatialPolygons or SpatialPolygonsDataFrame object.
OpenRange_sf( sf, directory, species.names.only = FALSE, return.species.list = TRUE, crop.ranges = FALSE, include.gid = FALSE, projection = 4326, scenario = "present", default_only = TRUE, ... )OpenRange_sf( sf, directory, species.names.only = FALSE, return.species.list = TRUE, crop.ranges = FALSE, include.gid = FALSE, projection = 4326, scenario = "present", default_only = TRUE, ... )
sf |
An object of class sf |
directory |
Directory that range maps should be saved in. |
species.names.only |
Return species names rather than spatial data? Default is FALSE. |
return.species.list |
Should a species list be returned in addition to downloading range maps? Default is FALSE |
crop.ranges |
Should the ranges be cropped to the focal area? Default is FALSE. |
include.gid |
Should the files returned have a unique GID appended to them? This is needed if downloading multiple maps for the same species. |
projection |
Numeric. What projection should maps be returned in? 4326 (default) or 3857 |
scenario |
Which climate scenario should be represented by maps? See BIEN_ranges_list_scenarios. |
default_only |
Logical. Should only default ranges be included? Default is TRUE. |
... |
Additional arguments passed to internal functions. |
All range maps that intersect the user-supplied shapefile.
Details on the construction of BIEN range maps is available at https://bien.nceas.ucsb.edu/bien/biendata/bien-3/
Other range functions:
OpenRange_api_load_species(),
OpenRange_api_species(),
OpenRange_get_license(),
OpenRange_get_stats(),
OpenRange_list_scenarios(),
OpenRange_load_species(),
OpenRange_species()
saguaro_poly <- OpenRange_load_species("Carnegiea gigantea") #Create a temp directory temp_dir <- file.path(tempdir(), "BIEN_temp") #Get range maps for all species with ranges that overlap the range range of saguaros OpenRange_sf(sf = saguaro_poly, directory = temp_dir) #Note that this will save many sfs to the directory (or working directory)saguaro_poly <- OpenRange_load_species("Carnegiea gigantea") #Create a temp directory temp_dir <- file.path(tempdir(), "BIEN_temp") #Get range maps for all species with ranges that overlap the range range of saguaros OpenRange_sf(sf = saguaro_poly, directory = temp_dir) #Note that this will save many sfs to the directory (or working directory)
OpenRange_species extracts range maps for the specified species.
OpenRange_species( species, directory, default_only = TRUE, matched = TRUE, match_names_only = FALSE, include_id = TRUE, projection = 4326, scenario = "present", ... )OpenRange_species( species, directory, default_only = TRUE, matched = TRUE, match_names_only = FALSE, include_id = TRUE, projection = 4326, scenario = "present", ... )
species |
A single species or a vector of species. |
directory |
Directory that range maps should be saved in. |
default_only |
Logical. Should only default ranges be included? Default is TRUE. |
matched |
Return a list of taxa that were downloaded. Default is TRUE. |
match_names_only |
Check for range maps for the taxa specified without downloading range maps. Default is FALSE. |
include_id |
Logical. Should the range_id be appended to the file name? Needed to save multiple maps per species. |
projection |
Numeric. What projection should maps be returned in? 4326 (default) or 3857 |
scenario |
Which climate scenario should be represented by maps? See BIEN_ranges_list_scenarios. |
... |
Additional arguments passed to internal functions. |
Range maps for specified species.
Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/
Other range functions:
OpenRange_api_load_species(),
OpenRange_api_species(),
OpenRange_get_license(),
OpenRange_get_stats(),
OpenRange_list_scenarios(),
OpenRange_load_species(),
OpenRange_sf()
library(maps) #a convenient source of maps library(sf) species_vector <- c("Abies_lasiocarpa","Abies_amabilis") #check whether the species are available OpenRange_species(species_vector,match_names_only = TRUE) #Create a temp directory temp_dir <- file.path(tempdir(), "BIEN_temp") #Download ranges OpenRange_species(species = species_vector, directory = temp_dir)#saves ranges to a temporary directory #Reading files Abies_poly <- st_read(dsn = temp_dir, layer = "Abies_amabilis_117684") #Plotting files plot(Abies_poly[,1])#plots the range, but doesn't mean much without any reference map('world', fill = TRUE, col = "grey")#plots a world map (WGS84 projection), in grey plot(Abies_poly,col="forest green",add=TRUE) #adds the range of Abies lasiocarpa to the map #Getting data from the files Abies_poly |> st_drop_geometry()library(maps) #a convenient source of maps library(sf) species_vector <- c("Abies_lasiocarpa","Abies_amabilis") #check whether the species are available OpenRange_species(species_vector,match_names_only = TRUE) #Create a temp directory temp_dir <- file.path(tempdir(), "BIEN_temp") #Download ranges OpenRange_species(species = species_vector, directory = temp_dir)#saves ranges to a temporary directory #Reading files Abies_poly <- st_read(dsn = temp_dir, layer = "Abies_amabilis_117684") #Plotting files plot(Abies_poly[,1])#plots the range, but doesn't mean much without any reference map('world', fill = TRUE, col = "grey")#plots a world map (WGS84 projection), in grey plot(Abies_poly,col="forest green",add=TRUE) #adds the range of Abies lasiocarpa to the map #Getting data from the files Abies_poly |> st_drop_geometry()