Title:	Code to Access Open Access Species Range Maps
Version:	0.0.1
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.
License:	MIT + file LICENSE
Encoding:	UTF-8
RoxygenNote:	7.3.2
Depends:	R (≥ 3.2.1), RPostgreSQL
Imports:	DBI, sf, httr, jsonlite
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), maps, tidyverse, vcr, ggplot2
VignetteBuilder:	knitr
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2025-01-12 16:30:14 UTC; Brian Maitner
Author:	Brian Maitner [aut, cre], Cory Merow [aut], Brad Boyle [aut], Xiao Feng [aut], Rethvick Sriram Yugendra Babu [aut], Brian Enquist [aut]
Maintainer:	Brian Maitner <bmaitner@usf.edu>
Repository:	CRAN
Date/Publication:	2025-01-14 13:00:05 UTC

Check that value is character

Description

Helper function to check data format.

Usage

.is_char(x)

Check that value is logical

Description

Helper function to check data format.

Usage

.is_log(x)

Check that value is logical or null

Description

Helper function to check data format.

Usage

.is_log_or_null(x)

Check that value is numeric

Description

Helper function to check data format.

Usage

.is_num(x)

Load range maps for given species using the API.

Description

OpenRange_api_load_species extracts range maps for the specified species.

Usage

OpenRange_api_load_species(species, ...)

Arguments

Value

Range maps for specified species.

Note

Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: OpenRange_api_species(), OpenRange_get_license(), OpenRange_get_stats(), OpenRange_list_scenarios(), OpenRange_load_species(), OpenRange_sf(), OpenRange_species()

Examples

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()

Download range maps for given species using the API.

Description

OpenRange_api_species downloads range maps for the specified species.

Usage

OpenRange_api_species(species, directory, include_id = TRUE, ...)

Arguments

Value

NULL. Called for its side effect of downloading range maps.

Note

Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: OpenRange_api_load_species(), OpenRange_get_license(), OpenRange_get_stats(), OpenRange_list_scenarios(), OpenRange_load_species(), OpenRange_sf(), OpenRange_species()

Examples

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()

Download license information

Description

OpenRange_get_license provides information on model licenses.

Usage

OpenRange_get_license(...)

Arguments

Value

Data.frame containing information on the license associated with the maps.

See Also

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()

Examples

range_license_info <- OpenRange_get_license()

Download model performance statistics

Description

OpenRange_get_stats provides information on model performance.

Usage

OpenRange_get_stats(...)

Arguments

Value

List object containing one data.frame for each of the three modeling frameworks.

See Also

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()

Examples

range_stats <- OpenRange_get_stats()

Download information on available climate change scenarios

Description

OpenRange_list_scenarios provides information on climate scenarios with range projections available.

Usage

OpenRange_list_scenarios(...)

Arguments

Value

Data.frame containing climate change scenarios available in BIEN.

Note

Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

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()

Examples

## Not run: 

cc_scenarios <- OpenRange_list_scenarios()


## End(Not run)

Load Open Range maps for specified species.

Description

OpenRange_load_species returns spatial data for the specified species.

Usage

OpenRange_load_species(
  species,
  default_only = TRUE,
  projection = 4326,
  scenario = "present",
  ...
)

Arguments

Value

A SpatialPolygonsDataFrame containing range maps for the specified species.

See Also

Other range functions: OpenRange_api_load_species(), OpenRange_api_species(), OpenRange_get_license(), OpenRange_get_stats(), OpenRange_list_scenarios(), OpenRange_sf(), OpenRange_species()

Examples

#' 
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()

Download range maps that intersect a user-supplied sf object.

Description

OpenRange_sf extracts range maps that intersect a specified SpatialPolygons or SpatialPolygonsDataFrame object.

Usage

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,
  ...
)

Arguments

Value

All range maps that intersect the user-supplied shapefile.

Note

Details on the construction of BIEN range maps is available at https://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: OpenRange_api_load_species(), OpenRange_api_species(), OpenRange_get_license(), OpenRange_get_stats(), OpenRange_list_scenarios(), OpenRange_load_species(), OpenRange_species()

Examples

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)

Download range maps for given species.

Description

OpenRange_species extracts range maps for the specified species.

Usage

OpenRange_species(
  species,
  directory,
  default_only = TRUE,
  matched = TRUE,
  match_names_only = FALSE,
  include_id = TRUE,
  projection = 4326,
  scenario = "present",
  ...
)

Arguments

Value

Range maps for specified species.

Note

Details on the construction of BIEN range maps is available at http://bien.nceas.ucsb.edu/bien/biendata/bien-3/

See Also

Other range functions: OpenRange_api_load_species(), OpenRange_api_species(), OpenRange_get_license(), OpenRange_get_stats(), OpenRange_list_scenarios(), OpenRange_load_species(), OpenRange_sf()

Examples

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()

Run an SQL query on the OpenRange database.

Description

ranges_sql is an internal function used to submit SQL queries.

Usage

ranges_sql(
  query,
  user = "public_bien",
  password = "bien_public",
  ranges = NULL,
  limit = NULL,
  return.query = FALSE,
  schema = "analytical_db",
  db_name = "vegbien",
  print.query = FALSE
)

Arguments

Value

A dataframe returned by the query.