Retrieve checklists overlapping with a shape file or a set of coordinates.
Usage
GIFT_spatial(
shp = NULL,
coordinates = NULL,
overlap = "centroid_inside",
entity_ID = NULL,
GIFT_version = "latest",
api = "https://gift.uni-goettingen.de/api/extended/"
)Arguments
- shp
Shapefile provided by the user. Its Coordinate Reference System (CRS) must be set to WGS84 (EPSG code 4326).
- coordinates
Custom set of coordinates. The format is a two columns data.frame, the first one being longitudes and the second being latitudes of the vertices of a polygon. If the data.frame only includes two rows, the function assumes that the values are the four limits (min and max. longitude and latitude) of a bounding box.
- overlap
A character string defining the criteria to use in order to retrieve checklists. Available options are
centroid_inside,extent_intersect,shape_intersectandshape_inside. For example,extent_intersectmeans that every polygon from GIFT for which the extent intersects the provided shape/coordinates will be retrieved.- entity_ID
Constrain the list of regions to be received by a predefined set of entity_IDs. E.g. this list could come from GIFT_checklists_conditional().
- GIFT_version
character string defining the version of the GIFT database to use. The function retrieves by default the
lateststable version. If set tobeta, the most up-to-date version which is still subject to changes and edits is used.- api
character string defining from which API the data will be retrieved.
Value
A data frame with 3 columns: entity_ID the identification number of a polygon, geo_entity_ref its name, and coverage which indicates the percentage of overlap between the provided shape and the different polygons of GIFT.
References
Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
access the Global Inventory of Floras and Traits. Methods in Ecology
and Evolution, 14, 2738-2748.
https://doi.org/10.1111/2041-210X.14213
Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
https://doi.org/10.1111/jbi.13623Examples
# \donttest{
# With a shapefile
data("western_mediterranean")
ex <- GIFT_spatial(shp = western_mediterranean, overlap = "centroid_inside")
#> You are asking for the latest stable version of GIFT which is 3.2.
# With a shapefile coming from GIFT
spain <- GIFT_shapes(entity_ID = 10071)
#> You are asking for the latest stable version of GIFT which is 3.2.
#> ================================================================================
ex_spain <- GIFT_spatial(shp = spain)
#> You are asking for the latest stable version of GIFT which is 3.2.
# With a point
custom_point <- cbind(9.9, 51)
ex2 <- GIFT_spatial(coordinates = custom_point,
overlap = "extent_intersect")
#> You are asking for the latest stable version of GIFT which is 3.2.
# With an extent
custom_extent <- cbind(c(-13, -18), c(27.5, 29.3))
ex3 <- GIFT_spatial(coordinates = custom_extent,
overlap = "extent_intersect")
#> You are asking for the latest stable version of GIFT which is 3.2.
#> 4 coordinates provided: an extent box was drawn, assuming that
#> minimum X and Y are on row 1, and maximum X and Y on row 2.
# With a custom polygon
custom_polygon <- cbind(c(-18, -16.9, -13, -13, -18, -18),
c(29.3, 33, 29.3, 27.5, 27.5, 29.3))
ex4 <- GIFT_spatial(coordinates = custom_polygon,
overlap = "extent_intersect")
#> You are asking for the latest stable version of GIFT which is 3.2.
#With a linestring
custom_linestring <- rbind(c(9.9, 51), c(2.35, 48.9))
custom_linestring <- sf::st_as_sf(as.data.frame(custom_linestring),
coords = c("V1", "V2"))
custom_linestring <- dplyr::summarise(custom_linestring,
geometry = sf::st_combine(geometry))
sf::st_crs(custom_linestring) <- sf::st_crs(western_mediterranean)
ex5 <- GIFT_spatial(shp = custom_linestring, overlap = "extent_intersect")
#> You are asking for the latest stable version of GIFT which is 3.2.
# }