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Fetch maps of GBIF occurrences

Source: R/map_fetch.R
map_fetch.Rd

This function is a wrapper for the GBIF mapping api version 2.0. The mapping API is a web map tile service making it straightforward to visualize GBIF content on interactive maps, and overlay content from other sources. It returns tile maps with number of GBIF records per area unit that can be used in a variety of ways, for example in interactive leaflet web maps. Map details are specified by a number of query parameters, some of them optional. Full documentation of the GBIF mapping api can be found at https://www.gbif.org/developer/maps

Usage

map_fetch(
  source = "density",
  x = 0:1,
  y = 0,
  z = 0,
  format = "@1x.png",
  srs = "EPSG:4326",
  bin = NULL,
  hexPerTile = NULL,
  squareSize = NULL,
  style = NULL,
  taxonKey = NULL,
  datasetKey = NULL,
  country = NULL,
  publishingOrg = NULL,
  publishingCountry = NULL,
  year = NULL,
  basisOfRecord = NULL,
  return = "png",
  base_style = NULL,
  plot_terra = TRUE,
  curlopts = list(http_version = 2),
  ...
)

Arguments

source

(character) Either density for fast, precalculated tiles, or adhoc for any search. Default: density

x

(integer sequence) the column. Default: 0:1

y

(integer sequence) the row. Default: 0

z

(integer) the zoom. Default: 0

format

(character) The data format, one of:

  • @Hx.png for a 256px raster tile

  • @1x.png for a 512px raster tile (the default)

  • @2x.png for a 1024px raster tile

  • @3x.png for a 2048px raster tile

  • @4x.png for a 4096px raster tile

srs

(character) Spatial reference system. One of:

  • EPSG:3857 (Web Mercator)

  • EPSG:4326 (WGS84 plate care?)

  • EPSG:3575 (Arctic LAEA on 10 degrees E)

  • EPSG:3031 (Antarctic stereographic)

bin

(character) square or hex to aggregate occurrence counts into squares or hexagons. Points by default.

hexPerTile

(integer) sets the size of the hexagons (the number horizontally across a tile).

squareSize

(integer) sets the size of the squares. Choose a factor of 4096 so they tessalate correctly: probably from 8, 16, 32, 64, 128, 256, 512.

style

(character) for raster tiles, choose from the available styles. Defaults to classic.point for source="density" and "scaled.circle" for source="adhoc".

taxonKey

(integer/numeric/character) search by taxon key, can only supply 1.

datasetKey

(character) search by taxon key, can only supply 1.

country

(character) search by taxon key, can only supply 1.

publishingOrg

(character) search by taxon key, can only supply 1.

publishingCountry

(character) search by taxon key, can only supply 1.

year

(integer) integer that limits the search to a certain year or, if passing a vector of integers, multiple years, for example 1984 or c(2016, 2017, 2018) or 2010:2015 (years 2010 to 2015). optional

basisOfRecord

(character) one or more basis of record states to include records with that basis of record. The full list is: c("OBSERVATION", "HUMAN_OBSERVATION", "MACHINE_OBSERVATION", "MATERIAL_SAMPLE", "PRESERVED_SPECIMEN", "FOSSIL_SPECIMEN", "LIVING_SPECIMEN", "LITERATURE", "UNKNOWN").

return

(character) Either "png" or "terra".

base_style

(character) The style of the base map.

plot_terra

(logical) Set whether the terra map be default plotted.

curlopts

options passed on to crul::HttpClient

...

additional arguments passed to the adhoc interface.

Value

a magick-image or terra::SpatRaster object.

Details

The default settings, return='png', will return a magick-image png. This image will be a composite image of the the occurrence tiles fetched and a base map. This map is primarily useful as a high quality image of occurrence records.

The args x and y can both be integer sequences. For example, x=0:3 or y=0:1. Note that the tile index starts at 0. Higher values of z, will will produce more tiles that can be fetched and stitched together. Selecting a too high value for x or y will produce a blank image.

Setting return='terra' will return a terra::SpatRaster object. This is primarily useful if you were interested in the underlying aggregated occurrence density data.

See the article

References

https://www.gbif.org/developer/maps

https://api.gbif.org/v2/map/demo.html

https://api.gbif.org/v2/map/demo13.html

See also

mvt_fetch()

Author

John Waller and Laurens Geffert laurensgeffert@gmail.com

Examples

if (FALSE) {

# all occurrences
map_fetch()
# get artic map
map_fetch(srs='EPSG:3031') 
# only preserved specimens
map_fetch(basisOfRecord="PRESERVED_SPECIMEN")

# Map of occ in Great Britain
map_fetch(z=3,y=1,x=7:8,country="GB")
# Peguins with artic projection
map_fetch(srs='EPSG:3031',taxonKey=2481660,style='glacier.point', 
base_style="gbif-dark")

# occ from a long time ago
map_fetch(year=1600) 
# polygon style 
map_fetch(style="iNaturalist.poly",bin="hex")
# iNaturalist dataset plotted 
map_fetch(datasetKey="50c9509d-22c7-4a22-a47d-8c48425ef4a7",
  style="iNaturalist.poly")
 
# use source="adhoc" for more filters
map_fetch(z=1,
  source="adhoc",
  iucn_red_list_category="CR",
  style="scaled.circles",
  base_style='gbif-light')

# cropped map of Hawaii
map_fetch(z=5,x=3:4,y=12,source="adhoc",gadmGid="USA.12_1")


}