rgbif: map_fetch – R documentation

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map_fetch

Fetch aggregated density maps of GBIF occurrences

Description

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,
  y = 0,
  z = 0,
  format = "@1x.png",
  srs = "EPSG:4326",
  bin = NULL,
  hexPerTile = NULL,
  squareSize = NULL,
  style = "classic.point",
  taxonKey = NULL,
  datasetKey = NULL,
  country = NULL,
  publishingOrg = NULL,
  publishingCountry = NULL,
  year = NULL,
  basisOfRecord = NULL,
  ...
)

Arguments

`source`	(character) Either `density` for fast, precalculated tiles, or `adhoc` for any search. Default: `density`
`x`	(integer) the column. Default: 0
`y`	(integer) 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. optional
`hexPerTile`	(integer) sets the size of the hexagons (the number horizontally across a tile). optional
`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. optional
`style`	(character) for raster tiles, choose from the available styles. Defaults to classic.point. optional. THESE DON'T WORK YET.
`taxonKey`	(integer/numeric/character) search by taxon key, can only supply 1. optional
`datasetKey`	(character) search by taxon key, can only supply 1. optional
`country`	(character) search by taxon key, can only supply 1. optional
`publishingOrg`	(character) search by taxon key, can only supply 1. optional
`publishingCountry`	(character) search by taxon key, can only supply 1. optional
`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")`. optional
`...`	curl options passed on to crul::HttpClient

Details

This function uses the arguments passed on to generate a query to the GBIF web map API. The API returns a web tile object as png that is read and converted into an R raster object. The break values or nbreaks generate a custom colour palette for the web tile, with each bin corresponding to one grey value. After retrieval, the raster is reclassified to the actual break values. This is a somewhat hacky but nonetheless functional solution in the absence of a GBIF raster API implementation.

We add extent and set the projection for the output. You can reproject after retrieving the output.

Value

an object of class RasterLayer

Note

Styles don't work yet, sorry, we'll try to fix it asap.

Author(s)

Laurens Geffert laurensgeffert@gmail.com

References

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

Examples

## Not run: 
if (
 requireNamespace("png", quietly = TRUE) &&
 requireNamespace("raster", quietly = TRUE)
) {
  x <- map_fetch(taxonKey = 2480498, year = 2007:2011)
  x
  # gives a RasterLayer object
  class(x)
  # visualize
  library(raster)
  plot(x)

  # different srs
  ## 3857
  y <- map_fetch(taxonKey = 2480498, year = 2010, srs = "EPSG:3857")
  plot(y)
  ## 3031
  z <- map_fetch(taxonKey = 2480498, year = 2010, srs = "EPSG:3031", verbose = TRUE)
  plot(z)
  # 3575
  z <- map_fetch(taxonKey = 2480498, year = 2010, srs = "EPSG:3575")
  plot(z)

  # bin
  plot(map_fetch(taxonKey = 212, year = 1998, bin = "hex",
     hexPerTile = 30, style = "classic-noborder.poly"))

  # styles
  plot(map_fetch(taxonKey = 2480498, style = "purpleYellow.point"))

  # query with basisOfRecord
  map_fetch(taxonKey = 2480498, year = 2010,
    basisOfRecord = "HUMAN_OBSERVATION")
  map_fetch(taxonKey = 2480498, year = 2010,
    basisOfRecord = c("HUMAN_OBSERVATION", "LIVING_SPECIMEN"))
 }

## End(Not run)

rgbif

Interface to the Global 'Biodiversity' Information Facility API

v3.5.2

MIT + file LICENSE

Authors

Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>), Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>), Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>), Laurens Geffert [ctb], Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>), Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>), rOpenSci [fnd] (https://ropensci.org/)

Initial release