A data.frame is returned as grid cells by species with values in each cell being the number of occurrences of each species. No null (all zero species should be returned. The coordinates returned are the TOP-LEFT corner of the grid cell.
sites_by_species( taxon, wkt, gridsize = 0.1, SPdata.frame = FALSE, verbose = ala_config()$verbose )
| taxon | string: the identifier to get the species data from the ala
biocache. E.g. "genus:Heleioporus". See
|
|---|---|
| wkt | string: Bounding area in Well Known Text (WKT) format. E.g. "POLYGON((118 -30,146 -30,146 -11,118 -11,118 -30))". |
| gridsize | numeric: size of output grid cells in decimal degrees. E.g. 0.1 (=~10km) |
| SPdata.frame | logical: should the output be returned as a SpatialPointsDataFrame of the sp package? |
| verbose | logical: show additional progress information? [default is set by ala_config()] |
A dataframe or a SpatialPointsDataFrame containing the species by
sites data. Columns will include longitude, latitude, and each species
present. Values for species are record counts (i.e. number of recorded
occurrences of that taxon in each grid cell). The guid attribute of
the data frame gives the guids of the species (columns) as a named
character vector
Associated web services: https://spatial.ala.org.au/ws/capabilities see PointsToGrid/sitesBySpecies
http://www.geoapi.org/3.0/javadoc/org/opengis/referencing/doc-files/WKT.html
if (FALSE) { # Eucalyptus in Tasmania based on a 0.1 degree grid ss <- sites_by_species(taxon = "genus:Eucalyptus", wkt = "POLYGON((144 -43,148 -43,148 -40, 144 -40,144 -43))", gridsize = 0.1, verbose = TRUE) head(ss[, 1:6]) ## get the guid of the first species attr(ss,"guid")[1] # Steps: 1. POST webservice creates a task # (use single quotes around data-binary argument) #curl 'https://spatial.ala.org.au/ws/tasks/create?userId=0' # --data-binary name=PointsToGrid #&input={"area":[{"name":"Current extent" #,"wkt":"POLYGON((144 -43,148 -43,148 -40,144 -40,144 -43))"}] #,"occurrenceDensity":false,"sitesBySpecies":true,"speciesRichness":false #,"species":{"q":["genus:Eucalyptus"] #,"bs":"https://biocache-ws.ala.org.au/ws/","name":"genus:Eucalyptus"} #,"gridCellSize":0.1,"resolution":0.01,"movingAverage":"1x1 (no moving average)"}' #resp eg '{"name":"PointsToGrid","created":1552881125953,"email":"null","history":{} #,"tag":"null","userId":"0","sessionId":"null","status":0,"id":<id>} # 2. check status values: 0 = in_queue, 1 = running, 2 = cancelled, 3 = error, 4 = finished #curl 'https://spatial.ala.org.au/ws/tasks/status/<id>' #waiting: {"status":1,"message":"getting species data","id":<id>,"name":"PointsToGrid"} #complete:{"status":4,"message":"finished","id":<id>,"name":"PointsToGrid" #,"history":{"1552879452131":"finished","1552879452155":"finished (id:<id>)"} #,"output":[{"name":"files","file":"SitesBySpecies.csv","taskId":<id>,"id":33111} #,{"name":"sxs_metadata.html","taskId":<id>,"file":"sxs_metadata.html","id":33109} #,{"file":"download.zip","taskId":<id>,"name":"download.zip","id":33110}]} #failed: {"status":4,"message":"finished","id":<id>,"name":"PointsToGrid" #,"history":{"1552881921817":"failed (id:<id>)"}} # 3. download the zip and extract the file # https://spatial.ala.org.au/ws/tasks/output/<id>/download.zip # https://spatial.ala.org.au/ws/tasks/output/<id>/SitesBySpecies.csv }