# NOT RUN {
# Single data sources
(res <- occ(query = 'Accipiter striatus', from = 'gbif', limit = 5))
res$gbif
(res <- occ(query = 'Accipiter', from = 'ecoengine', limit = 50))
res$ecoengine
(res <- occ(query = 'Accipiter striatus', from = 'ebird', limit = 50))
res$ebird
(res <- occ(query = 'Danaus plexippus', from = 'inat', limit = 50))
res$inat
(res <- occ(query = 'Bison bison', from = 'bison', limit = 50))
res$bison
(res <- occ(query = 'Bison bison', from = 'vertnet', limit = 5))
res$vertnet
res$vertnet$data$Bison_bison
occ2df(res)
# Paging
one <- occ(query = 'Accipiter striatus', from = 'gbif', limit = 5)
two <- occ(query = 'Accipiter striatus', from = 'gbif', limit = 5, start = 5)
one$gbif
two$gbif
# Restrict to records with coordinates
occ(query = "Acer", from = "idigbio", limit = 5, has_coords = TRUE)
# Data from AntWeb
# By species
(by_species <- occ(query = "linepithema humile", from = "antweb", limit = 10))
# or by genus
(by_genus <- occ(query = "acanthognathus", from = "antweb"))
occ(query = 'Setophaga caerulescens', from = 'ebird', ebirdopts = list(region='US'))
occ(query = 'Spinus tristis', from = 'ebird', ebirdopts =
list(method = 'ebirdgeo', lat = 42, lng = -76, dist = 50))
# idigbio data
## scientific name search
occ(query = "Acer", from = "idigbio", limit = 5)
occ(query = "Acer", from = "idigbio", idigbioopts = list(offset = 5, limit = 3))
## geo search
bounds <- c(-120, 40, -100, 45)
occ(from = "idigbio", geometry = bounds, limit = 10)
## just class arachnida, spiders
occ(idigbioopts = list(rq = list(class = 'arachnida')), from = "idigbio", limit = 10)
## search certain recordsets
sets <- c("1ffce054-8e3e-4209-9ff4-c26fa6c24c2f",
"8dc14464-57b3-423e-8cb0-950ab8f36b6f",
"26f7cbde-fbcb-4500-80a9-a99daa0ead9d")
occ(idigbioopts = list(rq = list(recordset = sets)), from = "idigbio", limit = 10)
# You can pass on limit param to all sources even though its a different param in that source
## ecoengine example
res <- occ(query = 'Accipiter striatus', from = 'ecoengine', ecoengineopts=list(limit = 5))
res$ecoengine
## This is particularly useful when you want to set different limit for each source
(res <- occ(query = 'Accipiter striatus', from = c('gbif','ecoengine'),
gbifopts=list(limit = 10), ecoengineopts=list(limit = 5)))
# Many data sources
(out <- occ(query = 'Pinus contorta', from=c('gbif','bison','vertnet'), limit=10))
## Select individual elements
out$gbif
out$gbif$data
out$vertnet
## Coerce to combined data.frame, selects minimal set of
## columns (name, lat, long, provider, date, occurrence key)
occ2df(out)
# Pass in limit parameter to all sources. This limits the number of occurrences
# returned to 10, in this example, for all sources, in this case gbif and inat.
occ(query='Pinus contorta', from=c('gbif','inat'), limit=10)
# Geometry
## Pass in geometry parameter to all sources. This constraints the search to the
## specified polygon for all sources, gbif and bison in this example.
## Check out http://arthur-e.github.io/Wicket/sandbox-gmaps3.html to get a WKT string
occ(query='Accipiter', from='gbif',
geometry='POLYGON((30.1 10.1, 10 20, 20 60, 60 60, 30.1 10.1))')
occ(query='Helianthus annuus', from='bison', limit=50,
geometry='POLYGON((-111.06 38.84, -110.80 39.37, -110.20 39.17, -110.20 38.90,
-110.63 38.67, -111.06 38.84))')
## Or pass in a bounding box, which is automatically converted to WKT (required by GBIF)
## via the bbox2wkt function. The format of a bounding box is
## [min-longitude, min-latitude, max-longitude, max-latitude].
occ(query='Accipiter striatus', from='gbif', geometry=c(-125.0,38.4,-121.8,40.9))
## Bounding box constraint with ecoengine
## Use this website: http://boundingbox.klokantech.com/ to quickly grab a bbox.
## Just set the format on the bottom left to CSV.
occ(query='Accipiter striatus', from='ecoengine', limit=10,
geometry=c(-125.0,38.4,-121.8,40.9))
## lots of results, can see how many by indexing to meta
res <- occ(query='Accipiter striatus', from='gbif',
geometry='POLYGON((-69.9 49.2,-69.9 29.0,-123.3 29.0,-123.3 49.2,-69.9 49.2))')
res$gbif
## You can pass in geometry to each source separately via their opts parameter, at
## least those that support it. Note that if you use rinat, you reverse the order, with
## latitude first, and longitude second, but here it's the reverse for consistency across
## the spocc package
bounds <- c(-125.0,38.4,-121.8,40.9)
occ(query = 'Danaus plexippus', from="inat", geometry=bounds)
## Passing geometry with multiple sources
occ(query = 'Danaus plexippus', from=c("inat","gbif","ecoengine"), geometry=bounds)
## Using geometry only for the query
### A single bounding box
occ(geometry = bounds, from = "gbif", limit=50)
### Many bounding boxes
occ(geometry = list(c(-125.0,38.4,-121.8,40.9), c(-115.0,22.4,-111.8,30.9)), from = "gbif")
## Many geometry and many names
res <- occ(query = c('Danaus plexippus', 'Accipiter striatus'),
geometry = list(c(-125.0,38.4,-121.8,40.9), c(-115.0,22.4,-111.8,30.9)), from = "bison")
res
## Geometry only with WKT
wkt <- 'POLYGON((-98.9 44.2,-89.1 36.6,-116.7 37.5,-102.5 39.6,-98.9 44.2))'
occ(from = "gbif", geometry = wkt, limit = 10)
# Specify many data sources, another example
ebirdopts = list(region = 'US'); gbifopts = list(country = 'US')
out <- occ(query = 'Setophaga caerulescens', from = c('gbif','inat','bison','ebird'),
gbifopts = gbifopts, ebirdopts = ebirdopts, limit=20)
occ2df(out)
# Pass in many species names, combine just data to a single data.frame, and
# first six rows
spnames <- c('Accipiter striatus', 'Setophaga caerulescens', 'Spinus tristis')
(out <- occ(query = spnames, from = 'gbif', gbifopts = list(hasCoordinate = TRUE), limit=25))
df <- occ2df(out)
head(df)
# no query, geometry, or ids passed
## many dataset keys to gbif
dsets <- c("14f3151a-e95d-493c-a40d-d9938ef62954", "f934f8e2-32ca-46a7-b2f8-b032a4740454")
occ(limit = 20, from = "gbif", gbifopts = list(datasetKey = dsets))
## class name to idigbio
occ(limit = 20, from = "idigbio", idigbioopts = list(rq = list(class = 'arachnida')))
## limit to ecoengine
occ(from = "ecoengine", ecoengineopts = list(limit = 3))
# taxize integration
## You can pass in taxonomic identifiers
library("taxize")
(ids <- get_ids(names=c("Chironomus riparius","Pinus contorta"), db = c('itis','gbif')))
occ(ids = ids[[1]], from='bison', limit=20)
occ(ids = ids, from=c('bison','gbif'), limit=20)
(ids <- get_ids(names="Chironomus riparius", db = 'gbif'))
occ(ids = ids, from='gbif', limit=20)
(ids <- get_gbifid("Chironomus riparius"))
occ(ids = ids, from='gbif', limit=20)
(ids <- get_tsn('Accipiter striatus'))
occ(ids = ids, from='bison', limit=20)
# SpatialPolygons/SpatialPolygonsDataFrame integration
library("sp")
## Single polygon in SpatialPolygons class
one <- Polygon(cbind(c(91,90,90,91), c(30,30,32,30)))
spone = Polygons(list(one), "s1")
sppoly = SpatialPolygons(list(spone), as.integer(1))
out <- occ(geometry = sppoly, limit=50)
out$gbif$data
## Two polygons in SpatialPolygons class
one <- Polygon(cbind(c(-121.0,-117.9,-121.0,-121.0), c(39.4, 37.1, 35.1, 39.4)))
two <- Polygon(cbind(c(-123.0,-121.2,-122.3,-124.5,-123.5,-124.1,-123.0),
c(44.8,42.9,41.9,42.6,43.3,44.3,44.8)))
spone = Polygons(list(one), "s1")
sptwo = Polygons(list(two), "s2")
sppoly = SpatialPolygons(list(spone, sptwo), 1:2)
out <- occ(geometry = sppoly, limit=50)
out$gbif$data
## Two polygons in SpatialPolygonsDataFrame class
sppoly_df <- SpatialPolygonsDataFrame(sppoly, data.frame(a=c(1,2), b=c("a","b"), c=c(TRUE,FALSE),
row.names=row.names(sppoly)))
out <- occ(geometry = sppoly_df, limit=50)
out$gbif$data
# curl debugging
library('httr')
occ(query = 'Accipiter striatus', from = 'gbif', limit=10, callopts=verbose())
# occ(query = 'Accipiter striatus', from = 'ebird', limit=10, callopts=verbose())
occ(query = 'Accipiter striatus', from = 'bison', limit=10, callopts=verbose())
occ(query = 'Accipiter striatus', from = 'ecoengine', limit=10, callopts=verbose())
occ(query = 'Accipiter striatus', from = c('ebird','bison'), limit=10, callopts=verbose())
# occ(query = 'Accipiter striatus', from = 'ebird', limit=10, callopts=timeout(seconds = 0.1))
occ(query = 'Accipiter striatus', from = 'inat', callopts=verbose())
occ(query = 'Mola mola', from = 'obis', limit = 200, callopts = verbose())
## notice that callopts is ignored when from='antweb'
occ(query = 'linepithema humile', from = 'antweb', callopts=verbose())
########## More thorough data source specific examples
# idigbio
## scientific name search
res <- occ(query = "Acer", from = "idigbio", limit = 5)
res$idigbio
## geo search
### bounding box
bounds <- c(-120, 40, -100, 45)
occ(from = "idigbio", geometry = bounds, limit = 10)
### wkt
# wkt <- 'POLYGON((-69.9 49.2,-69.9 29.0,-123.3 29.0,-123.3 49.2,-69.9 49.2))'
wkt <- 'POLYGON((-98.9 44.2,-89.1 36.6,-116.7 37.5,-102.5 39.6,-98.9 44.2))'
occ(from = "idigbio", geometry = wkt, limit = 10)
## limit fields returned
occ(query = "Acer", from = "idigbio", limit = 5,
idigbioopts = list(fields = "scientificname"))
## offset and max_items
occ(query = "Acer", from = "idigbio", limit = 5,
idigbioopts = list(offset = 10))
## sort
occ(query = "Acer", from = "idigbio", limit = 5,
idigbioopts = list(sort = TRUE))$idigbio
occ(query = "Acer", from = "idigbio", limit = 5,
idigbioopts = list(sort = FALSE))$idigbio
## more complex queries
### parameters passed to "rq", get combined with the name queried
occ(query = "Acer", from = "idigbio", limit = 5,
idigbioopts = list(rq = list(basisofrecord="fossilspecimen")))$idigbio
#### NOTE: no support for multipolygons yet
## WKT's are more flexible than bounding box's. You can pass in a WKT with multiple
## polygons like so (you can use POLYGON or MULTIPOLYGON) when specifying more than one
## polygon. Note how each polygon is in it's own set of parentheses.
# occ(query='Accipiter striatus', from='gbif',
# geometry='MULTIPOLYGON((30 10, 10 20, 20 60, 60 60, 30 10),
# (30 10, 10 20, 20 60, 60 60, 30 10))')
# OBIS examples
## basic query
(res <- occ(query = 'Mola mola', from = 'obis', limit = 200))
## get to obis data
res$obis
## get obis + gbif data
(res <- occ(query = 'Mola mola', from = c('obis', 'gbif'), limit = 200))
res$gbif
res$obis
## no match found
(res <- occ(query = 'Linguimaera thomsonia', from = 'obis'))
## geometry query
geometry <- "POLYGON((8.98 48.05,15.66 48.05,15.66 45.40,8.98 45.40,8.98 48.05))"
(res <- occ(from = 'obis', geometry = geometry, limit = 50))
res$obis
## Pass in spatial classes
library("sp")
one <- Polygon(cbind(c(45,30,30,45), c(35,35,30,30)))
spone = Polygons(list(one), "s1")
sppoly = SpatialPolygons(list(spone), as.integer(1))
(res <- occ(from = 'obis', geometry = sppoly, limit = 50))
## Do paging
(res1 <- occ(query = 'Mola mola', from = 'obis', limit = 10))
(res2 <- occ(query = 'Mola mola', from = 'obis', limit = 10, start = 20))
res1$obis
res2$obis
## Pass in any occurrence route parameters to obisopts as a list
(res <- occ(query = 'Mola mola', from = 'obis',
obisopts = list(year = 2005)))
unique(res$obis$data$Mola_mola$yearcollected)
# ALA examples
## basic query
(res <- occ(query = 'Alaba vibex', from = 'ala', limit = 200))
## get to ala data
res$ala
occ2df(res)
# geometry search
(x <- occ(query = "Macropus", from = 'ala',
geometry = "POLYGON((145 -37,150 -37,150 -30,145 -30,145 -37))"))
x$ala
occ2df(x)
# }
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