,
Chris Ray [ctb],
Vijay Barve [ctb],
Dave Slager [aut, cre, cph] | Title: | Search 'Vertnet', a 'Database' of Vertebrate Specimen Records |
|---|---|
| Description: | Retrieve, map and summarize data from the 'VertNet.org' archives (<https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email. |
| Authors: | Scott Chamberlain [aut, cph] ,
Chris Ray [ctb],
Vijay Barve [ctb],
Dave Slager [aut, cre, cph] |
| Maintainer: | Dave Slager <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.8.4.9000 |
| Built: | 2024-08-29 22:58:42 UTC |
| Source: | https://github.com/ropensci/rvertnet |
There are a variety of ways to search VertNet
Search for Aves in the state of California, limit to 10 records, e.g.:
searchbyterm(class = "Aves", state = "California", lim = 10,
verbose = FALSE)
Search for Mustela nigripes in the states of Wyoming or South Dakota, limit to 20 records, e.g.:
searchbyterm(genus = "Mustela", specificepithet = "nigripes",
state = "(wyoming OR south dakota)", limit = 20, verbose=FALSE)
Specifies a termwise search (like searchbyterm()), but requests that all
available records be made available for download as a tab-delimited
text file.
bigsearch(genus = "ochotona", rf = "pikaRecords",
email = "[email protected]")
spatialsearch(lat = 33.529, lon = -105.694, radius = 2000, limit = 10,
verbose = FALSE)
Find records using a global full-text search of VertNet archives.
vertsearch(taxon = "aves", state = "california")
It's possible to get no results when requesting data from VertNet, then run the same function again 10 seconds later, and you do get a result. I'm not sure why this is, something having to do with Vertnet's infrastucture that I'm not aware of. Point is, if you are sure you haven't made any mistakes with the parameters, etc., then simply run the function call again.
Maintainer: Dave Slager [email protected] (ORCID) [copyright holder]
Authors:
Scott Chamberlain [email protected] (ORCID) [copyright holder]
Other contributors:
Chris Ray [contributor]
Vijay Barve [contributor]
Useful links:
Report bugs at https://github.com/ropensci/rvertnet/issues
Specifies a term-wise search (like searchbyterm) and requests
that all available records be made available for download as a
tab-delimited text file.
bigsearch(..., rfile, email, messages = TRUE, callopts = list())bigsearch(..., rfile, email, messages = TRUE, callopts = list())
... |
arguments, must be named, see |
rfile |
A name for the results file that you will download (character). Required. |
email |
An email address where you can be contacted when your records are ready for download (character). Required. |
messages |
(logical) Print progress and information messages.
Default: |
callopts |
(named list) Curl arguments passed on to crul::verb-GET |
bigsearch allows you to request records as a
tab-delimited text file. This is the best way to access a large number of
records, such as when your search results indicate that >1000 records are
available. You will be notified by email when your records are ready
for download.
Prints messages on progress, but returns NULL
We suggest reading data in with data.table::fread() - as it's very
fast for the sometimes large datasets
you will get from using this function, and is usually robust to
formatting issues.
https://github.com/VertNet/webapp/wiki/The-API-search-function
## Not run: # replace "[email protected]" with your own email address bigsearch(genus = "ochotona", rfile = "pikaRecords", email = "[email protected]") # Pass in curl options for curl debugging bigsearch(genus = "ochotona", rfile = "pikaRecords", email = "[email protected]", verbose = TRUE) # Use more than one year query bigsearch(class = "aves", year = c(">=1976", "<=1986"), rfile = "test-bigsearch1", email = "[email protected]") ## End(Not run)## Not run: # replace "[email protected]" with your own email address bigsearch(genus = "ochotona", rfile = "pikaRecords", email = "[email protected]") # Pass in curl options for curl debugging bigsearch(genus = "ochotona", rfile = "pikaRecords", email = "[email protected]", verbose = TRUE) # Use more than one year query bigsearch(class = "aves", year = c(">=1976", "<=1986"), rfile = "test-bigsearch1", email = "[email protected]") ## End(Not run)
vertavailablemaps: Function is now defunct, i.e., not available anymore.
vertlocations: Function is now defunct, i.e., not available anymore.
vertoccurrence: Function is now defunct, i.e., not available anymore.
vertoccurrencecount: Function is now defunct, i.e., not available anymore.
vertproviders: Function is now defunct, i.e., not available anymore.
verttaxa: Function is now defunct, i.e., not available anymore.
Flexible search for records using keywords/terms
searchbyterm( ..., limit = 1000, compact = TRUE, messages = TRUE, only_dwc = TRUE, callopts = list() )searchbyterm( ..., limit = 1000, compact = TRUE, messages = TRUE, only_dwc = TRUE, callopts = list() )
... |
arguments, must be named, see section |
limit |
(numeric) Limit on the number of records returned. If >1000
results, we use a cursor internally, but you should still get up to the
results you asked for. See also |
compact |
(logical) Return a compact data frame |
messages |
(logical) Print progress and information messages.
Default: |
only_dwc |
(logical) whether or not to return only Darwin Core term
fields. Default: |
callopts |
(named list) Curl arguments passed on to crul::verb-GET |
searchbyterm() builds a query from input parameters
based on Darwin Core (dwc) terms (for the full list of terms, see
https://code.google.com/p/darwincore/wiki/DarwinCoreTerms).
A list with two slots:
meta: a named list of metadata for the search results
data: a data frame of search results, columns vary
All these parameters can be passed in to searchbyterm(). All others
will be silently dropped.
See https://github.com/VertNet/webapp/wiki/The-API-search-function for more details
taxon
kingdom (character) Taxonomic kingdom
phylum (character) Taxonomic phylum
class (character) Taxonomic class
order (character) Taxonomic order
family (character) Taxonomic family
genus (character) Taxonomic genus
specificepithet (character) Taxonomic specific epithet, e.g. (sapiens in Homo sapiens)
infraspecificepithet (character) Taxonomic infraspecific epithet
scientificname (character) scientific name
vernacularname (character) a verncular name
event
year (numeric) Year or range of years designated by comparison operators "<", ">", "<=" or ">=". You can pass in more than one of these queries, in a vector. See example below
month (numeric) month or range of months designated by comparison operators "<", ">", "<=" or ">=". You can pass in more than one of these queries, in a vector. See example below
day (numeric) day or range of days designated by comparison operators "<", ">", "<=" or ">=". You can pass in more than one of these queries, in a vector. See example below
eventdate Event date associated with this occurrence record; yyyy-mm-dd or the range yyyy-mm-dd/yyyy-mm-dd (character)
record level
institutioncode (character) Code name for the provider/institution of record
occurrenceid (character) Provider's unique identifier for this occurrence record
catalognumber (character) Provider's catalog number or other ID for this record
collectioncode (character) collection code
license (dcterms:license) license string
iptlicense (eml:intellectualRights) license string
basisofrecord (character) one of PreservedSpecimen, FossilSpecimen, MaterialSample, Occurrence, MachineObservation, HumanObservation
hasmedia (logical) Record also references associated media, such as a film or video
isfossil (logical) dwc:basisOfRecord is FossilSpecimen or collection
is a paleo collection
haslicense (logical) dcterms:license or eml:intellectualRights has a
license designated
identification
typestatus (character) a type status
hastypestatus (logical) type status known or not
occurrence
iptrecordid (character) (same as dwc:occurrenceID)
recordedby (character) Collector name
recordnumber (character) record number
fieldnumber (character) field number
establishmentmeans (character) establishment means
wascaptive (logical) (dwc:establishmentMeans or occurrenceRemarks suggests
it was captive)
wasinvasive (logical) (was the organism recorded to be invasive where and when it occurred)
sex (character) standardized sex from original sex field or extracted from elsewhere in the record
lifestage (character) lifeStage from original sex field or extracted from elsewhere in the record
preparations (not sure what this means)
hastissue (logical) Record is likely to reference tissues
reproductivecondition (not sure what this means)
location
continent (character) Continent to search for occurrence
country (character) Country to search for occurrence
stateprovince (character) State or province to search for occurrence
county (character) County to search for occurrence
island (character) Island to search for occurrence
igroup (character) Island group to search for occurrence
municipality (character)
waterbody (character)
geodeticdatum (character)
georeferencedby (character)
georeferenceverificationstatus (character)
location a Google GeoField of the dwc:decimalLatitude,
dwc:decimalLongitude
mappable (logical) Record includes valid coordinates in decimal latitude and decimal longitude
geological context
bed (character) geological bed
formation (character) geological formation
group (character) geological group
member (character) geological member
traits
haslength (logical) (was a value for length extracted?)
hasmass (logical) (was a value for mass extraccted?)
hassex (logical) (does the record have sex?)
haslifestage (logical) (does the record have life stage?)
lengthtype (character) type of length measurement extracted from the record, can refer to a number or to a range) ('total length', 'standard length', 'snout-vent length','head-body length', 'fork length', 'total length range', 'standard length range', 'snout-vent length range', 'head-body length range', 'fork length range'
lengthinmm (numeric) length measurement extracted from the record
massing (numeric) mass measurement extracted from the record (For detailed information about trait extraction and aggregation and querying via the VertNet portal, see http://vertnet.org/resources/traitsguide.html
data set
gbifdatasetid (character) GBIF identifier for the data set
gbifpublisherid (character) GBIF identifier for the data publishing organization
lastindexed (character) date (YYYY-MM-DD) the record was most recently indexed into VertNet
networks (character) one of MaNIS, ORNIS, HerpNET, FishNet, VertNet, Arctos, Paleo
migrator (character) the version of the migrator used to process the data set, a date of form (YYYY-MM-DD)
orgcountry (character) the country where the organization is located
orgstateprovince (character) the first-level administrative unit where the organization is located
index
rank (character) a higher number means the record is more complete with respect to georeferences, scientific names, and event dates
vntype (character) Type of record; "specimen" or "observation"
hashid (integer) a value to distribute records in 10k bins; 0-9998
other
coordinateuncertaintyinmeters (character) Coordinate uncertainty in meters (numeric) or range of uncertainty values designated by comparison operators "<", ">", "<=", or ">="
It's possible to get no results with a call to searchbyterm(),
then run it again 10 seconds later, and you do get a result.
I'm not sure why this is, something having to do with Vertnet's
infrastucture that I'm not aware of. Point is, if you are sure
you haven't made any mistakes with the parameters, etc., then
simply run the function call again.
https://github.com/VertNet/webapp/wiki/The-API-search-function
## Not run: # Find multiple species out <- searchbyterm(genus = "ochotona", specificepithet = "(princeps OR collaris)", limit=10) # iptrecordid searchbyterm(iptrecordid = "7108667e-1483-4d04-b204-6a44a73a5219") # you can pass more than one, as above, in a single string in parens records <- "(7108667e-1483-4d04-b204-6a44a73a5219 OR 1efe900e-bde2-45e7-9747-2b2c3e5f36c3)" searchbyterm(iptrecordid = records, callopts = list(verbose = TRUE)) # Specifying a range (in meters) for uncertainty in spatial location # (use quotes) out <- searchbyterm(class = "aves", stateprovince = "nevada", coordinateuncertaintyinmeters = "<25") out <- searchbyterm(class = "aves", stateprovince = "california", year = 1976, coordinateuncertaintyinmeters = "<=1000") # Specifying records by event date (use quotes) out <- searchbyterm(class = "aves", stateprovince = "california", eventdate = "2009-03-25") # ...but specifying a date range may not work out <- searchbyterm(specificepithet = "nigripes", eventdate = "1935-09-01/1935-09-30") # Pass in curl options for curl debugging out <- searchbyterm(class = "aves", limit = 10, callopts = list(verbose = TRUE)) # Use more than one year query searchbyterm(genus = "mustela", specificepithet = "nigripes", year = c('>=1900', '<=1940')) searchbyterm(sex = "male", limit = 30)$data$sex searchbyterm(lifestage = "juvenile", limit = 30)$data$lifestage ## End(Not run)## Not run: # Find multiple species out <- searchbyterm(genus = "ochotona", specificepithet = "(princeps OR collaris)", limit=10) # iptrecordid searchbyterm(iptrecordid = "7108667e-1483-4d04-b204-6a44a73a5219") # you can pass more than one, as above, in a single string in parens records <- "(7108667e-1483-4d04-b204-6a44a73a5219 OR 1efe900e-bde2-45e7-9747-2b2c3e5f36c3)" searchbyterm(iptrecordid = records, callopts = list(verbose = TRUE)) # Specifying a range (in meters) for uncertainty in spatial location # (use quotes) out <- searchbyterm(class = "aves", stateprovince = "nevada", coordinateuncertaintyinmeters = "<25") out <- searchbyterm(class = "aves", stateprovince = "california", year = 1976, coordinateuncertaintyinmeters = "<=1000") # Specifying records by event date (use quotes) out <- searchbyterm(class = "aves", stateprovince = "california", eventdate = "2009-03-25") # ...but specifying a date range may not work out <- searchbyterm(specificepithet = "nigripes", eventdate = "1935-09-01/1935-09-30") # Pass in curl options for curl debugging out <- searchbyterm(class = "aves", limit = 10, callopts = list(verbose = TRUE)) # Use more than one year query searchbyterm(genus = "mustela", specificepithet = "nigripes", year = c('>=1900', '<=1940')) searchbyterm(sex = "male", limit = 30)$data$sex searchbyterm(lifestage = "juvenile", limit = 30)$data$lifestage ## End(Not run)
Used internally by vert_id() to filter data to Darwin core terms only. Get in touch with us if these terms need correcting or are out of date.
simple_dwc_termssimple_dwc_terms
simple_dwc_termsA character vector
https://raw.githubusercontent.com/tdwg/dwc/master/dist/simple_dwc_vertical.csv
Searches by decimal latitude and longitude to return any occurrence record within the input distance (radius) of the input point.
spatialsearch( lat, long, radius, limit = 1000, compact = TRUE, messages = TRUE, ... )spatialsearch( lat, long, radius, limit = 1000, compact = TRUE, messages = TRUE, ... )
lat |
(numeric) Latitude of the central point, in decimal degrees required. |
long |
(numeric) Longitude of the central point, in decimal degrees required. |
radius |
(numeric) Radius to search, in meters. There is no default value for this parameter. required. |
limit |
(integer) Limit on the number of records returned. If >1000
results, we use a cursor internally, but you should still get up to the
results you asked for. See also |
compact |
(logical) Return a compact data frame. default: |
messages |
(logical) Print progress and information messages.
Default: |
... |
Curl arguments passed on to crul::HttpClient |
spatialsearch() finds all records of any taxa having
decimal lat/long coordinates within a given radius (in meters) of
your coordinates.
A list with two slots:
meta: a named list of metadata for the search results
data: a data frame of search results, columns vary
https://github.com/VertNet/webapp/wiki/The-API-search-function
## Not run: res <- spatialsearch(lat = 33.529, long = -105.694, radius = 2000, limit = 10) # Pass in curl options for curl debugging out <- spatialsearch(lat = 33.529, long = -105.694, radius = 2000, limit = 10, verbose = TRUE) ## End(Not run)## Not run: res <- spatialsearch(lat = 33.529, long = -105.694, radius = 2000, limit = 10) # Pass in curl options for curl debugging out <- spatialsearch(lat = 33.529, long = -105.694, radius = 2000, limit = 10, verbose = TRUE) ## End(Not run)
Trait focused search
traitsearch( taxon = NULL, has_mass = FALSE, has_length = FALSE, has_sex = FALSE, has_lifestage = FALSE, length_type = NULL, length = NULL, mass = NULL, limit = 1000, compact = TRUE, messages = TRUE, callopts = list(), ... )traitsearch( taxon = NULL, has_mass = FALSE, has_length = FALSE, has_sex = FALSE, has_lifestage = FALSE, length_type = NULL, length = NULL, mass = NULL, limit = 1000, compact = TRUE, messages = TRUE, callopts = list(), ... )
taxon |
(character) Taxonomic identifier or other text to search for |
has_mass |
(logical) limit to records that have mass data (stored in
|
has_length |
(logical) limit to records that have length data (stored
in |
has_sex |
(logical) limit to records that have sex data (stored in
|
has_lifestage |
(logical) limit to records that have lifestage data
(stored in |
length_type |
(character) length type, one of 'total length',
'standard length', 'snout-vent length', 'head-body length', 'fork length',
'total length range', 'standard length range', 'snout-vent length range',
'head-body length range', 'fork length range'. (stored in |
length |
(list) list of query terms for length, e.g., "< 100" |
mass |
(list) list of query terms for mass, e.g., "< 100" |
limit |
(numeric) Limit on the number of records returned. If >1000
results, we use a cursor internally, but you should still get up to the
results you asked for. See also
|
compact |
Return a compact data frame (boolean) |
messages |
Print progress and information messages. Default: TRUE |
callopts |
curl options in a list passed on to
|
... |
(character) Additional search terms. These must be unnamed |
Wraps vertsearch, with some of the same parameters,
but with additional parameters added to make querying for traits easy.
a list, same as returned by vertsearch, with data
in the data slot
## Not run: traitsearch(has_mass = TRUE, limit = 3) traitsearch(has_lifestage = TRUE) traitsearch(has_mass = TRUE, has_length = TRUE) res <- traitsearch(length_type = "total length", length = list(">= 300", "<= 1000")) summary(as.numeric(res$data$lengthinmm)) res <- traitsearch(has_mass = TRUE, mass = list(">= 20", "<= 500")) summary(as.numeric(res$data$massing)) traitsearch(taxon = "aves", has_mass = TRUE, limit = 100) ## End(Not run)## Not run: traitsearch(has_mass = TRUE, limit = 3) traitsearch(has_lifestage = TRUE) traitsearch(has_mass = TRUE, has_length = TRUE) res <- traitsearch(length_type = "total length", length = list(">= 300", "<= 1000")) summary(as.numeric(res$data$lengthinmm)) res <- traitsearch(has_mass = TRUE, mass = list(">= 20", "<= 500")) summary(as.numeric(res$data$massing)) traitsearch(taxon = "aves", has_mass = TRUE, limit = 100) ## End(Not run)
Search by Vertnet occurrence ID
vert_id(ids, compact = TRUE, messages = TRUE, ...)vert_id(ids, compact = TRUE, messages = TRUE, ...)
ids |
(character) VertNet IDs, one or more. Required. |
compact |
(logical) Return a compact data frame. That is, remove
empty columns. Default: |
messages |
(logical) Print progress and information messages.
Default: |
... |
Curl arguments passed on to crul::HttpClient |
VertNet IDs can be a variety of things, some URIs
(i.e., with http://...), while others start with urn.
Internally in this function we filter data to darwin core terms only. To
see what terms we use, see:
print(simple_dwc_terms).
See documentation for more information:
?simple_dwc_terms
A list, with data frame of search results, and list of metadata
## Not run: vert_id(ids = "urn:catalog:CM:Herps:116520") ids <- c("http://arctos.database.museum/guid/MSB:Mamm:56979?seid=1643089", "urn:catalog:CM:Herps:116520", "urn:catalog:AUM:Fish:13271") res <- vert_id(ids) res$data$occurrenceid out <- vertsearch(taxon = "aves", state = "california", limit = 5) (ids <- out$data$occurrenceid) res <- vert_id(ids) identical(sort(res$data$occurrenceid), sort(ids)) ## End(Not run)## Not run: vert_id(ids = "urn:catalog:CM:Herps:116520") ids <- c("http://arctos.database.museum/guid/MSB:Mamm:56979?seid=1643089", "urn:catalog:CM:Herps:116520", "urn:catalog:AUM:Fish:13271") res <- vert_id(ids) res$data$occurrenceid out <- vertsearch(taxon = "aves", state = "california", limit = 5) (ids <- out$data$occurrenceid) res <- vert_id(ids) identical(sort(res$data$occurrenceid), sort(ids)) ## End(Not run)
Plots record locations on a world or regional map using latitude/longitude data returned by a VertNet search.
vertmap( input = NULL, mapdatabase = "world", region = ".", geom = geom_point, jitter = NULL )vertmap( input = NULL, mapdatabase = "world", region = ".", geom = geom_point, jitter = NULL )
input |
Output from |
mapdatabase |
The base map on which your data are displayed; what you choose here determines what you can choose in the region parameter; one of: county, state, usa, world, world2, france, italy, or nz |
region |
The region in which your data are displayed; to see region names
for the "world" database layer, run
|
geom |
Specifies the type of object being plotted; one of: |
jitter |
If |
vertmap uses decimal latitude and longitude data in records generated by
an rvertnet search to display returned records on a specified base map. Taxa
are color-coded by scientific name, if available. Adapt the vertmap code to
construct maps according to your own specifications.
Map of record locations displayed on the selected base map
## Not run: out <- vertsearch("Junco hyemalis") # get occurrence records vertmap(out) # map occurrence records # Records are color coded by dwc term "scientificname" - sometimes unavailble out <- vertsearch("mustela nigripes") vertmap(input = out, mapdatabase = "state") # Use searchbyterm() to match records with mapped region spec <- searchbyterm(genus = "ochotona", specificepithet = "princeps", state = "california", limit = 200) vertmap(input = spec, mapdatabase = "state", region = "california") # Many species splist <- c("Accipiter erythronemius", "Aix sponsa", "Haliaeetus leucocephalus", "Corvus corone", "Threskiornis molucca", "Merops malimbicus") out <- lapply(splist, function(x) vertsearch(t=x, lim=100)) out <- dplyr::bind_rows(lapply(out, "[[", "data")) vertmap(out) ## jitter points library("ggplot2") vertmap(out, geom = geom_jitter, jitter = position_jitter(1, 6)) ## End(Not run)## Not run: out <- vertsearch("Junco hyemalis") # get occurrence records vertmap(out) # map occurrence records # Records are color coded by dwc term "scientificname" - sometimes unavailble out <- vertsearch("mustela nigripes") vertmap(input = out, mapdatabase = "state") # Use searchbyterm() to match records with mapped region spec <- searchbyterm(genus = "ochotona", specificepithet = "princeps", state = "california", limit = 200) vertmap(input = spec, mapdatabase = "state", region = "california") # Many species splist <- c("Accipiter erythronemius", "Aix sponsa", "Haliaeetus leucocephalus", "Corvus corone", "Threskiornis molucca", "Merops malimbicus") out <- lapply(splist, function(x) vertsearch(t=x, lim=100)) out <- dplyr::bind_rows(lapply(out, "[[", "data")) vertmap(out) ## jitter points library("ggplot2") vertmap(out, geom = geom_jitter, jitter = position_jitter(1, 6)) ## End(Not run)
Returns any record containing your target text in any field of the record.
vertsearch( taxon = NULL, ..., limit = 1000, compact = TRUE, messages = TRUE, only_dwc = TRUE, callopts = list() )vertsearch( taxon = NULL, ..., limit = 1000, compact = TRUE, messages = TRUE, only_dwc = TRUE, callopts = list() )
taxon |
(character) Taxonomic identifier or other text to search for |
... |
(character) Additional search terms. These must be unnamed |
limit |
(numeric) Limit on the number of records returned. If >1000
results, we use a cursor internally, but you should still get up to the
results you asked for. See also
|
compact |
Return a compact data frame (boolean) |
messages |
Print progress and information messages. Default: TRUE |
only_dwc |
(logical) whether or not to return only Darwin Core term
fields. Default: |
callopts |
curl options in a list passed on to
|
vertsearch performs a nonspecific search for your
input within every record and field of the VertNet archives. For a more
specific search, try searchbyterm
A data frame of search results
https://github.com/VertNet/webapp/wiki/The-API-search-function
## Not run: out <- vertsearch(taxon = "aves", "california", limit=3) # Limit the number of records returned (under 1000) out <- vertsearch("(kansas state OR KSU)", limit = 200) # Use bigsearch() to retrieve >1000 records # Find multiple species using searchbyterm(): # a) returns a specific result out <- searchbyterm(genus = "mustela", species = "(nivalis OR erminea)") vertmap(out) # b) returns a non-specific result out <- vertsearch(taxon = "(mustela nivalis OR mustela erminea)") vertmap(out) # c) returns a non-specific result splist <- c("mustela nivalis", "mustela erminea") out <- lapply(splist, function(x) vertsearch(taxon = x, lim = 500)) out <- dplyr::bind_rows(lapply(out, "[[", "data")) vertmap(out) # curl options vertsearch(taxon = "Aves", limit = 10, callopts = list(verbose = TRUE)) # vertsearch(taxon = "Aves", limit = 10, callopts = list(timeout_ms = 10)) ## End(Not run)## Not run: out <- vertsearch(taxon = "aves", "california", limit=3) # Limit the number of records returned (under 1000) out <- vertsearch("(kansas state OR KSU)", limit = 200) # Use bigsearch() to retrieve >1000 records # Find multiple species using searchbyterm(): # a) returns a specific result out <- searchbyterm(genus = "mustela", species = "(nivalis OR erminea)") vertmap(out) # b) returns a non-specific result out <- vertsearch(taxon = "(mustela nivalis OR mustela erminea)") vertmap(out) # c) returns a non-specific result splist <- c("mustela nivalis", "mustela erminea") out <- lapply(splist, function(x) vertsearch(taxon = x, lim = 500)) out <- dplyr::bind_rows(lapply(out, "[[", "data")) vertmap(out) # curl options vertsearch(taxon = "Aves", limit = 10, callopts = list(verbose = TRUE)) # vertsearch(taxon = "Aves", limit = 10, callopts = list(timeout_ms = 10)) ## End(Not run)
Creates a simple summary of data returned by a VertNet search.
vertsummary(input, verbose = TRUE)vertsummary(input, verbose = TRUE)
input |
Output from |
verbose |
Print progress and information messages. Default: TRUE |
vertsummary provides information on the sources,
types and extent of data returned by a VertNet search.
A list of summary statistics
## Not run: # get occurrence records recs <- vertsearch("Junco hyemalis", limit = 10) # summarize occurrence records vertsummary(recs) vertsummary(vertsearch("Oncorhynchus clarki henshawi")) ## End(Not run)## Not run: # get occurrence records recs <- vertsearch("Junco hyemalis", limit = 10) # summarize occurrence records vertsummary(recs) vertsummary(vertsearch("Oncorhynchus clarki henshawi")) ## End(Not run)