Download the number of records available for different collections filtered
by location (if provided). If authorization is provided, the collections are
filtered to only those available to the user (unless using show = "all").
Without authorization all collections are returned.
nc_count(
collections = NULL,
project_ids = NULL,
species = NULL,
years = NULL,
doy = NULL,
region = NULL,
site_type = NULL,
show = "available",
username = NULL,
timeout = 120,
verbose = TRUE
)Character vector. The collection codes from which to download data. NULL (default) downloads data from all available collections
Character/Numeric vector. The project ids from which to
download data. First the collections associated with a project_id are
determined, and then data is downloaded for each collection. If both
collections and project_ids are supplied, they are combined.
Numeric vector. Numeric species ids (see details)
Numeric vector. The start/end years of data to download. Can use NA for either start or end, or a single value to return data from a single year.
Character/Numeric vector. The start/end day-of-year to download (1-366 or dates that can be converted to day of year). Can use NA for either start or end
List. Named list with one of the following options:
country, statprov, subnational2, iba, bcr, utm_squares, bbox.
See details
Character vector. The type of site to return (e.g., IBA).
Character. Either "all" or "available". "all" returns counts from all data sources. "available" only returns counts for data available for the username provided. If no username is provided, defaults to "all".
Character vector. Username for http://naturecounts.ca. If provided, the user will be prompted for a password. If left NULL, only public collections will be returned.
Numeric. Number of seconds before connecting to the server times out.
Logical. Show messages?
Data frame
The akn_level column describes the level of data access for that collection
(see descriptions online).
The access column describes the accessibility of a collection for a given
username (or no access if no username supplied). See the section on Access
and request_ids for more details.
All public data is available with a username/password
(sign up
for a free NatureCounts account). However, to access private/semi-public
projects/collections you must request access. See the Access and
request_ids section for more information.
species)Numeric species id codes can determined from the functions
search_species() or search_species_code(). See also the article on
species codes
for more information.
doy)The format for day of year (doy) is fairly flexible and can be a whole
number between 1 and 366 or anything recognized by
lubridate-package's ymd()
function. However, it must have the order of year, month, day. Note that
year is ignored when converting to day of year, except that it will result
in a 1 day offset for leap years.
region)Regions are defined by codes reflecting the country, state/province,
subnational (level 2), Important Bird Areas (IBA), and Bird Conservation
Regions (BCR) (see search_region() for codes). They can also be defined
by providing specific UTM squares to download or a bounding box area which
specifies the min/max longitude and min/max latitude (bbox). See the
article on regional filters
for more information.
request_idsAccess to a data collection is either available as "full" or "by request".
Use nc_count(username = "USER", show = "all"), to see the accessibility of
collections.
"Full" access means that data can be immediately requested directly through
the naturecounts R package. "By request" means that a request must be
submitted online and
approved before the data can be downloaded through naturecounts.
This means that there are two types of data requests: ones made through this
naturecounts R package (API requests) and those made through the online
Web Request Form (Web
requests). Every request (from either method) generates a request_id which
identifies the filter set and collections requested. Details of all of
requests can be reviewed with the nc_requests() function.
To download data with "full" access, users can either specify filters, or if
they are repeating a download, can use the request_id from nc_requests().
Otherwise, if the user doesn't have "full" access, they must supply an
approved request_id to the nc_data_dl() function (e.g.,
nc_data_dl(request_id = 152000, username = "USER")). Use nc_requests() to
see request_ids, filters, and approval status.
Requests for "full" access to additional collections can be made online through the Web Request Form by checking the "Full access?" box in Step 2 of the form.
# Count all publicly available records:
# \donttest{
nc_count()
#> Without a username, using 'show = "all"'
#> # A tibble: 440 × 4
#> collection akn_level access nrecords
#> <chr> <int> <chr> <int>
#> 1 ABATLAS1 5 full 123364
#> 2 ABATLAS2 5 full 201357
#> 3 ABBIRDRECS 5 full 357264
#> 4 ATBANS 3 by request 102
#> 5 ATOWLS 4 by request 25268
#> 6 BBS 5 full 5735895
#> 7 BBS50 5 full 0
#> 8 BBS50-CAN 5 full 4543180
#> 9 BBS50-US-EAST 5 full 10761296
#> 10 BBS50-US-WEST 5 full 11665251
#> # ℹ 430 more rows
# }
# Count publicly available records for Manitoba, Canada
# \donttest{
nc_count(region = list(statprov = "MB"))
#> Without a username, using 'show = "all"'
#> Using filters: statprov (MB)
#> # A tibble: 103 × 4
#> collection akn_level access nrecords
#> <chr> <int> <chr> <int>
#> 1 ABBIRDRECS 5 full 357
#> 2 BBS 5 full 86997
#> 3 BBS50-CAN 5 full 493120
#> 4 CBC 2 no access 20507
#> 5 CMMN-DET-DMBO 2 no access 93013
#> 6 EBIRD-CA-PR 4 by request 3367908
#> 7 EBIRD-CA-SENS 3 by request 4898
#> 8 EBUTTERFLY 5 full 224
#> 9 GBBC 4 by request 20996
#> 10 GBIF_040C5662 5 full 217
#> # ℹ 93 more rows
# }
# Count all records for all collections user "sample" has access to
if (FALSE) {
nc_count(username = "sample")
}
# Count records with house finches in Ontario
search_species("house finch")
#> # A tibble: 3 × 5
#> species_id scientific_name english_name french_name taxon_group
#> <int> <chr> <chr> <chr> <chr>
#> 1 20350 Haemorhous mexicanus House Finch Roselin fa… BIRDS
#> 2 42255 Haemorhous mexicanus [mexican… House Finch… Roselin fa… BIRDS
#> 3 42256 Haemorhous mexicanus mcgregori House Finch… Roselin fa… BIRDS
nc_count(species = 20350, region = list(statprov = "ON"), username = "sample")
#> Using filters: species (20350); statprov (ON)
#> # A tibble: 2 × 4
#> collection akn_level access nrecords
#> <chr> <int> <chr> <int>
#> 1 SAMPLE1 0 full 8
#> 2 SAMPLE2 0 full 11
# Count all records available in the Christmas Bird Count and Breeding Bird
# Survey collections (regardless of user permissions)
nc_count(collections = c("CBC", "BBS"), show = "all", username = "sample")
#> Using filters: collections (CBC, BBS)
#> # A tibble: 2 × 4
#> collection akn_level access nrecords
#> <chr> <int> <chr> <int>
#> 1 BBS 5 by request 5735895
#> 2 CBC 2 no access 7570427