Description Usage Arguments Details Value Geographic Subsetting Author(s) References See Also Examples
Assemble North American Breeding Bird Survey 10-stop count data into a data
frame, optionally subset to select regions, years, and/or species. The
underlying data come from state/province-specific zipped csv files within the
BBS folder /States/. These csv files do not include counts of zero
(i.e. when a species is not observed during a given survey), but counts of
zero can optionally be built in (see argument zeros
).
Note: Without counts of zero the full 10-stop dataset for 2017
includes 6.4 million rows. With zeros it includes 90 million rows, which will
take some time to build and require a few gigabytes of memory. If building
with zeros, consider subsetting to regions, years, and/or species of
interest.
1 2 |
bbs_dir |
Local directory from which to load BBS data. Must be an existing directory with the same structure as the USGS BBS directory (ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/DataFiles/). |
zeros |
Build in counts of zero? Defaults to |
countries |
Vector of country names to subset to. Defaults to all available. Case insensitive. (See section Geographic Subsetting) |
states |
Vector of state/province/territory names to subset to. Defaults to all available. Case insensitive. (See section Geographic Subsetting) |
bcr |
Vector of Bird Conservation Region integer codes to subset to. Defaults to all available. (See section Geographic Subsetting) |
strata |
Vector of physiographic strata integer codes to subset to. Defaults to all available. (See section Geographic Subsetting) |
aou |
Vector of integer species id codes to subset to. Defaults to all available. (See BBS file SpeciesList.txt) |
years |
Vector of survey years to subset to. Defaults to all available. |
If zeros = TRUE
, counts of zero are built in as follows:
1. Find every unique combination of route-year-rpid matching the given subset arguments (or the whole dataset if no subset arguments given).
2. Find every unique species (aou) that was recorded on those route-year-rpid (subject to aou subset argument, if given).
3. Create a data frame with every combination of those route-year-rpid and aou, and merge with the non-zero count data. Any route-year-rpid-aou rows with missing count data are then filled in with counts of zero.
Note that this method is potentially inefficient in that it will yield counts of zero for species even in regions where they have never been observed.
A data.frame
with the following columns (all integer):
route_data_id |
code for unique combinations of country_num, state, route, rpid, and year |
country_num |
code for country: 124 (Canada), 484 (Mexico), or 840 (United States) |
state_num |
code for state/province/territory (see BBS file RegionCodes.txt) |
route |
code for route (unique within states) |
rpid |
code for Run Protocol ID (see BBS file RunProtocolID.txt) |
year |
survey year |
aou |
species code from American Ornithological Union |
count_10 |
total individuals of the species recorded on stops 1-10 |
count_20 |
total individuals of the species recorded on stops 11-20 |
count_30 |
total individuals of the species recorded on stops 21-30 |
count_40 |
total individuals of the species recorded on stops 31-40 |
count_50 |
total individuals of the species recorded on stops 41-50 |
stop_total |
number of stops out of 50 on which the species was recorded |
species_total |
total individuals recorded on that run of the route (sum from all stops) |
For country and state names see bbs_meta_regions
. For integer
bcr codes see bbs_meta_bcr
, and for integer strata codes see
bbs_meta_strata
.
Geographic subsetting may done by countries and/or states OR bcr and/or strata, but not by both. Subsets are additive, so specifying
bbs_build_10('.', countries = 'Canada', states = 'Montana')
will return data for all Canadian provinces/territories plus the state of Montana. Likewise, the following lines are equivalent, and will both return data for all American states:
bbs_build_10('.', countries = 'United States', states = 'Florida')
bbs_build_10('.', countries = 'United States')
Bob O'Hara
Patrick Barks <patrick.barks@gmail.com>
Pardieck, K.L., D.J. Ziolkowski Jr., M. Lutmerding and M.-A.R. Hudson. 2018. North American Breeding Bird Survey Dataset 1966-2017, version 2017.0. U.S. Geological Survey, Patuxent Wildlife Research Center. https://doi.org/10.5066/F76972V8
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
# build whole dataset excluding counts of zero
bbs <- bbs_build_10(bbs_dir = ".")
# build with Canadian routes only, including counts of zero
bbs <- bbs_build_10(bbs_dir = ".", zeros = TRUE, countries = 'Canada')
# build for species Gray Jay (aou 4840), including counts of zero
bbs <- bbs_build_10(bbs_dir = ".", zeros = TRUE, aou = 4840)
## End(Not run)
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