auk (version 0.8.0)

auk_rollup: Roll up eBird taxonomy to species

Description

The eBird Basic Dataset (EBD) includes both true species and every other field-identifiable taxon that could be relevant for birders to report. This includes taxa not identifiable to a species (e.g. hybrids) and taxa reported below the species level (e.g. subspecies). This function produces a list of observations of true species, by removing the former and rolling the latter up to the species level. In the resulting EBD data.frame, category will be "species" for all records and the subspecies fields will be dropped. By default, read_ebd() calls ebd_rollup() when importing an eBird data file.

Usage

auk_rollup(x, taxonomy_version, drop_higher = TRUE)

Value

A data frame of the eBird data with taxonomic rollup applied.

Arguments

x

data.frame; data frame of eBird data, typically as imported by read_ebd()

taxonomy_version

integer; the version (i.e. year) of the taxonomy. In most cases, this should be left empty to use the version of the taxonomy included in the package. See get_ebird_taxonomy().

drop_higher

logical; whether to remove taxa above species during the rollup process, e.g. "spuhs" like "duck sp.".

Details

When rolling observations up to species level the observed counts are summed across any taxa that resolve to the same species. However, if any of these taxa have a count of "X" (i.e. the observer did not enter a count), then the rolled up record will get an "X" as well. For example, if an observer saw 3 Myrtle and 2 Audubon's Warblers, this will roll up to 5 Yellow-rumped Warblers. However, if an "X" was entered for Myrtle, this would roll up to "X" for Yellow-rumped Warbler.

The eBird taxonomy groups taxa into eight different categories. These categories, and the way they are treated by auk_rollup() are as follows:

• Species: e.g., Mallard. Combined with lower level taxa if present on the same checklist.

• ISSF or Identifiable Sub-specific Group: Identifiable subspecies or group of subspecies, e.g., Mallard (Mexican). Rolled-up to species level.

• Intergrade: Hybrid between two ISSF (subspecies or subspecies groups), e.g., Mallard (Mexican intergrade. Rolled-up to species level.

• Form: Miscellaneous other taxa, including recently-described species yet to be accepted or distinctive forms that are not universally accepted (Red-tailed Hawk (Northern), Upland Goose (Bar-breasted)). If the checklist contains multiple taxa corresponding to the same species, the lower level taxa are rolled up, otherwise these records are left as is.

• Spuh: Genus or identification at broad level -- e.g., duck sp., dabbling duck sp.. Dropped by auk_rollup().

• Slash: Identification to Species-pair e.g., American Black Duck/Mallard). Dropped by auk_rollup().

• Hybrid: Hybrid between two species, e.g., American Black Duck x Mallard (hybrid). Dropped by auk_rollup().

• Domestic: Distinctly-plumaged domesticated varieties that may be free-flying (these do not count on personal lists) e.g., Mallard (Domestic type). Dropped by auk_rollup().

The rollup process is based on the eBird taxonomy, which is updated once a year in August. The auk package includes a copy of the eBird taxonomy, current at the time of release; however, if the EBD and auk versions are not aligned, you may need to explicitly specify which version of the taxonomy to use, in which case the eBird API will be queried to get the correct version of the taxonomy.

References

Consult the eBird taxonomy page for further details.

See Also

Other pre: auk_unique()

Examples

# get the path to the example data included in the package
# in practice, provide path to ebd, e.g. f <- "data/ebd_relFeb-2018.txt
f <- system.file("extdata/ebd-rollup-ex.txt", package = "auk")
# read in data without rolling up
ebd <- read_ebd(f, rollup = FALSE)
# rollup
ebd_ru <- auk_rollup(ebd)
# keep higher taxa
ebd_higher <- auk_rollup(ebd, drop_higher = FALSE)

# all taxa not identifiable to species are dropped
unique(ebd$category)
unique(ebd_ru$category)
unique(ebd_higher$category)

# yellow-rump warbler subspecies rollup
library(dplyr)
# without rollup, there are three observations
ebd %>%
  filter(common_name == "Yellow-rumped Warbler") %>% 
  select(checklist_id, category, common_name, subspecies_common_name, 
         observation_count)
# with rollup, they have been combined
ebd_ru %>%
  filter(common_name == "Yellow-rumped Warbler") %>% 
  select(checklist_id, category, common_name, observation_count)