eBird Data Extraction and Processing in R

Extract and process bird sightings records from eBird (< http://ebird.org>), an online tool for recording bird observations. Public access to the full eBird database is via the eBird Basic Dataset (EBD; see < http://ebird.org/ebird/data/download> for access), a downloadable text file. This package is an interface to AWK for extracting data from the EBD based on taxonomic, spatial, or temporal filters, to produce a manageable file size that can be imported into R.


News

auk 0.3.1

auk 0.3.1

  • rlang::UQ() and rlang::UQS() deprecated, switching to !! and !!!
  • auk_unique() now keeps track of all sampling event and observer IDs that comprise a group checklist

auk 0.3.0

  • Updated to 2018 taxonomy; new function get_ebird_taxonomy() to get taxonomy via the eBird API
  • Better handling of taxonomy versions, many functions now take a taxonomy_version argument and use the eBird API to get the taxonomy
  • auk_getpath() renamed auk_get_awk_path(), and added auk_set_awk_path()
  • Added auk_set_ebd_path() and auk_get_ebd_path() to set and get the EBD_PATH environment variable. Now users only need to set this once and just refer to the file name, rather than specifying the full path every time.
  • Functions to prepare data for occupancy modeling: filter_repeat_visits() and format_unmarked_occu()
  • New auk_bcr() function to extract data from BCRs
  • Added bcr_codes data frame to look up BCR names and codes
  • "Area" protocol added to auk_protocol() filter.
  • auk_extent() renamed auk_bbox(); auk_extent() deprecated and redirects to auk_bbox()
  • auk_zerofill() now checks for complete checklists and gives option to not rollup
  • auk_rollup() now gives the option of keeping higher taxa via drop_higher argument
  • auk_clean() deprecated
  • Fixed package load error when EBD_PATH is invalid
  • Fixed bug when reading files with a blank column using readr

auk 0.2.2

  • Updated to work with EDB version 1.9
  • Modified tests to be more general to all sample data
  • ebird_species() now returns 6-letter species codes
  • Fixed bug causing auk to fail on files downloaded via custom download form
  • Fixed bug with normalizePath() use on Windows
  • Fixed bug with system2() on Windows

auk 0.2.1

  • Patch release fixing a couple bugs
  • Removed all non-ASCII characters from example files, closes issue #14
  • Fixed issue with state filtering not working, closes issue $16

auk 0.2.0

  • New function, auk_split(), splits EBD up into multiple files by species
  • New object, auk_sampling, and associated methods for working with the sampling data only
  • New function, auk_select(), for selecting a subset of columns
  • auk_date() now allows filtering date ranges across years using wildcards, e.g. date = c("*-05-01", "*-06-30") for observations from May and June of any year
  • New function, auk_state() for filtering by state
  • Now using AWK arrays to speed up country and species filtering; ~20% speed up when filtering on many species/countries
  • Allow selection of a subset of columns when filtering
  • Remove free text columns in auk_clean() to decrease file size
  • Updated to work with Feb 2018 version of EBD
  • Fixed broken dependency on countrycode package

auk 0.1.0

  • eBird taxonomy update to August 2017 version, users should download the most recent EBD to ensure the taxonomy is in sync with the new package
  • Manually set AWK path with environment variable AWK_PATH in .Renviron file
  • auk_distance, auk_breeding, auk_protocol, and auk_project filters added
  • Users can now specify a subset of columns to return when calling auk_filter using the keep and drop arguments
  • Many changes suggested by rOpenSci package peer review process, see https://github.com/ropensci/onboarding/issues/136 for details
  • New vignette added to aid those wanting to contribute to package development

auk 0.0.2

  • Patch release converting ebird_taxonomy to ASCII to pass CRAN checks

auk 0.0.1

  • First CRAN release

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("auk")

0.4.0 by Matthew Strimas-Mackey, 21 days ago


https://github.com/CornellLabofOrnithology/auk, http://CornellLabofOrnithology.github.io/auk/


Report a bug at https://github.com/CornellLabofOrnithology/auk/issues


Browse source code at https://github.com/cran/auk


Authors: Matthew Strimas-Mackey [aut, cre] , Eliot Miller [aut] , Wesley Hochachka [aut] , Cornell Lab of Ornithology [cph]


Documentation:   PDF Manual  


GPL-3 license


Imports assertthat, countrycode, dplyr, httr, magrittr, rlang, stringi, stringr, tidyr, utils

Suggests covr, data.table, knitr, readr, rmarkdown, testthat, unmarked


See at CRAN