Introduction to the rebird package
Sebastian Pardo, Rafael Maia
2021-01-25
Source:vignettes/rebird_vignette.Rmd
rebird_vignette.RmdA programmatic interface to the eBird database. Find out more about eBird at their website.
Installation
You can install the stable version from CRAN
install.packages("rebird")Or the development version from Github
install.packages("devtools")
devtools::install_github("ropensci/rebird")Then load the package into the R session
Usage
The eBird API server requires users to provide an API key, which is linked to your eBird user account. You can pass it to the ‘key’ argument in rebird functions, but we highly recommend storing it as an environment variable called EBIRD_KEY in your .Renviron file. If you don’t have a key, you can obtain one from https://ebird.org/api/keygen.
You can keep your .Renviron file in your global R home directory (R.home()), your user’s home directory (Sys.getenv("HOME")), or your current working directory (getwd()). Remember that .Renviron is loaded once when you start R, so if you add your API key to the file you will have to restart your R session. See ?Startup for more information on R’s startup files.
Furthermore, functions now use species codes, rather than scientific names, for species-specific requests. We’ve made the switch easy by providing the species_code function, which converts a scientific name to its species code:
species_code('sula variegata')## Peruvian Booby (Sula variegata): perboo1## [1] "perboo1"The species_code function can be called within other rebird functions, or the species code can be specified directly.
eBird Taxonomy
The eBird taxonomy is internally stored in rebird and can be called using
rebird::tax## # A tibble: 17,064 × 15
## sciName comName speciesCode category taxonOrder bandingCodes comNameCodes
## <chr> <chr> <chr> <chr> <dbl> <chr> <chr>
## 1 Struthio c… Common… ostric2 species 2 <NA> COOS
## 2 Struthio m… Somali… ostric3 species 7 <NA> SOOS
## 3 Struthio c… Common… y00934 slash 8 <NA> SOOS,COOS
## 4 Rhea ameri… Greate… grerhe1 species 10 <NA> GRRH
## 5 Rhea penna… Lesser… lesrhe2 species 16 <NA> LERH
## 6 Rhea penna… Lesser… lesrhe4 issf 17 <NA> LERH
## 7 Rhea penna… Lesser… lesrhe3 issf 20 <NA> LERH
## 8 Nothocercu… Tawny-… tabtin1 species 22 <NA> TBTI
## 9 Nothocercu… Highla… higtin1 species 23 HITI <NA>
## 10 Nothocercu… Highla… higtin2 issf 24 <NA> HITI
## # ℹ 17,054 more rows
## # ℹ 8 more variables: sciNameCodes <chr>, order <chr>, familyCode <chr>,
## # familyComName <chr>, familySciName <chr>, reportAs <chr>, extinct <lgl>,
## # extinctYear <int>While the internal taxonomy is kept up to date with each package release, it could be outdated if a new taxonomy is made available before the package is updated. You can obtain the latest eBird taxonomy by
new_tax <- ebirdtaxonomy()Sightings at location determined by latitude/longitude
Search for bird occurrences by latitude and longitude point
ebirdgeo(species = species_code('spinus tristis'), lat = 42, lng = -76)## American Goldfinch (Spinus tristis): amegfi## # A tibble: 31 × 13
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 amegfi America… Spinus… L144… Heart … 2024… 10 41.8 -75.8 TRUE
## 2 amegfi America… Spinus… L982… Hazel … 2024… 1 42.1 -76.1 TRUE
## 3 amegfi America… Spinus… L243… 71 Wil… 2024… 12 42.2 -75.9 TRUE
## 4 amegfi America… Spinus… L124… Happy … 2024… 7 42.1 -75.9 TRUE
## 5 amegfi America… Spinus… L197… esther… 2024… 4 42.1 -75.9 TRUE
## 6 amegfi America… Spinus… L299… 184 Sw… 2024… 4 42.2 -76.0 TRUE
## 7 amegfi America… Spinus… L300… 194 Sw… 2024… 6 42.2 -75.9 TRUE
## 8 amegfi America… Spinus… L210… 1099 P… 2024… 2 42.1 -76.0 TRUE
## 9 amegfi America… Spinus… L131… Vestal 2024… 1 42.1 -76.1 TRUE
## 10 amegfi America… Spinus… L447… Bingha… 2024… 2 42.1 -76.0 TRUE
## # ℹ 21 more rows
## # ℹ 3 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>Recent observations at a region
Search for bird occurrences by region and species name
ebirdregion(loc = 'US', species = 'btbwar')## # A tibble: 15 × 13
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 btbwar Black-… Setoph… L129… Cave C… 2024… 1 31.9 -109. TRUE
## 2 btbwar Black-… Setoph… L584… Treasu… 2024… 1 27.8 -80.4 TRUE
## 3 btbwar Black-… Setoph… L300… 11300 … 2024… 1 27.8 -80.4 TRUE
## 4 btbwar Black-… Setoph… L127… Lettuc… 2024… 1 28.1 -82.4 TRUE
## 5 btbwar Black-… Setoph… L195… 1 My H… 2024… 1 27.0 -80.1 TRUE
## 6 btbwar Black-… Setoph… L582… Southe… 2024… 1 25.4 -80.6 TRUE
## 7 btbwar Black-… Setoph… L661… Memori… 2024… 1 29.6 -95.6 TRUE
## 8 btbwar Black-… Setoph… L214… Saxapa… 2024… 1 35.9 -79.3 TRUE
## 9 btbwar Black-… Setoph… L149… Jackso… 2024… 1 30.3 -81.5 TRUE
## 10 btbwar Black-… Setoph… L127… Key We… 2024… 2 24.6 -81.7 TRUE
## 11 btbwar Black-… Setoph… L127… Key La… 2024… 1 25.2 -80.4 TRUE
## 12 btbwar Black-… Setoph… L385… My Yard 2024… 1 25.7 -80.3 TRUE
## 13 btbwar Black-… Setoph… L823… J. N. … 2024… 1 26.5 -82.1 TRUE
## 14 btbwar Black-… Setoph… L682… Univer… 2024… 1 25.7 -80.3 TRUE
## 15 btbwar Black-… Setoph… L130… Castle… 2024… 1 29.6 -81.2 TRUE
## # ℹ 3 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>Recent observations at hotspots
Search for bird occurrences by a given hotspot
ebirdregion(loc = 'L99381')## # A tibble: 62 × 14
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 gadwal Gadwall Mareca… L993… Stewar… 2024… 6 42.5 -76.5 TRUE
## 2 amewig America… Mareca… L993… Stewar… 2024… 2 42.5 -76.5 TRUE
## 3 mallar3 Mallard Anas p… L993… Stewar… 2024… 25 42.5 -76.5 TRUE
## 4 ambduc America… Anas r… L993… Stewar… 2024… 2 42.5 -76.5 TRUE
## 5 commer Common … Mergus… L993… Stewar… 2024… 6 42.5 -76.5 TRUE
## 6 killde Killdeer Charad… L993… Stewar… 2024… 2 42.5 -76.5 TRUE
## 7 ribgul Ring-bi… Larus … L993… Stewar… 2024… NA 42.5 -76.5 TRUE
## 8 gbbgul Great B… Larus … L993… Stewar… 2024… NA 42.5 -76.5 TRUE
## 9 doccor Double-… Nannop… L993… Stewar… 2024… 2 42.5 -76.5 TRUE
## 10 amecro America… Corvus… L993… Stewar… 2024… 4 42.5 -76.5 TRUE
## # ℹ 52 more rows
## # ℹ 4 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>,
## # exoticCategory <chr>Nearest observations of a species
Search for a species’ occurrences near a given latitude and longitude
nearestobs(species_code('branta canadensis'), 42, -76)## Canada Goose (Branta canadensis): cangoo## # A tibble: 67 × 13
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 cangoo Canada … Branta… L179… "Bingh… 2024… 2 42.1 -75.9 TRUE
## 2 cangoo Canada … Branta… L144… "Heart… 2024… 2 41.8 -75.8 TRUE
## 3 cangoo Canada … Branta… L116… "Lake … 2024… 2 41.8 -75.9 TRUE
## 4 cangoo Canada … Branta… L465… "Bingh… 2024… 8 42.1 -75.9 TRUE
## 5 cangoo Canada … Branta… L300… "Our L… 2024… 2 42.1 -75.9 TRUE
## 6 cangoo Canada … Branta… L145… "Lake … 2024… 2 41.8 -75.8 TRUE
## 7 cangoo Canada … Branta… L204… "McDon… 2024… 4 41.8 -75.9 TRUE
## 8 cangoo Canada … Branta… L936… "Bolan… 2024… 6 42.2 -75.9 TRUE
## 9 cangoo Canada … Branta… L186… "Otsin… 2024… 10 42.1 -75.9 TRUE
## 10 cangoo Canada … Branta… L717… "PA-SQ… 2024… 2 41.9 -75.9 TRUE
## # ℹ 57 more rows
## # ℹ 3 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>Recent notable sightings
Search for notable sightings at a given latitude and longitude
ebirdnotable(lat = 42, lng = -70)## # A tibble: 3,200 × 14
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 osprey Osprey Pandio… L300… 100 Gr… 2024… 1 41.7 -72.6 FALSE
## 2 fiespa Field S… Spizel… L514… Pinnac… 2024… 1 43.1 -72.4 FALSE
## 3 chispa Chippin… Spizel… L586… High S… 2024… 2 42.9 -70.8 FALSE
## 4 palwar3 Palm Wa… Setoph… L250… Hampto… 2024… 1 42.9 -70.8 FALSE
## 5 bkhgul Black-h… Chroic… L829… Dowses… 2024… 5 41.6 -70.4 FALSE
## 6 rosgoo Ross's … Anser … L279… Hardar… 2024… 1 42.9 -70.8 FALSE
## 7 osprey Osprey Pandio… L675… Longme… 2024… 2 42.1 -72.6 FALSE
## 8 yebsap Yellow-… Sphyra… L458… Waldob… 2024… 1 44.1 -69.4 FALSE
## 9 yebsap Yellow-… Sphyra… L458… Waldob… 2024… 1 44.1 -69.4 FALSE
## 10 baleag Bald Ea… Haliae… L226… W Basi… 2024… 1 41.4 -70.8 FALSE
## # ℹ 3,190 more rows
## # ℹ 4 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>,
## # exoticCategory <chr>or a region
ebirdnotable(locID = 'US-NY-109')## # A tibble: 84 × 13
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 veggul1 Herring… Larus … L212… Steven… 2024… 1 42.4 -76.4 FALSE
## 2 sancra Sandhil… Antigo… L212… Steven… 2024… 9 42.4 -76.4 FALSE
## 3 sancra Sandhil… Antigo… L212… Steven… 2024… 9 42.4 -76.4 FALSE
## 4 veggul1 Herring… Larus … L212… Steven… 2024… 1 42.4 -76.4 FALSE
## 5 veggul1 Herring… Larus … L212… Steven… 2024… 1 42.4 -76.4 FALSE
## 6 veggul1 Herring… Larus … L212… Steven… 2024… 1 42.4 -76.4 FALSE
## 7 eastow1 Eastern… Pipilo… L117… Ringwo… 2024… 1 42.4 -76.4 FALSE
## 8 eastow1 Eastern… Pipilo… L117… Ringwo… 2024… 1 42.4 -76.4 FALSE
## 9 eastow1 Eastern… Pipilo… L117… Ringwo… 2024… 1 42.4 -76.4 FALSE
## 10 eastow1 Eastern… Pipilo… L117… Ringwo… 2024… 1 42.4 -76.4 FALSE
## # ℹ 74 more rows
## # ℹ 3 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>Historic Observations
Obtain a list of species reported on a specific date in a given region
ebirdhistorical(loc = 'US-VA-003', date = '2019-02-14',max = 10)## # A tibble: 10 × 13
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 cangoo Canada … Branta… L139… Lickin… 2019… 30 38.1 -78.7 TRUE
## 2 mallar3 Mallard Anas p… L139… Lickin… 2019… 5 38.1 -78.7 TRUE
## 3 gnwtea Green-w… Anas c… L139… Lickin… 2019… 8 38.1 -78.7 TRUE
## 4 killde Killdeer Charad… L139… Lickin… 2019… 1 38.1 -78.7 TRUE
## 5 baleag Bald Ea… Haliae… L139… Lickin… 2019… 1 38.1 -78.7 TRUE
## 6 belkin1 Belted … Megace… L139… Lickin… 2019… 1 38.1 -78.7 TRUE
## 7 carwre Carolin… Thryot… L139… Lickin… 2019… 1 38.1 -78.7 TRUE
## 8 whtspa White-t… Zonotr… L139… Lickin… 2019… 2 38.1 -78.7 TRUE
## 9 norcar Norther… Cardin… L139… Lickin… 2019… 1 38.1 -78.7 TRUE
## 10 canvas Canvasb… Aythya… L331… Montic… 2019… 19 38.0 -78.5 TRUE
## # ℹ 3 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>or a hotspot
ebirdhistorical(loc = 'L196159', date = '2019-02-14', fieldSet = 'full')## # A tibble: 14 × 27
## speciesCode comName sciName locId locName obsDt howMany lat lng obsValid
## <chr> <chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl> <lgl>
## 1 annhum Anna's … Calypt… L196… Vancou… 2019… 4 49.3 -123. TRUE
## 2 ribgul Ring-bi… Larus … L196… Vancou… 2019… 4 49.3 -123. TRUE
## 3 glwgul Glaucou… Larus … L196… Vancou… 2019… 29 49.3 -123. TRUE
## 4 amecro America… Corvus… L196… Vancou… 2019… 100 49.3 -123. TRUE
## 5 bkcchi Black-c… Poecil… L196… Vancou… 2019… 16 49.3 -123. TRUE
## 6 bushti Bushtit Psaltr… L196… Vancou… 2019… 20 49.3 -123. TRUE
## 7 pacwre1 Pacific… Troglo… L196… Vancou… 2019… 1 49.3 -123. TRUE
## 8 houfin House F… Haemor… L196… Vancou… 2019… 2 49.3 -123. TRUE
## 9 purfin Purple … Haemor… L196… Vancou… 2019… 3 49.3 -123. TRUE
## 10 amegfi America… Spinus… L196… Vancou… 2019… 15 49.3 -123. TRUE
## 11 daejun Dark-ey… Junco … L196… Vancou… 2019… 37 49.3 -123. TRUE
## 12 sonspa Song Sp… Melosp… L196… Vancou… 2019… 12 49.3 -123. TRUE
## 13 spotow Spotted… Pipilo… L196… Vancou… 2019… 1 49.3 -123. TRUE
## 14 rewbla Red-win… Agelai… L196… Vancou… 2019… 6 49.3 -123. TRUE
## # ℹ 17 more variables: obsReviewed <lgl>, locationPrivate <lgl>, subId <chr>,
## # subnational2Code <chr>, subnational2Name <chr>, subnational1Code <chr>,
## # subnational1Name <chr>, countryCode <chr>, countryName <chr>,
## # userDisplayName <chr>, obsId <chr>, checklistId <chr>, presenceNoted <lgl>,
## # hasComments <lgl>, firstName <chr>, lastName <chr>, hasRichMedia <lgl>Information on a given region or hotspot
Obtain detailed information on any valid eBird region
ebirdregioninfo("CA-BC-GV")## # A tibble: 1 × 5
## region minX maxX minY maxY
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 Metro Vancouver, British Columbia, Canada -123. -122. 49.0 49.6or hotspot
ebirdregioninfo("L196159")## # A tibble: 1 × 16
## locId name latitude longitude countryCode countryName subnational1Name
## <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
## 1 L196159 Vancouver… 49.3 -123. CA Canada British Columbia
## # ℹ 9 more variables: subnational1Code <chr>, subnational2Code <chr>,
## # subnational2Name <chr>, isHotspot <lgl>, locName <chr>, lat <dbl>,
## # lng <dbl>, hierarchicalName <chr>, locID <chr>Obtain a list of eBird species codes for all species recorded in a region
ebirdregionspecies("GB-ENG-LND")## # A tibble: 383 × 1
## speciesCode
## <chr>
## 1 wfwduc1
## 2 fuwduc
## 3 bahgoo
## 4 empgoo
## 5 snogoo
## 6 rosgoo
## 7 gragoo
## 8 swagoo1
## 9 gwfgoo
## 10 lwfgoo
## # ℹ 373 more rowsor a hotspot
ebirdregionspecies("L5803024")## # A tibble: 181 × 1
## speciesCode
## <chr>
## 1 gragoo
## 2 gwfgoo
## 3 pifgoo
## 4 bargoo
## 5 cangoo
## 6 x00758
## 7 mutswa
## 8 whoswa
## 9 egygoo
## 10 comshe
## # ℹ 171 more rowsObtain a list of all subregions within an eBird region
ebirdsubregionlist("subnational1","US")## # A tibble: 51 × 2
## code name
## <chr> <chr>
## 1 US-AL Alabama
## 2 US-AK Alaska
## 3 US-AZ Arizona
## 4 US-AR Arkansas
## 5 US-CA California
## 6 US-CO Colorado
## 7 US-CT Connecticut
## 8 US-DE Delaware
## 9 US-DC District of Columbia
## 10 US-FL Florida
## # ℹ 41 more rowsChecklist Feed
Obtain a list of checklists submitted on a given date at a region or hotspot
ebirdchecklistfeed(loc = "L207391", date = "2020-03-24", max = 5)## # A tibble: 5 × 9
## locId subId userDisplayName numSpecies obsDt obsTime isoObsDate subID loc
## <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr> <chr>
## 1 L207391 S6617… David Wood 10 24 M… 14:47 2020-03-2… S661… L207…
## 2 L207391 S6617… Sofia Prado-Ir… 15 24 M… 14:31 2020-03-2… S661… L207…
## 3 L207391 S6619… Jeffrey Gantz 19 24 M… 13:30 2020-03-2… S661… L207…
## 4 L207391 S6617… Ann Gurka 21 24 M… 13:00 2020-03-2… S661… L207…
## 5 L207391 S7098… Barbara Olson 20 24 M… 10:30 2020-03-2… S709… L207…View Checklist
Obtain all information on a specific checklist
ebirdchecklist("S139153079")## # A tibble: 99 × 24
## subId protocolId locId groupId durationHrs allObsReported subComments
## <chr> <chr> <chr> <chr> <dbl> <lgl> <chr>
## 1 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 2 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 3 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 4 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 5 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 6 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 7 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 8 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 9 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## 10 S139153079 P22 L17 G10310841 11.2 TRUE "There are …
## # ℹ 89 more rows
## # ℹ 17 more variables: creationDt <chr>, lastEditedDt <chr>, obsDt <chr>,
## # obsTimeValid <lgl>, checklistId <chr>, numObservers <int>,
## # effortDistanceKm <dbl>, effortDistanceEnteredUnit <chr>,
## # subnational1Code <chr>, userDisplayName <chr>, numSpecies <int>,
## # speciesCode <chr>, obsId <chr>, howManyStr <chr>, obsComments <chr>,
## # photoCounts <int>, videoCounts <int>Hotspots in a region or nearby coordinates
Obtain a list of hotspots within a region
ebirdhotspotlist("CA-NS-HL")## # A tibble: 290 × 9
## locId locName countryCode subnational1Code subnational2Code lat lng
## <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
## 1 L2334369 Abraham … CA CA-NS CA-NS-HL 45.2 -62.6
## 2 L7003818 Admiral … CA CA-NS CA-NS-HL 44.7 -63.7
## 3 L1765807 Admiral … CA CA-NS CA-NS-HL 44.8 -63.1
## 4 L12227034 Armdale-… CA CA-NS CA-NS-HL 44.6 -63.6
## 5 L12690538 Armdale-… CA CA-NS CA-NS-HL 44.6 -63.6
## 6 L2390509 Bald Roc… CA CA-NS CA-NS-HL 44.5 -63.6
## 7 L7598385 Bayers L… CA CA-NS CA-NS-HL 44.6 -63.7
## 8 L11019120 Beaver B… CA CA-NS CA-NS-HL 44.8 -63.7
## 9 L1872934 Bedford … CA CA-NS CA-NS-HL 44.7 -63.7
## 10 L12134597 Bedford-… CA CA-NS CA-NS-HL 44.7 -63.7
## # ℹ 280 more rows
## # ℹ 2 more variables: latestObsDt <chr>, numSpeciesAllTime <int>or within a radius of up to 50 kilometers, from a given set of coordinates.
ebirdhotspotlist(lat = 30, lng = -90, dist = 10)## No region code provided, locating hotspots using lat/lng## # A tibble: 54 × 9
## locId locName countryCode subnational1Code subnational2Code lat lng
## <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
## 1 L6025517 Algiers P… US US-LA US-LA-071 30.0 -90.1
## 2 L3886471 Armstrong… US US-LA US-LA-071 30.0 -90.1
## 3 L727179 Audubon L… US US-LA US-LA-071 30.0 -90.0
## 4 L6665071 BAEA Nest… US US-LA US-LA-087 30.0 -90.0
## 5 L6666949 BAEA Nest… US US-LA US-LA-071 29.9 -90.0
## 6 L2423926 Bayou Bie… US US-LA US-LA-071 30.0 -90.0
## 7 L725034 Bayou Sau… US US-LA US-LA-071 30.1 -89.9
## 8 L727232 Chalmette… US US-LA US-LA-087 29.9 -90.0
## 9 L453412 City Park… US US-LA US-LA-071 30.0 -90.1
## 10 L5229399 City Park… US US-LA US-LA-071 30.0 -90.1
## # ℹ 44 more rows
## # ℹ 2 more variables: latestObsDt <chr>, numSpeciesAllTime <int>