Introduction to the rebird package

Sebastian Pardo, Rafael Maia

2021-01-25

A 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

library("rebird")

Usage

The eBird API server has been updated and thus there are a couple major changes in the way rebird works. API requests to eBird now require 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: 16,513 x 14
##    sciName comName speciesCode category taxonOrder bandingCodes comNameCodes
##    <chr>   <chr>   <chr>       <chr>         <dbl> <chr>        <chr>       
##  1 Struth… Common… ostric2     species           1 <NA>         COOS        
##  2 Struth… Somali… ostric3     species           6 <NA>         SOOS        
##  3 Struth… Common… y00934      slash             7 <NA>         SOOS,COOS   
##  4 Rhea a… Greate… grerhe1     species           8 <NA>         GRRH        
##  5 Rhea p… Lesser… lesrhe2     species          14 <NA>         LERH        
##  6 Rhea p… Lesser… lesrhe4     issf             15 <NA>         LERH        
##  7 Rhea p… Lesser… lesrhe3     issf             18 <NA>         LERH        
##  8 Nothoc… Tawny-… tabtin1     species          19 <NA>         TBTI        
##  9 Nothoc… Highla… higtin1     species          20 HITI         <NA>        
## 10 Nothoc… Highla… higtin2     issf             21 <NA>         HITI        
## # … with 16,503 more rows, and 7 more variables: sciNameCodes <chr>,
## #   order <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: 17 x 13
##    speciesCode comName sciName locId locName obsDt howMany   lat   lng obsValid
##    <chr>       <chr>   <chr>   <chr> <chr>   <chr>   <int> <dbl> <dbl> <lgl>   
##  1 amegfi      Americ… Spinus… L133… "545 R… 2021…       8  42.0 -76.1 TRUE    
##  2 amegfi      Americ… Spinus… L197… "esthe… 2021…      12  42.1 -75.9 TRUE    
##  3 amegfi      Americ… Spinus… L275… "Home " 2021…       8  42.1 -76.0 TRUE    
##  4 amegfi      Americ… Spinus… L109… "Hillc… 2021…       1  42.2 -75.9 TRUE    
##  5 amegfi      Americ… Spinus… L186… "Otsin… 2021…       1  42.1 -75.9 TRUE    
##  6 amegfi      Americ… Spinus… L895… "Nowla… 2021…       2  42.1 -75.9 TRUE    
##  7 amegfi      Americ… Spinus… L207… "Workw… 2021…       4  42.1 -75.9 TRUE    
##  8 amegfi      Americ… Spinus… L133… "4457 … 2021…       2  42.0 -75.9 TRUE    
##  9 amegfi      Americ… Spinus… L870… "325 D… 2021…       1  42.2 -76.0 TRUE    
## 10 amegfi      Americ… Spinus… L121… "1312 … 2021…       3  42.1 -76.0 TRUE    
## 11 amegfi      Americ… Spinus… L133… "216 W… 2021…       1  42.1 -76.0 TRUE    
## 12 amegfi      Americ… Spinus… L524… "Victo… 2021…       4  42.1 -76.0 TRUE    
## 13 amegfi      Americ… Spinus… L505… "Bolan… 2021…       1  42.2 -75.9 TRUE    
## 14 amegfi      Americ… Spinus… L850… "Sandy… 2021…      20  42.1 -75.9 TRUE    
## 15 amegfi      Americ… Spinus… L351… "Anson… 2021…      16  42.1 -76.1 TRUE    
## 16 amegfi      Americ… Spinus… L270… "Gripp… 2021…       1  42.1 -76.1 TRUE    
## 17 amegfi      Americ… Spinus… L564… "Kinne… 2021…       1  42.1 -76.2 TRUE    
## # … with 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: 81 x 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… L577… Merrit… 2021…       1  28.6 -80.7 TRUE    
##  2 btbwar      Black-… Setoph… L863… 104 7t… 2021…       1  32.0 -80.8 TRUE    
##  3 btbwar      Black-… Setoph… L407… Thomps… 2021…       1  38.9 -77.1 TRUE    
##  4 btbwar      Black-… Setoph… L193… Rye     2021…       1  43.0 -70.8 TRUE    
##  5 btbwar      Black-… Setoph… L195… 1 My H… 2021…       1  27.0 -80.1 TRUE    
##  6 btbwar      Black-… Setoph… L104… Feathe… 2021…       1  25.6 -80.3 TRUE    
##  7 btbwar      Black-… Setoph… L324… Wither… 2021…       1  31.0 -82.9 TRUE    
##  8 btbwar      Black-… Setoph… L128… Zoo Mi… 2021…       1  25.6 -80.4 TRUE    
##  9 btbwar      Black-… Setoph… L992… Kendal… 2021…       1  25.7 -80.4 TRUE    
## 10 btbwar      Black-… Setoph… L133… 603 S … 2021…       1  26.2 -98.2 TRUE    
## # … with 71 more rows, and 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: 38 x 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… L993… Stewar… 2021…     300  42.5 -76.5 TRUE    
##  2 mallar3     Mallard Anas p… L993… Stewar… 2021…      20  42.5 -76.5 TRUE    
##  3 commer      Common… Mergus… L993… Stewar… 2021…       2  42.5 -76.5 TRUE    
##  4 ribgul      Ring-b… Larus … L993… Stewar… 2021…      NA  42.5 -76.5 TRUE    
##  5 hergul      Herrin… Larus … L993… Stewar… 2021…      NA  42.5 -76.5 TRUE    
##  6 gbbgul      Great … Larus … L993… Stewar… 2021…       3  42.5 -76.5 TRUE    
##  7 baleag      Bald E… Haliae… L993… Stewar… 2021…       1  42.5 -76.5 TRUE    
##  8 eursta      Europe… Sturnu… L993… Stewar… 2021…      40  42.5 -76.5 TRUE    
##  9 doccor      Double… Phalac… L993… Stewar… 2021…       5  42.5 -76.5 TRUE    
## 10 ambduc      Americ… Anas r… L993… Stewar… 2021…       1  42.5 -76.5 TRUE    
## # … with 28 more rows, and 3 more variables: obsReviewed <lgl>,
## #   locationPrivate <lgl>, subId <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: 25 x 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… L109… Hillcr… 2021…      34  42.2 -75.9 TRUE    
##  2 cangoo      Canada… Branta… L186… Otsini… 2021…     117  42.1 -75.9 TRUE    
##  3 cangoo      Canada… Branta… L186… Cheri … 2021…       4  42.1 -75.9 TRUE    
##  4 cangoo      Canada… Branta… L809… Port D… 2021…      74  42.1 -75.9 TRUE    
##  5 cangoo      Canada… Branta… L527… R Tee … 2021…     100  42.2 -75.9 TRUE    
##  6 cangoo      Canada… Branta… L133… I-81 N… 2021…      45  42.1 -75.9 TRUE    
##  7 cangoo      Canada… Branta… L245… Water … 2021…       3  42.1 -75.9 TRUE    
##  8 cangoo      Canada… Branta… L116… Homest… 2021…     230  42.1 -76.0 TRUE    
##  9 cangoo      Canada… Branta… L106… IBM CC… 2021…       1  42.1 -76.0 TRUE    
## 10 cangoo      Canada… Branta… L273… Schnur… 2021…       2  42.1 -75.8 TRUE    
## # … with 15 more rows, and 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: 3,578 x 13
##    speciesCode comName sciName locId locName obsDt howMany   lat   lng obsValid
##    <chr>       <chr>   <chr>   <chr> <chr>   <chr>   <int> <dbl> <dbl> <lgl>   
##  1 foxsp1      Fox Sp… Passer… L382… Yard    2021…       1  42.2 -71.3 FALSE   
##  2 foxsp1      Fox Sp… Passer… L276… Standi… 2021…       1  42.3 -71.3 FALSE   
##  3 reshaw      Red-sh… Buteo … L575… The 20… 2021…       1  44.2 -69.4 FALSE   
##  4 gadwal      Gadwall Mareca… L143… Holyok… 2021…       2  42.2 -72.6 FALSE   
##  5 lbbgul      Lesser… Larus … L106… Goulds… 2021…       1  42.2 -71.4 FALSE   
##  6 pinwar      Pine W… Setoph… L919… Northb… 2021…       1  42.1 -71.7 FALSE   
##  7 bnhcow      Brown-… Moloth… L825… Westwo… 2021…       1  42.2 -71.2 FALSE   
##  8 comred      Common… Acanth… L358… Fort H… 2021…       2  41.8 -70.0 FALSE   
##  9 redcro10    Red Cr… Loxia … L480… West B… 2021…       2  41.7 -70.4 FALSE   
## 10 foxsp1      Fox Sp… Passer… L276… Standi… 2021…       1  42.3 -71.3 FALSE   
## # … with 3,568 more rows, and 3 more variables: obsReviewed <lgl>,
## #   locationPrivate <lgl>, subId <chr>

or a region

ebirdnotable(locID = 'US-NY-109')
## # A tibble: 81 x 13
##    speciesCode comName sciName locId locName obsDt howMany   lat   lng obsValid
##    <chr>       <chr>   <chr>   <chr> <chr>   <chr>   <int> <dbl> <dbl> <lgl>   
##  1 blkvul      Black … Coragy… L212… Steven… 2021…       1  42.4 -76.4 FALSE   
##  2 redcro      Red Cr… Loxia … L550… Cornel… 2021…       1  42.5 -76.5 FALSE   
##  3 yerwar      Yellow… Setoph… L351… Fuerte… 2021…       1  42.5 -76.5 FALSE   
##  4 redcro      Red Cr… Loxia … L123… Boyer … 2021…       5  42.3 -76.3 FALSE   
##  5 whwcro      White-… Loxia … L550… Cornel… 2021…       2  42.5 -76.5 FALSE   
##  6 x00684      Canvas… Aythya… L140… East S… 2021…       1  42.5 -76.5 FALSE   
##  7 x00684      Canvas… Aythya… L140… East S… 2021…       1  42.5 -76.5 FALSE   
##  8 blksco2     Black … Melani… L353… Salt P… 2021…       1  42.5 -76.5 FALSE   
##  9 evegro      Evenin… Coccot… L133… 571 So… 2021…      17  42.3 -76.4 FALSE   
## 10 hoared2     Hoary … Acanth… L686… George… 2021…       1  42.5 -76.3 FALSE   
## # … with 71 more rows, and 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 x 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-… Anas c… L139… Lickin… 2019…       8  38.1 -78.7 TRUE    
##  4 killde      Killde… Charad… L139… Lickin… 2019…       1  38.1 -78.7 TRUE    
##  5 baleag      Bald E… 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      Caroli… Thryot… L139… Lickin… 2019…       1  38.1 -78.7 TRUE    
##  8 whtspa      White-… Zonotr… L139… Lickin… 2019…       2  38.1 -78.7 TRUE    
##  9 norcar      Northe… Cardin… L139… Lickin… 2019…       1  38.1 -78.7 TRUE    
## 10 canvas      Canvas… Aythya… L331… Montic… 2019…      19  38.0 -78.5 TRUE    
## # … with 3 more variables: obsReviewed <lgl>, locationPrivate <lgl>,
## #   subId <chr>

or a hotspot

ebirdhistorical(loc = 'L196159', date = '2019-02-14', fieldSet = 'full')
## # A tibble: 14 x 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-b… Larus … L196… Vancou… 2019…       4  49.3 -123. TRUE    
##  3 glwgul      Glauco… Larus … L196… Vancou… 2019…      29  49.3 -123. TRUE    
##  4 norcro      Northw… Corvus… L196… Vancou… 2019…     100  49.3 -123. TRUE    
##  5 bkcchi      Black-… Poecil… L196… Vancou… 2019…      16  49.3 -123. TRUE    
##  6 bushti      Bushtit Psaltr… L196… Vancou… 2019…      20  49.3 -123. TRUE    
##  7 pacwre1     Pacifi… Troglo… L196… Vancou… 2019…       1  49.3 -123. TRUE    
##  8 houfin      House … Haemor… L196… Vancou… 2019…       2  49.3 -123. TRUE    
##  9 purfin      Purple… Haemor… L196… Vancou… 2019…       3  49.3 -123. TRUE    
## 10 amegfi      Americ… Spinus… L196… Vancou… 2019…      15  49.3 -123. TRUE    
## 11 daejun      Dark-e… Junco … L196… Vancou… 2019…      37  49.3 -123. TRUE    
## 12 sonspa      Song S… Melosp… L196… Vancou… 2019…      12  49.3 -123. TRUE    
## 13 spotow      Spotte… Pipilo… L196… Vancou… 2019…       1  49.3 -123. TRUE    
## 14 rewbla      Red-wi… Agelai… L196… Vancou… 2019…       6  49.3 -123. TRUE    
## # … with 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 x 5
##   region                                     minX  maxX  minY  maxY
##   <chr>                                     <dbl> <dbl> <dbl> <dbl>
## 1 Metro Vancouver, British Columbia, Canada -123. -122.  49.0  49.6

or hotspot

ebirdregioninfo("L196159")
## # A tibble: 1 x 16
##   locId name  latitude longitude countryCode countryName subnational1Name
##   <chr> <chr>    <dbl>     <dbl> <chr>       <chr>       <chr>           
## 1 L196… Vanc…     49.3     -123. CA          Canada      British Columbia
## # … with 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: 304 x 1
##    speciesCode
##    <chr>      
##  1 bahgoo     
##  2 snogoo     
##  3 gragoo     
##  4 gwfgoo     
##  5 tunbeg1    
##  6 pifgoo     
##  7 brant      
##  8 bargoo     
##  9 cangoo     
## 10 rebgoo1    
## # … with 294 more rows

or a hotspot

ebirdregionspecies("L5803024")
## # A tibble: 156 x 1
##    speciesCode
##    <chr>      
##  1 gragoo     
##  2 gwfgoo     
##  3 bargoo     
##  4 cangoo     
##  5 mutswa     
##  6 egygoo     
##  7 comshe     
##  8 manduc     
##  9 gargan     
## 10 norsho     
## # … with 146 more rows

Obtain a list of all subregions within an eBird region

ebirdsubregionlist("subnational1","US")
## # A tibble: 51 x 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             
## # … with 41 more rows

Checklist 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 x 8
##   locId  subId  userDisplayName  numSpecies obsDt obsTime subID loc             
##   <chr>  <chr>  <chr>                 <int> <chr> <chr>   <chr> <chr>           
## 1 L2073… S6617… David Wood               10 24 M… 14:47   S661… L207391,Mt. Aub…
## 2 L2073… S6617… Sofia Prado-Irw…         15 24 M… 14:31   S661… L207391,Mt. Aub…
## 3 L2073… S6619… Jeffrey Gantz            19 24 M… 13:30   S661… L207391,Mt. Aub…
## 4 L2073… S6617… Ann Gurka                21 24 M… 13:00   S661… L207391,Mt. Aub…
## 5 L2073… S7098… Barbara Olson            20 24 M… 10:30   S709… L207391,Mt. Aub…

Hotspots in a region or nearby coordinates

Obtain a list of hotspots within a region

ebirdhotspotlist("CA-NS-HL")
## # A tibble: 220 x 9
##    locId locName countryCode subnational1Code subnational2Code   lat   lng
##    <chr> <chr>   <chr>       <chr>            <chr>            <dbl> <dbl>
##  1 L233… Abraha… CA          CA-NS            CA-NS-HL          45.2 -62.6
##  2 L700… Admira… CA          CA-NS            CA-NS-HL          44.7 -63.7
##  3 L176… Admira… CA          CA-NS            CA-NS-HL          44.8 -63.1
##  4 L584… Albro … CA          CA-NS            CA-NS-HL          44.7 -63.6
##  5 L437… Aldern… CA          CA-NS            CA-NS-HL          44.7 -63.6
##  6 L122… Armdal… CA          CA-NS            CA-NS-HL          44.6 -63.6
##  7 L624… Atlant… CA          CA-NS            CA-NS-HL          44.7 -63.3
##  8 L239… Bald R… CA          CA-NS            CA-NS-HL          44.5 -63.6
##  9 L759… Bayers… CA          CA-NS            CA-NS-HL          44.6 -63.7
## 10 L642… Beaufo… CA          CA-NS            CA-NS-HL          44.7 -63.5
## # … with 210 more rows, and 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: 52 x 9
##    locId locName countryCode subnational1Code subnational2Code   lat   lng
##    <chr> <chr>   <chr>       <chr>            <chr>            <dbl> <dbl>
##  1 L602… Algier… US          US-LA            US-LA-071         30.0 -90.1
##  2 L388… Armstr… US          US-LA            US-LA-071         30.0 -90.1
##  3 L727… Audubo… US          US-LA            US-LA-071         30.0 -90.0
##  4 L666… BAEA N… US          US-LA            US-LA-087         30.0 -90.0
##  5 L666… BAEA N… US          US-LA            US-LA-071         29.9 -90.0
##  6 L242… Bayou … US          US-LA            US-LA-071         30.0 -90.0
##  7 L725… Bayou … US          US-LA            US-LA-071         30.1 -89.9
##  8 L727… Chalme… US          US-LA            US-LA-087         29.9 -90.0
##  9 L453… City P… US          US-LA            US-LA-071         30.0 -90.1
## 10 L522… City P… US          US-LA            US-LA-071         30.0 -90.1
## # … with 42 more rows, and 2 more variables: latestObsDt <chr>,
## #   numSpeciesAllTime <int>

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