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Wrapper to the eBird API

Home Page: https://docs.ropensci.org/rebird

License: Other

Makefile 0.73% R 99.27%

ebird rstats birds ebird-api r ebird-webservices spocc r-package

rebird's Introduction

rebird's People

Contributors

Stargazers

Watchers

Forkers

ateucher sebpardo strategist922 graceli8 youngforever222 gbabineau r-forks-to-learn mfoos mpadge mengchiehfeng vlucet dbradnum sussyfuss slager richardlitt

rebird's Issues

A way to get older observations?

Currently, the documentation for ebirdloc says that it can only go back 30 days. It would be useful to be able to go back farther (e.g. to take a 30-day chunk from last summer).

Thanks for making such a cool package!

update taxonomy

Taxonomy needs a refresh

https://github.com/ropensci/rebird/commits/master/R/sysdata.rda

Have tets run on travis once tests done

Travis-ci and Coveralls not updating

I noticed that travis-ci and coveralls are not being ran with the latest commits/releases; travis-ci last ran on an commit from 8 months ago while coveralls last ran 5 years ago. Obviously this isn't any issue with rebird itself, but I wonder if we should update the badges? @sckott ?

Add `skip_on_cran()` to tests

As per rOpenSci's packaging guidelines, we should use testthat::skip_on_cran() in tests that use the API

Add vignette

@rmaia I'm adding this posthumously (spelling?) - in that I already added the vignette in a recent push today

I just basically took examples from each functions examples section. Hope that's okay. I played around a bit with the knitr docco style. Check it out when you install, then load the package. Do change if you want.

Also updated readme with a few examples. Hope that's okay.

All ebirdfreq requests failing

giving 404 response, not found

looks like the url that the fxn gets data from http://ebird.org/ebird/BarChart is down

@ateucher @sebpardo

Get species for location / region

I recently helped a fellow eBirder answer a question about the total number of species seen at hotspots within a distance of his home. This involved a couple of eBird API functions that aren't yet included in rebird:

I've got R code up and running for both of these now, and am happy to tidy it up and submit as pull requests for the package - hopefully it'll be useful for other people.
I can see that #83 is already open for the first API call, so I'm raising this to cover the second one.

Hope this all sounds OK? Do let know if there's anything I should bear in mind, or I inadvertantly go astray with the fork > branch > pull request process!

Wrapper to part of the eBird API

Would it be possible to clarify which webservice(s) from the eBird API are wrapped in this package? I think it'd be an useful addition to the docs.

Once the package has been switched to the new API, asking for contributors to add new endpoints wrappers might be a good way to have first-time contributors?

put lat/lng from ip in a function

I've started on this here: https://github.com/ateucher/rebird/blob/latlng_func/R/getlatlng.R

ebirdfreq failure - URL directs to login page(?)

Hi,

I'm consistently getting a failure from the ebirdfreq() function. When I try the examples in the package documentation, I get an error as follows:

> ebirdfreq(loctype = 'hotspots', loc = 'L196159')
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘    .January-1’, ‘.January-1’, ‘</a>.January-1’, ‘</div>.January-1’, ‘</g>.January-1’, ‘</label>.January-1’, ‘</svg>.January-1’, ‘<g class=LogoLab-ofOrnithology fill=#000 transform=translate(335.03 17.285)>.January-1’, ‘<g class=LogoLab-sapsucker transform=translate(242.966)>.January-1’, ‘<g class=LogoLab-theCornellLab fill=#000 transform=translate(0 17.285)>.January-1’, ‘<path d=M0.138375929,2.72872008 C0.138375929,3.83301149 1.01946082,4.71324377 2.12749183,4.71324377 C3.23285288,4.71324377 4.11393777,3.83301149 4.11660773,2.72872008 C4.11393777,1.6217613 3.23018292,0.741529015 2.12749183,0.738861644 C1.02213078,0.741529015 0.138375929,1.6217613 0.138375929,2.72872008 L0.138375929,2.72872008 Z/>.January-1’, ‘<path d=M134.835358 31.9764382C132.958381 31.9737709 131.81297 30.8268015 131.8103 28.9116295L131.8103 15.0039594 137.881776 15.0039594 137.881776 12.683347 131.8103 12.683347 131.8103 6.57240105 129.212435 6.57240105 129.212435 12.683 [... truncated]

It seems that the call to the URL is returning an HTML document rather than a TSV as expected. I can see that when I try to construct the URL myself - eg https://ebird.org/ebird/barchartData?byr=1900&eyr=2020&bmo=1&emo=12&r=L196159&fmt=tsv - and plug it into Chrome, I get the file I expect.... but I have to be logged in first.

Having now dug into the package source a bit, and stepped through the code up to here, it looks like the web response we're getting in R is the eBird log-in page, rather than the lovely TSV data file we want :-(

I guess maybe something has changed on eBird's end? Worth noting that I do have an ebird access token, and other functions (eg nearestobs(), ebirdregion()) are working fine. But I think this one isn't connected up to the same API, so it's a different case.

Any suggestions for getting this working again would be much appreciated - and do let me know if you need any more info or I can help otherwise.

Session Info

> devtools::session_info() - Session info ------------------------------------------------------------------------------------------------------ setting value version R version 4.0.3 (2020-10-10) os Windows 10 x64 system x86_64, mingw32 ui RStudio language (EN) collate English_United Kingdom.1252 ctype English_United Kingdom.1252 tz Europe/London date 2020-10-22

Packages ----------------------------------------------------------------------------------------------------------
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.3)
backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.3)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.3)
cli 2.1.0 2020-10-12 [1] CRAN (R 4.0.3)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.3)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.3)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.3)
devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.3)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.3)
dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.3)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.3)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.3)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.3)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.3)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.3)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.3)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.3)
jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.3)
knitr 1.30 2020-09-22 [1] CRAN (R 4.0.3)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.3)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.3)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.3)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.3)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.3)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.3)
processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.3)
ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.3)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.3)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.3)
rebird * 1.1.0 2019-10-24 [1] CRAN (R 4.0.3)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.3)
rlang 0.4.8 2020-10-08 [1] CRAN (R 4.0.3)
rmarkdown 2.4 2020-09-30 [1] CRAN (R 4.0.3)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.3)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.3)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.3)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.3)
tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.3)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.3)
usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.3)
vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.3)
withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.3)
xfun 0.18 2020-09-29 [1] CRAN (R 4.0.3)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.3)

[1] C:/Users/dbrad/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.3/library

Retrieving observations more than 30 days back

Why do the functions make it impossible to retrieve observations more than 30 days back?

As of 2017-04-06, ebirdfreq returns a 404 error

For example, this piece of code from the examples is not working anymore :
ebirdfreq(loctype = 'hotspots', loc = 'L196159')

From looking at the code, it seems the url is constructed with a capitalized version of the url :
url <- "http://ebird.org/ebird/BarChart" which, as of today does not seem to be supported.

For example, compare these :
http://ebird.org/ebird/barchart?byr=1900&eyr=2017&bmo=1&emo=12&r=US-AL
http://ebird.org/ebird/BarChart?byr=1900&eyr=2017&bmo=1&emo=12&r=US-AL

This happens with version 0.3.0, latest version on CRAN

Use httr::GET instead of RCurl::getForm

If the ebird API receives invalid input parameters it returns a 400 error and then sends a JSON object with an informative error message (https://confluence.cornell.edu/display/CLOISAPI/eBird-1.1-ErrorHandling).

RCurl::getForm errors on the 400 and exits, but httr can handle the redirect to the JSON object; could then parse the error message out and pass it to the user.

Allow ebirdfreq to merge data from multiple hotspots

If providing a list of hotspot codes, then calculate a combined frequency of observations for all species seen in those hotspots based on sample size and frequency in each separate hotspot.

ebirdregion should return all observations, but fails to return a few, although these may be retrievable by ebirdnotable

Hello

I love this package. I am wondering how the search is performed though, as there seems to be some inconsistencies..

Consider for instance this checklist from yesterday, Oct 17th: https://ebird.org/view/checklist/S49257480
It contains 72 species. By calling ebirdregion(loc = 'DK') and followingly filtering out that particular location and date, I only get 62 out of 72 observations. 10 are missing, including the notable observation "Dusky Warbler 3".

If I, however use ebirdnotable(loc='DK'), I get two observations that INCLUDES the "Dusky Warbler 3" observation. I suspect there is some delay for recently submitted observations before they are accessible for extraction and this is likely on eBird API's end. In any case though, I would like to hear some feedback from you, whether this is a known issue.

I originally discovered the error simply because ebirdnotable() was able to find this dusky warbler record, while the call ebirdregion(loc = 'DK', species = 'duswar') couldn't. Both functions could however properly extract another Dusky Warbler observation from October 16th, so I will not be surprised if by tomorrow, the ebirdregion() call will be able to retrieve all 72 observations from the checklist in consideration.

So: any explanation for the possible delay and inevitable inconsitency between ebirdnotable and ebirdregion?

Mathias

Helper fxn for GET requests across all fxns

New API coming

I just noticed that there is a new API coming: https://documenter.getpostman.com/view/664302/ebird-api-20/2HTbHW

I don't know the timeline for full implementation, but it looks like the ones documented there are already functional. It looks like it will require an API key for most calls

Push v0.2 to CRAN soon?

Seems like we've had many changes in this package lately. Should we push a new version v0.2 to CRAN soon?

I made a milestone for this v0.2 we can assign issues to.

API v2?

@sebpardo looks like they want everyone to move to using the v2 api

https://documenter.getpostman.com/view/664302/ebird-api-20/2HTbHW

do you have time to work on making the switch?

rbind_all() deprecated, replace with bind_rows()

Hi,

The ebirdregion() function isn't work. This is the error message:

Warning message:
`rbind_all()` is deprecated. Please use `bind_rows()` instead.

Rownames error using ebirdfreq

Simply running the example in the doc throws in a rownames error. Maybe related to recent updates in the tidyverse suite of packages?

freqs <- ebirdfreq(loctype = "hotspots", loc = 'L196159')

Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘    .January-1’, ‘.January-1’, ‘</a>.January-1’, ‘</div>.January-1’, ‘</g>.January-1’, ‘</label>.January-1’, ‘</svg>.January-1’, ‘<g class=LogoLab-ofOrnithology fill=#000 transform=translate(335.03 17.285)>.January-1’, ‘<g class=LogoLab-sapsucker transform=translate(242.966)>.January-1’, ‘<g class=LogoLab-theCornellLab fill=#000 transform=translate(0 17.285)>.January-1’, ‘<path d=M0.138375929,2.72872008 C0.138375929,3.83301149 1.01946082,4.71324377 2.12749183,4.71324377 C3.23285288,4.71324377 4.11393777,3.83301149 4.11660773,2.72872008 C4.11393777,1.6217613 3.23018292,0.741529015 2.12749183,0.738861644 C1.02213078,0.741529015 0.138375929,1.6217613 0.138375929,2.72872008 L0.138375929,2.72872008 Z/>.January-1’, ‘<path d=M134.835358 31.9764382C132.958381 31.9737709 131.81297 30.8268015 131.8103 28.9116295L131.8103 15.0039594 137.881776 15.0039594 137.881776 12.683347 131.8103 12.683347 131.8103 6.57 [... truncated]

Session Info

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 20.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.0   stringr_1.4.0   dplyr_1.0.2     purrr_0.3.4     readr_1.4.0     tidyr_1.1.2     tibble_3.0.4   
 [8] ggplot2_3.3.2   tidyverse_1.3.0 raster_3.4-5    sp_1.4-4        rebird_1.1.2    sf_0.9-6       

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0   haven_2.3.1        lattice_0.20-41    colorspace_1.4-1   vctrs_0.3.5        generics_0.1.0    
 [7] blob_1.2.1         rlang_0.4.9        e1071_1.7-4        pillar_1.4.7       withr_2.3.0        glue_1.4.2        
[13] DBI_1.1.0          dbplyr_1.4.4       modelr_0.1.8       readxl_1.3.1       lifecycle_0.2.0    munsell_0.5.0     
[19] gtable_0.3.0       cellranger_1.1.0   rvest_0.3.6        codetools_0.2-16   curl_4.3           class_7.3-17      
[25] fansi_0.4.1        broom_0.7.1        Rcpp_1.0.5         KernSmooth_2.23-17 backports_1.1.9    scales_1.1.1      
[31] classInt_0.4-3     jsonlite_1.7.1     fs_1.5.0           hms_0.5.3          stringi_1.5.3      grid_4.0.3        
[37] cli_2.2.0          tools_4.0.3        magrittr_2.0.1     crayon_1.3.4       pkgconfig_2.0.3    ellipsis_0.3.1    
[43] xml2_1.3.2         reprex_0.3.0       lubridate_1.7.9    assertthat_0.2.1   httr_1.4.2         rstudioapi_0.11   
[49] R6_2.5.0           units_0.6-7        compiler_4.0.3

Is it possible to map the locations of the bird observations?

Hi,

Is it possible to map (google maps, OpenStreetMap) multiple locations of the bird observations via R rebird or other R package?
For instance the locations (Long. and lat.) of a specific bird in the USA found with ebirdregion function:

Example:
ebirdregion(region = 'US', species = 'Passer domesticus')

Best,
Cordny
the Netherlands

Curl options

Most or all fxns have a ... parameter to pass on curl options, but internally there is no way to catch and pass on these options.

Regional statistics on a date

Hi all, thank you for this package—it’s been useful for many projects I’ve been involved with!

I’m wondering about the status of a function for the “Regional statistics on a date” endpoint. Is there a specific reason it’s not been added or is it simply that nobody has given it a try yet? Thought I’d ask before trying myself!

Location precedence in ebirdnotable

Sort out what to do when > 1 location type provided. I suggest most specific takes precedence (lat/lng > hotspot > region). I've started on this.

Change license?

Currently BSD https://github.com/ropensci/rebird/blob/master/DESCRIPTION#L6

I think it's deprecated for CRAN packages now at least

Replace RJSONIO with jsonlite

spocc integration: Pass warning/message on http error if not done already

Looks like already using warn_for_status() in ebirdgeo(), but make sure this works smoothly in spocc to allow searches to proceed even if some sources fail

related to ropensci/spocc#53

export taxonomy?

It could be useful for the package to export the internal taxonomy data object so that other packages can reference that object without getting R CMD CHECK warnings. Happy to do a PR for this if you're amenable to it.

GitHub Action checks failing due to missing API key

GitHub Actions checks are failing as they require an eBird API key to properly run the tests. I'm unsure of how to securely store an API key for those checks without making it public.

Getting nearby hotspots

Hi, awesome package. Was wondering if there was a way to get a list of hotspots nearby given coordinates. I cannot find an example in the doc. It would basically wrap a querry to this address in the api doc.

Session Info

error behavior

noticed when fixing spocc's ebird integration that error behavior could be better.

when the API key is not found or not set, there's a nice error message about this. 👍

But if the API key is bad/not known by eBird, the error behavior is pretty bad:

library(rebird)

# works fine
ebirdregion(loc = 'US', species = 'btbwar') 

# unset api key
Sys.unsetenv('EBIRD_KEY')

# fails nicely
ebirdregion(loc = 'US', species = 'btbwar')
#> Error: You must provide an API key from eBird.
#>     You can pass it to the 'key' argument or store 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.

# change API key to an obvisouly bad value
Sys.setenv(EBIRD_KEY = 'a')

# now fails badly
ebirdregion(loc = 'US', species = 'btbwar')
#> Error: parse error: premature EOF
#> 
#>                      (right here) ------^

The problem is the data from eBird is being processed before checking for any errors - here https://github.com/ropensci/rebird/blob/master/R/zzz.R#L37-L38 There i a proper error on the above request (403 http status code), so you should be able to catch that and then proceed accordingly with a nice error for the user.

ebirdhistorical error for loc = "AR"

Hello,

I am trying to download data for Argentina using the ebirdhistorical function:

ebirdhistorical(loc="AR",date="2020-05-09",key = EBIRD_KEY)

This gives the error:
Error in ebird_GET(url, args, key = key, ...) : 500 -- http.status.500 -- PreparedStatementCallback; SQL ORA-01013: user requested cancel of current operation; nested exception is java.sql.SQLTimeoutException: ORA-01013: user requested cancel of current operation

I have also tried:
ebirdhistorical(loc="AR",date="2020-05-09",key = BIRD_KEY, config= httr::timeout(60*10)), max=10000)
I get the same error.

The function works for other regions (including US, CO & KE) just fine, but not AR. What could the issue be?
Date of my download attempt = "2020-05-31"

Many thanks,

Pete S

use dplyr::bind_rows instead of dplyr::rbind_all

ebird_GET() : Unknown species: Genus%20species = double url encoding ?

I couldn't use ebird_GET() without a warning like :
In ebird_GET(url, args, ...) : Unknown species: Anas%20platyrhynchos

It seems that the space charater ' ' is encoded two times : ' ' ->'%20' ->'%2520'

GET function use an url with 'Anas%2520platyrhynchos' instead of 'Anas%20platyrhynchos'.
See the following example with the verbose enabled :
``

ebirdgeo('Anas platyrhynchos', 39, -121, max=5, config=verbose())
-> GET /ws1.1/data/obs/geo_spp/recent?fmt=json&sci=Anas%20platyrhynchos&lat=39&lng=-121&maxResults=5 HTTP/1.1
-> Host: ebird.org
-> User-Agent: libcurl/7.59.0 r-curl/3.2 httr/1.3.1
-> Accept-Encoding: gzip, deflate
-> Accept: application/json, text/xml, application/xml, /
->
<- HTTP/1.1 302 Found
<- Date: Tue, 05 Jun 2018 13:39:33 GMT
<- Server: Apache
<- Location: https://ebird.org/ws1.1/data/obs/geo_spp/recent?fmt=json&sci=Anas%2520platyrhynchos&lat=39&lng=-121&maxResults=5
<- Content-Length: 312
<- Content-Type: text/html; charset=iso-8859-1
<- X-OSSProxy: OSSProxy 1.3.337.412 (Build 337.412 Win32 en-us)(Jan 11 2018 14:07:40)
<- Connection: keep-alive
<-
-> GET /ws1.1/data/obs/geo_spp/recent?fmt=json&sci=Anas%2520platyrhynchos&lat=39&lng=-121&maxResults=5 HTTP/1.1
-> Host: ebird.org
-> User-Agent: libcurl/7.59.0 r-curl/3.2 httr/1.3.1
-> Accept-Encoding: gzip, deflate
-> Accept: application/json, text/xml, application/xml, /
->
<- HTTP/1.1 400 400
<- Date: Tue, 05 Jun 2018 13:39:33 GMT
<- Server: Apache
<- Content-Encoding: gzip
<- Content-Type: application/json;charset=utf-8
<- Content-Length: 96
<- Connection: close
<-
[1] NA
Warning message:
In ebird_GET(url, args, ...) : Unknown species: Anas%20platyrhynchos
``

I tried it using the v0.4.0 in rstudio (windows) and with linux Rscripts, same issue when using the spocc package.
Do you know if it's a wrong use of the function or a bug with the request ?
Thank for your help

httr::content fixes for new httr version

publish release

@sebpardo looks like the release is in draft state for v0.4, can you publish that?

Would like to contribute a checklist feed function

Hi folks,

I wrote a function (and tests) to access the checklist feed API endpoint https://documenter.getpostman.com/view/664302/S1ENwy59?version=latest#4416a7cc-623b-4340-ab01-80c599ede73e

and then realized that the contributor guidelines say to post before making a PR. Also, I am working with a different version of roxygen, so I'm reluctant to include the man/(filename).Rd file in the commit because the formats are slightly different.

Any thoughts before I make a PR?

thanks!
M

Make `ebirdregioncheck()` and `ebirdloc()` defunct

ebirdregioncheck() has been marked as deprecated for several years now and it should be made defunct in the next version update.

@slager I'm flagging this here so you don't convert the tests for this function to vcr.

Bug from CRAN core

Package: rebird Version: 0.1
Check: DESCRIPTION meta-information ... NOTE
Deprecated license: BSD

Add Andy Teucher as an author

@ateucher made a bunch of contributions, lets add him as an author,

Add ebird as a resource

using rebird

Add test suite

Version, two or three digits to CRAN?

Currently rebird releases only two digits to CRAN, and uses the third one for the development versions. I've seen that most other packages (and what Hadley recommends in his book) is to release three digits to CRAN and use the fourth one for devel.

@sckott does ROpenSci have a standard for this?

ebirdhistorical returns incomplete data

I am trying to retrieve all the ebird data for a region on a specific date. I have either stumbled upon a bug or I am confused how the rebird package works.

library(rebird)
library(dplyr)
library(lubridate)

# pick date
x=as_date("2022-10-04")

# download ebird data
dd<-rebird::ebirdhistorical(loc = "US-CA-087",date = x,key = api_key,fieldSet = "full")

# print all the data associated with my userDisplayName
dd %>% 
    filter(userDisplayName=="Abram Fleishman") %>% 
    as.data.frame

  speciesCode                comName             sciName   locId       locName            obsDt howMany      lat       lng obsValid obsReviewed
1      linspa      Lincoln's Sparrow Melospiza lincolnii L279615 Bethany Curve 2022-10-04 12:15       1 36.95371 -122.0383     TRUE       FALSE
2      orcwar Orange-crowned Warbler  Leiothlypis celata L279615 Bethany Curve 2022-10-04 12:15       1 36.95371 -122.0383     TRUE       FALSE
  locationPrivate      subId subnational2Code subnational2Name subnational1Code subnational1Name countryCode   countryName userDisplayName
1           FALSE S119974903        US-CA-087       Santa Cruz            US-CA       California          US United States Abram Fleishman
2           FALSE S119974903        US-CA-087       Santa Cruz            US-CA       California          US United States Abram Fleishman
          obsId checklistId presenceNoted hasComments firstName  lastName hasRichMedia
1 OBS1532344704     CL22352         FALSE       FALSE     Abram Fleishman        FALSE
2 OBS1532344716     CL22352         FALSE       FALSE     Abram Fleishman        FALSE

The 2 species that are returned were indeed part of checklist S119974903, however, there are 19 other species that are missing from the data retrieved from rebird.

I do not understand how only some of the species are returned, and how would I return the full checklists?

Session Info

> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23 ucrt)
 os       Windows 10 x64 (build 19044)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       America/Los_Angeles
 date     2022-10-17
 rstudio  2022.07.1+554 Spotted Wakerobin (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.2.1)
 cachem        1.0.6   2021-08-19 [1] CRAN (R 4.2.1)
 callr         3.7.1   2022-07-13 [1] CRAN (R 4.2.1)
 cli           3.3.0   2022-04-25 [1] CRAN (R 4.2.1)
 colorspace    2.0-3   2022-02-21 [1] CRAN (R 4.2.1)
 crayon        1.5.1   2022-03-26 [1] CRAN (R 4.2.1)
 crosstalk     1.2.0   2021-11-04 [1] CRAN (R 4.2.1)
 curl          4.3.2   2021-06-23 [1] CRAN (R 4.2.1)
 data.table    1.14.2  2021-09-27 [1] CRAN (R 4.2.1)
 DBI           1.1.3   2022-06-18 [1] CRAN (R 4.2.1)
 devtools      2.4.4   2022-07-20 [1] CRAN (R 4.2.1)
 digest        0.6.29  2021-12-01 [1] CRAN (R 4.2.1)
 dplyr       * 1.0.9   2022-04-28 [1] CRAN (R 4.2.1)
 ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.2.1)
 fansi         1.0.3   2022-03-24 [1] CRAN (R 4.2.1)
 farver        2.1.1   2022-07-06 [1] CRAN (R 4.2.1)
 fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.2.1)
 fs            1.5.2   2021-12-08 [1] CRAN (R 4.2.1)
 generics      0.1.3   2022-07-05 [1] CRAN (R 4.2.1)
 ggplot2     * 3.3.6   2022-05-03 [1] CRAN (R 4.2.1)
 ggrepel     * 0.9.1   2021-01-15 [1] CRAN (R 4.2.1)
 glue          1.6.2   2022-02-24 [1] CRAN (R 4.2.1)
 gtable        0.3.0   2019-03-25 [1] CRAN (R 4.2.1)
 htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.2.1)
 htmlwidgets   1.5.4   2021-09-08 [1] CRAN (R 4.2.1)
 httpuv        1.6.5   2022-01-05 [1] CRAN (R 4.2.1)
 httr          1.4.3   2022-05-04 [1] CRAN (R 4.2.1)
 jsonlite      1.8.0   2022-02-22 [1] CRAN (R 4.2.1)
 labeling      0.4.2   2020-10-20 [1] CRAN (R 4.2.0)
 later         1.3.0   2021-08-18 [1] CRAN (R 4.2.1)
 lattice       0.20-45 2021-09-22 [2] CRAN (R 4.2.1)
 lazyeval      0.2.2   2019-03-15 [1] CRAN (R 4.2.1)
 lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.2.1)
 lubridate   * 1.8.0   2021-10-07 [1] CRAN (R 4.2.1)
 magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.2.1)
 Matrix        1.4-1   2022-03-23 [2] CRAN (R 4.2.1)
 memoise       2.0.1   2021-11-26 [1] CRAN (R 4.2.1)
 mgcv          1.8-40  2022-03-29 [2] CRAN (R 4.2.1)
 mime          0.12    2021-09-28 [1] CRAN (R 4.2.0)
 miniUI        0.1.1.1 2018-05-18 [1] CRAN (R 4.2.1)
 munsell       0.5.0   2018-06-12 [1] CRAN (R 4.2.1)
 nlme          3.1-157 2022-03-25 [2] CRAN (R 4.2.1)
 patchwork   * 1.1.1   2020-12-17 [1] CRAN (R 4.2.1)
 pillar        1.8.0   2022-07-18 [1] CRAN (R 4.2.1)
 pkgbuild      1.3.1   2021-12-20 [1] CRAN (R 4.2.1)
 pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.2.1)
 pkgload       1.3.0   2022-06-27 [1] CRAN (R 4.2.1)
 plotly      * 4.10.0  2021-10-09 [1] CRAN (R 4.2.1)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.2.1)
 processx      3.7.0   2022-07-07 [1] CRAN (R 4.2.1)
 profvis       0.3.7   2020-11-02 [1] CRAN (R 4.2.1)
 promises      1.2.0.1 2021-02-11 [1] CRAN (R 4.2.1)
 ps            1.7.1   2022-06-18 [1] CRAN (R 4.2.1)
 purrr       * 0.3.4   2020-04-17 [1] CRAN (R 4.2.1)
 R6            2.5.1   2021-08-19 [1] CRAN (R 4.2.1)
 ragg          1.2.2   2022-02-21 [1] CRAN (R 4.2.1)
 Rcpp          1.0.9   2022-07-08 [1] CRAN (R 4.2.1)
 rebird      * 1.3.0   2021-09-20 [1] CRAN (R 4.2.1)
 remotes       2.4.2   2021-11-30 [1] CRAN (R 4.2.1)
 rlang         1.0.4   2022-07-12 [1] CRAN (R 4.2.1)
 rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.2.1)
 scales        1.2.0   2022-04-13 [1] CRAN (R 4.2.1)
 sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.2.1)
 shiny         1.7.2   2022-07-19 [1] CRAN (R 4.2.1)
 stringi       1.7.8   2022-07-11 [1] CRAN (R 4.2.1)
 stringr       1.4.0   2019-02-10 [1] CRAN (R 4.2.1)
 systemfonts   1.0.4   2022-02-11 [1] CRAN (R 4.2.1)
 textshaping   0.3.6   2021-10-13 [1] CRAN (R 4.2.1)
 tibble        3.1.8   2022-07-22 [1] CRAN (R 4.2.1)
 tidyr       * 1.2.0   2022-02-01 [1] CRAN (R 4.2.1)
 tidyselect    1.1.2   2022-02-21 [1] CRAN (R 4.2.1)
 urlchecker    1.0.1   2021-11-30 [1] CRAN (R 4.2.1)
 usethis       2.1.6   2022-05-25 [1] CRAN (R 4.2.1)
 utf8          1.2.2   2021-07-24 [1] CRAN (R 4.2.1)
 vctrs         0.4.1   2022-04-13 [1] CRAN (R 4.2.1)
 viridisLite   0.4.0   2021-04-13 [1] CRAN (R 4.2.1)
 withr         2.5.0   2022-03-03 [1] CRAN (R 4.2.1)
 xtable        1.8-4   2019-04-21 [1] CRAN (R 4.2.1)
 yaml          2.3.5   2022-02-21 [1] CRAN (R 4.2.0)
 zoo           1.8-10  2022-04-15 [1] CRAN (R 4.2.1)

 [1] C:/Users/ConservationMetrics/AppData/Local/R/win-library/4.2
 [2] C:/Program Files/R/R-4.2.1/library

ropensci / rebird Goto Github PK

rebird's Introduction

rebird: wrapper to the eBird API

Install

Direct use of rebird

eBird Taxonomy

Sightings at location determined by latitude/longitude

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Nearest observations of a species

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