Extracting and Processing eBird Data

stefanie · August 7, 2018, 5:05pm

eBird is an online tool for recording bird observations. The eBird database currently contains over 500 million records of bird sightings, spanning every country and nearly every bird species, making it an extremely valuable resource for bird research and conservation. These data can be used to map the distribution and abundance of species, and assess how species’ ranges are changing over time.
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The auk package acts as a front end for AWK, allowing users to filter eBird data before import into R, and provides tools to perform some important pre-processing of the data. Them name of this package comes from the happy coincidence that the command line tool AWK, upon which the package is based, is pronounced the same as auk, the family of sea birds also known as Alcids.
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Read the full post here: https://ropensci.org/blog/2018/08/07/auk/

Toucan15 · November 20, 2019, 7:13pm

Hi, I’m wondering if auk works with the full eBird Reference dataset or only the eBird Basic Data? All of the info I have seen only refers to the eBird Basic Data.

Thanks

sckott · November 20, 2019, 7:17pm

Thanks for your question @Toucan15

@mstrimas Any thoughts on this?

mstrimas · November 20, 2019, 7:23pm

No, unfortunately not, auk only works for the EBD. Furthermore, we don’t really maintain or update the ERD any more, although the 2016 version is still available on the website.

Toucan15 · November 20, 2019, 7:35pm

Ok, thanks, I was coming to that same conclusion based on the number of errors I was getting. I was hoping to use the ERD because it has elevation but maybe I can estimate elevation based on lat long

sckott · November 20, 2019, 7:48pm

maybe @mstrimas has a favorite elevation tool - we do have an ropensci pkg that can do that:

geonames::GNsrtm3 - description: http://www.geonames.org/export/web-services.html#srtm3

mstrimas · November 20, 2019, 7:53pm

You might find this resource to be useful: http://strimas.com/ebird-best-practices/covariates.html

We cover how to attach land cover and elevation covariates to data extracted form the EBD. Lots of other useful stuff in there about working with eBird data!

Toucan15 · November 20, 2019, 9:53pm

Thank you both so much! I’ll see what I can do.

amarjeet_kaur · April 5, 2020, 1:25am

Hi. Thank you for providing these commands which are very easy to grasp.
I am working on eBird data from India, and I have followed the steps you have provided. But when i perform zero-filling, I am getting error that says “Error in auk_zerofill.data.frame(x = ebd, sampling_events = sed, species = species, :
Some checklists in EBD are missing from sampling event data.”

Can you please help me on this?
Thank you again.

mstrimas · April 5, 2020, 1:44pm

Hi, this can happen if you’ve applied different filters to the EBD and sampling event data or are using different versions of these files (i.e. downloaded at different times). If that’s not what’s causing this, I’d have to see your full code to assess the problem.