iNat Visualizations Using R

[whimbrelbirder]

If anyone is interested in visualizing their iNat data, I’m currently making a repository on GitHub that will be full of code for producing some cool graphics done with R. Also, if you have any suggestions for a visualization I don’t have yet in the repo or if you don’t know how to use R, dm me and I will make it for you.

If you notice any errors in the code or a way to make the visualizations better, feel free to file an issue in the repo.

The link to repository is here at: https://github.com/oliverburrus/iNat_Visualizations

Lastly, if you would like to contribute to the repo yourself lmk and I can make you a collaborator.

[cthawley]

@alexis18 and @pisum may have some good thoughts and have done some previous viz work with iNat and R: https://forum.inaturalist.org/t/what-things-are-misidentified-as-large-milkweed-bug/12571

[pisum]

i’m actually not an R person, but there are plenty of folks who have mentioned making things for iNat for and related to R (feel free to add to this wiki post, if you like):

@alexis18

Since you all were as excited about my last visualization about milkweed bug misidentifications as I was, I thought I’d share one I put together about invasive species.

This one takes a place_id and plots the introduced species as bubbles sized by the number of research-grade observations in that place. The colors correspond to the iconic taxon.

Bubble plots are a fun way to communicate biodiversity data, in my opinion, and can help you compare between sites at a glance.

The code for this visualization is here . It doesn’t handle huge numbers of observations super well, both in terms of speed and visualizations, so I recommend places with <50,000 total verifiable observations.

@gonzalopatagonia

I am working on a R code to produce dashboards with plots, tables and others, to show inaturalist data on a web site.

Some examples can be found here (view results).

Code here .

@jlayman

The app: https://jonathanlayman001.shinyapps.io/iNaturalist_user_trends/

@vojczech

For heatmap of either single species observations or single user observations check this online app.
https://github.com/Vojczech/iNaturalist_app

@hanly

Check out my iNat profile for installation instructions and examples of a beta R package that can handle this request: https://www.inaturalist.org/people/hanly

@loarie

Here’s the little R script I used to make that fig from the iNat API

A post from github I saw on twitter for making chloropleths of seasonal iNat observation data: https://github.com/alexkrohn/reptile-choropleth

[optilete]

Cool!

[crellow]

I don’t have much else to say at the moment, but this is great. Keen to see where this goes.

Actually I’m not sure whether the links that @pisum provided will mention it at all, but there’s also the rinat package here: https://github.com/ropensci/rinat.

[pisum]

@crellow

there’s also the rinat package

from what i can tell, the rinat package is a little dated at this point. it seems to hit the old iNaturalist API, which is deprecated at this point, and rinat doesn’t seem to be actively developed any more. i think it would be better to use hanly’s thing above, which hits the current v1 API, or just hit the API directly yourself. (the v2 API is currently in development. so even the current v1 API and anything built on it may be dated soon, too.)

@crellow

I’m not sure whether the links that @pisum provided will mention it at all

it’s definitely not all of it. the above items are only the things i remember of that relate to visualizations or ways to get data from the API into R. (i remember other people using R to do other things like modify EXIF data, etc.)

i just made my earlier post a wiki. so if you want to add to it, feel free to add to it, if you like.

[dataecologist]

I also made this visual not long ago to show the most popular species in each state

Note that observation are tallied so there is 1 “vote” per user per species/state/month. This minimizes the effect of super-users, and also makes it so top species on the website do not necessarily match

[sarahshearer]

@mikeakresh, check this out! Have you ever used iNat data for visualization using R?

[rion_science]

rinat

has been updated 3 months ago.

[pisum]

it may be updated, but as far as i can tell, it still hits the deprecated iNat API. is there any reason to use rinat for new development rather than hitting the current /v1 API directly or using some other wrapper package that hits the /v1 API? (just for example, rOpenSci also provides the spocc package which will allow you to get info from iNat’s /v1 API, along with other sources like GBIF, eBird, etc.)

[rion_science]

Thanks spocc is much better!