WIKI - External code, tools etc for working with iNat

Please add your code, links etc to tools to work with iNat to centralize being able to find them in 1 place.

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Developer Info

Tools

Sites/Apps Using iNaturalist’s API

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This will be WONDERFUL!!! Has this been decided on/set up yet? If yes, is there a link?

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World Tour figures for
https://forum.inaturalist.org/t/how-to-replicate-world-tour-figures/13109/8
eg:
the hard/inefficient part is positioning the markers on the map based on where the center of gravity of observations is for an observer. loarie describes generally how he’s doing it here: https://forum.inaturalist.org/t/china-inaturalist-world-tour/5440/4.
(http://api.inaturalist.org/v1/docs/#!/Observations/get_observations_observers), then downloading all observations in the area for each top observer, and then probably running it through some algorithm in R to find that center of gravity.

iNat Visualizations Using R

iNaturalist Visualization: Flexdashboard (R markdown)
https://forum.inaturalist.org/t/inaturalist-visualization-flexdashboard-r-markdown/13036

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Edits to wiki:

  • Fixed the heading markup (’# Heading’ rather than ‘=Heading=’).
  • Added link to “API recommended practices” and a couple projects (pyinaturalist, rinat)

This topic should probably be moved to the “Tutorials” category, rather than “General”.

@cmcheatle can we include examples that use iNat’s API, eg https://www.owlsnearme.com/ ?

I dont see any reason why not.

TLDR; I started a Slack workspace for coders, ecologists, datascientists who want to work with iNat data. message me if you want to join!

Hi Everyone who’s worked on this!

It’s cool to see some energy building on the forum around visualizing and processing the iNat data.
Like others, I’ve also been interested in resurrecting the rinat package and updating it to make use of new API. The authors of the rinat pacage at ROpenSci said that they’d like to hand off the project to some more active developers. If there’s a group of people here who want to work on it that would be great.

In general, it would be awesome to have a place for coders, data scientists and ecologists that are using iNat data to connect. I have a ton of ideas about how to use the data but I don’t make time to actually work on many of them (and I’m not sure any of my ideas are that useful to others). I’m sure there’s a lot of redundancy in the features that people want so working together could be efficient.

I started a Slack workspace for this. Let me know if you think this is a good way to connect. (also if there’s already a slack or discord for this topic let me know). Eventually I’d like to host a virtual meet up on zoom.

Message me if you want to join (I’m not sure I should post invite link publicly).

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for what it’s worth, @hanly already seems to have something that works with the v1 version of the iNaturalist API. the v2 API is still in development. so it might be too early to start developing something against it.

while there’s certainly an audience for it, i’m not entirely convinced that building an R package is necessarily the best way to open up the iNat data to the most people. for that, i think it would be better to have folks create 5-20 minute videos / tutorials that show people how to conceptually work with the data in various tools.

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I’m not sure the R package is that useful either. Especially since there are a few ways to access the GBIF data from R already. I’d also say lot of the region and taxa specific apps I’ve seen using iNat data just replicate features on iNaturalist itself.

But this is why I think it would be useful to have a place to discuss projects. What do people need help with? For instance, I think building a toolkit that allows people to more flexibly make maps and phenological charts of iNaturalist records could be useful. Developing a tool that can generate species area curves or species accumulation curves from iNat data is another thing I’d think would be useful.

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I think this is a great idea. What are the topics around data analysis data visualization people want to see covered in tutorial videos?

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I also agree, that was my conclusion also. I had considered taking over development of rinat, but then realized that for any scientific work GBIF is a better source (more comprehensive data set, citeable data queries, …). As it exists, rinat is a simple repackaging of the iNat v1 API, without the more useful tools for working with the data post-download, and the more recent ROpenSci plans don’t go much further than adding the v2 API to the same framework. From following the user requests on this forum, there seems to be more interest in tools for “social” summaries (searching and/or displaying a user’s contributions or summarizing project data) rather than the scientific/statistical apps that are R’s forte.

here are the videos that i think would be good as a starting point:

  1. (5-10 minutes) custom searches using URL parameters
  2. (5 minutes) downloading data from iNaturalist via CSV export
  3. (10 minutes) downloading iNaturalist data from GBIF (including pros and cons)
  4. (5-15 minutes) demystifying the API – part 1 (general overview – what is an API, what kind of data can be accessed via iNaturalist’s APIs, and what are pros and cons of API vs other ways to get data?)
  5. (5-15 minutes) demystifying the API – part 2 (conceptual walkthrough getting data from the observation endpoint using the Swagger interface)
  6. (10-15 minutes) demystifying the API – part 3 (example – get 1000 observations into R)
  7. (10 minutes) demystifying the API – part 4 (example – get histogram data – or other aggregated data – into Excel)
  8. (10-30 minutes) demystifying the API – part 5a (example – producing a tiled map visualization in QGIS, including pulling data from GBIF, too)
  9. (5 minutes) demystifying the API – part 5b (example – producing and sharing a tiled map visualization in ArcGIS Online in under 5 minutes)
  10. (5-10 minutes) demystifying the API – part 6 (general best practices and limitations of the API)
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