How does iNaturalist Count Taxa?

A common question to both help@inaturalist.org and the iNaturalist Google Group is why the species counts on Your Observations are different from species counts elsewhere on the site such as your Life List.

Unfortunately, counting species has some subtle complexities that make this trickier to explain that we'd like. On top of that, Life List functionality on iNaturalist works quite a bit differently than the Your Observation functionality which complicates things further.

We wrote a tutorial to try to explain some of these complexities about how iNaturalist counts taxa. We also provide some steps for how to sync up your Life List count with the count displayed on Your Observations. Read more

Posted by loarie loarie, October 16, 2018 07:21 PM

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Bravo. I've been curious about this for a long time. I would love an addendum about how place checklists are calculated!

Posted by muir about 2 months ago (Flag)
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I appreciate the explanation, it's all quite interesting. However, I only ever want to see terminal taxa. If I've observed Ivesia gordonii alpicola and Ivesia gordonii ursinorum, I have observed two things. Life List will count three things. Your Observations will count one thing. It's two things.

Posted by dgreenberger about 2 months ago (Flag)
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is this related at all to how the calendar page tracks life list firsts? i have noticed that it misses things a lot of the time.

Posted by charlie about 2 months ago (Flag)
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@dgreenberger do you mean 'leaves count' without roll rolling up infraspecies? To be clear, that would be all taxa minus ancestors. Thats how we initially launched the Species tab on the Your Observations / Explore page, but there were lots of complaints relating to the ordering by observation frequency. For example if I had 100 observations on a species and just 2 on a child ssp with the original leaves count the ssp with its 2 obs would likely be buried far down on the list, whereas with the current leaves count that rolls up infrataxa the species with its 100 obs would likely be towards the beginning.

Posted by loarie about 2 months ago (Flag)
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charlie - yes the calendar tracks life list firsts by using the 'first observation' stats on your Life List listed taxa which is one of the main things that can get out of sync. And similarly something that 'syncing' your Life List via the steps described should fix

Posted by loarie about 2 months ago (Flag)
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Thanks Scott, i will try that. I used to sometimes add things to my life list that weren't observations, but i don't do it much anymore so i guess i don't care too much if i lose those.

Posted by charlie about 2 months ago (Flag)
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charlie - even if you manually add things to your life list that shouldn't mess with the calendar life list firsts, and as for the counts with the default 'observed = yes' filter they should still match what you see on Your Observations

Posted by loarie about 2 months ago (Flag)
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Thank you! I like this option that I've overlooked this whole time, apparently. Lol.

On an only slightly related note, does anyone know what the "Observed" option means when filtering the stats in your life list? The options are yes, no, and any, but I don't understand why any of my observations would not be observed, seems counter-intuitive.

Posted by bennypoo about 2 months ago (Flag)
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bennypoo you can manually add things to your life list that you haven't observed. For example, I once saw a Tayra so I added it to my list but I don't have a corresponding obs. I can see that listing by filtering by 'observed=no' (1 taxa) https://www.inaturalist.org/lists/9413-loaries-Life-List?q=&taxon=&observed=f&rank=leaves&taxonomic_status=all
but by filtering by 'observed=yes' this listing isn't counted (5,697 taxa)
https://www.inaturalist.org/lists/9413-loaries-Life-List?q=&taxon=&observed=t&rank=leaves&taxonomic_status=all
but by filtering by 'observed=yes' this listing isn't counted and matches 'Your Observations' (5,697 taxa) https://www.inaturalist.org/observations?place_id=any&user_id=loarie&verifiable=any&view=species
and by choosing 'observed=any' it is counted (5,697 of 5,698 taxa observed)
https://www.inaturalist.org/lists/9413-loaries-Life-List?q=&taxon=&observed=any&rank=leaves&taxonomic_status=all

At least thats how its supposed to work when everything is synced up. But unfortunately, list functionality has a way of getting out of sync with observations so chances are unless you follow the steps to re-sync your list as I've done here, your listings are going to be a bit out of sync with what you've actually observed

Posted by loarie about 2 months ago (Flag)
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@loarie Yes, I wish my body of observations could be viewed through the lens of 'all taxa minus ancestors.' The current options don't accurately reflect the observations of those of us who strive to identify to subspecific rank whenever possible.

Like, if I've gone through the trouble to see every single variety of Eriogonum umbellatum, Your Observations will display "1 species" instead of 25. Ouch.

And at the same time, if I observe:
-Eriogonum umbellatum nevadense
-Eriogonum luteolum caninum
-Eriogonum wrightii subscaposum
-Eriogonum nudum nudum
-Eriogonum ovalifolium nivale
my Life List will sit at 10. Five plants, 10 taxa doesn't make sense either.

It's a niche concern but I thought I'd throw it out there.

Posted by dgreenberger about 2 months ago (Flag)
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dgreenberger - totally fair. One issue is that we're trying to find a count that is comparable across the site for things like leaderboards etc.
but also allow people to search for and count what they want.

I agree that 'all taxa minus ancestors' is a legit use case to be able to search for that we should add.

For the count that's comparable across the site, we had wanted verifiable 'leaves count' (all taxa minus ancestors while rolling up infraspecies) to be that count. But as I mentioned in the post, we haven't found a way to calculate the leaves count on leaderboard so at the moment they're showing verifiable 'species count' (all species while rolling up infraspecies) which is annoying.

Posted by loarie about 2 months ago (Flag)
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Thanks for this article, I’ve been confused on this for a while.

Posted by kemper about 2 months ago (Flag)
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Is it possible to use the explore tool to see all the genera/families/orders etc that I've seen?

For example, if I've observed 3 Lithobates clamitans, 2 Lithobates pipiens, 1 Lithobates of indeterminate species, and 2 Anaxyrus americanus, and sorted the observations to show genera, it would list 6 Lithobates and 2 Anaxyrus.

Posted by mws about 2 months ago (Flag)
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@loarie
Thanks for the tip! And thanks for the whole tutorial. It's fantastic!

Posted by bennypoo about 2 months ago (Flag)
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mws - not currently if you use the rank filters you can show only genera (e.g. https://www.inaturalist.org/observations?hrank=genus&lrank=genus&place_id=any&view=species) but it will only count observations sitting on those genus nodes - i.e. it won't 'roll up' as your describing. I agree that would be super cool and useful though. @pleary has spent some time exploring the limits of what we can do with the Species tab on the Explore tool, but we're having a hard time figuring out how to do anything to complicated and also have it be performative, work across all observations globally, and continue to work as the number of observations continues to scale

Posted by loarie about 2 months ago (Flag)
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It's disappointing that there's no higher-taxon-viewing functionality yet, but I'm glad to know that you guys are looking into it. I'm looking forwards to the future of the species tab.

Posted by mws about 2 months ago (Flag)
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Thank you mightily for creating this journal entry — I can’t even tell how many times I’ve been asked what’s up with the discrepancy between the various ‘life lists’ and ‘species observed’ etc... Normally, I just tell them to go out and observe more. Now I can keep telling them that and to read this entry. ;)
Keep up the awesome work — loving it all. :)

Posted by sambiology about 2 months ago (Flag)
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I've started looking at my life list after reading the article and discovered that many of my verified research grade observations are only found when using the setting observed = 'no', why is this?

Posted by colinchiu about 2 months ago (Flag)
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colinchiu did you re-sync your list using the steps described? If so and you're still seeing that, can you paste in a listed taxon URL that you think should be backed up by an observation but isn't?

Posted by loarie about 2 months ago (Flag)
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@laorie My apologies, I didn't click re-apply list rules, sorry for bothering.

Posted by colinchiu about 2 months ago (Flag)
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On my lists other than the life list, under the number of taxa it displays something like '569 of 718 observed'. What does this mean?

Posted by catherineklatt about 2 months ago (Flag)
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catherineklatt , your lists that are not your primary Life List default to showing all listed taxa regardless of whether they have been observed or are ‘leaves’. So that means there are 718 listed taxa on the list and you've observed 569 of them. If you change the filter from 'observed = any' to 'observed = yes' the count should change to 569

Posted by loarie about 2 months ago (Flag)
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The output of the leaf-count algorithm can be explained otherwise as returning the minimum observed species. By the given example, the actual observed species could be anywhere between 3 and 8. So it's like saying "You have observed at least 3 species. Could be more but not less". So a more accurate and descriptive label in such cases, like "Your Observations" tab, would be "at least N species". While the output of the node-counting (species or different rank) algorithm could be labeled as "N identified taxa".

Posted by exonie about 2 months ago (Flag)
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Friends I need some help with a rare bird ID: tentative is Red-breasted Sapsucker in NE Oklahoma (where it has no business being). The discussion is whether or not is a hybrid with a red-naped sapsucker (which also has no business in NE Oklahoma). I have three photo of the bird, and would great appreciate feedback. All of my field guides indicate this is a Red-breasted. Help?

Posted by nevusmom 3 days ago (Flag)
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I have photos of the bird under my observations. (3 photos)

Posted by nevusmom 3 days ago (Flag)
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@nevusmom i think your best bet is to just post an observation. Possible outlying bird occurrences get a lot of attention and people will probably help with ID. This is a thread about taxa number tracking where you probably won't find additional help (i don't know enough about birds to know either)

Posted by charlie 2 days ago (Flag)

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