Opting out of community taxon

General
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At the family level, usually. Penstemon were moved from Scrophulariaceae to Plantaginaceae, which caused “disagreements” on iNaturalist observations.
At the genus level, you might not be safe. Escobaria vivipara is now transitioning to Pelecyphora vivipara.
At the species level, it’s all kind of wibbly wobbly as new species are described regularly and old species split or refined. Cylindropuntia spinosior became Cylindropuntia imbricata spinosior.

Are all those old IDs wrong? If I understand correctly, that’s Patrick’s biggest complaint about the current systems. Since taxonomy is unstable, it’s reasonable for users to opt out of automatic changes and community taxon to retain control over their data.

There are cases where opting out is a true hindrance, but I say you have to be a goldfish. Add your ID/DQA, move on, and forget.

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Yup @joe_fish is on taxonomy strike.

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In practice, the “right” answer is taken to be whichever one was published the most recently. Where there is conflicting evidence, people make a subjective judgment as to which evidence they feel is more important.

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I advise against this practice. :-)

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If you choose to adopt an interpretation contrary to what people have told you when asked to explain their viewpoint, well, I guess I can’t stop you. :-)

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I think I consider a right / wrong evaluation to be much less important than most other people in this discussion believe it to be. The name is a label used for retrieving observations. Can I retrieve the right set of observations with the name under which I know the taxon?

With regard to my own observations, opting out increases the odds that the answer is “yes”.

For what it’s worth, the only method I’ve found in the current iNaturalist structure that allows reliable retrieval of the set of observations to which I would apply a particular name is: Create an observation field that includes that name as one of its allowed values. In other words, have a parallel taxonomy that completely bypasses the iNaturalist taxonomy. This is not ideal, for various reasons…

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In my (admittedly still limited) knowledge of mycology, one that comes to mind is the genus Lepista. I’ve seen some mycologists argue that it shouldn’t be its on genus and that it should never have been split off from Clitocybe. Inat goes with lepista, though, and i feel like most people in to mushrooms would just… under stand the wibbly-wobbliness of fungal taxonomy and not fight to keep a blewit as Clitocybe nuda instead of Lepista nuda.

At least, i havent seen anyone doing this so far. Personally if i cared sufficiently enough about a give taxon to care that a name change happened, i also would…be aware of alternate names.

Theres a whole host of fungi this would apply for, if you look at some mushroom ID sites (the bolete filter, for example) there will be a quite a large list of recent synonyms for some groups

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You are coming from the very few obs, where a skilled identifier is defending a different taxonomy.

We are coming from the many where Opted Out is either much too broad, or heading for Maverick because they are simply wrong.

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I certainly recognize that my viewpoint may not be representative. I don’t know what the average opter-out on the street thinks, just what I happen to think.

I’m a little curious about the perception that this is a significant problem. My identifications counter currently sits at 64279 and I’ve certainly encountered “stuck” observations from people opting out but no longer being engaged on the platform. I know the problem does exist. My experience, though, is that this is a very rare and minor irritant. I’m not sure if it’s much more frequent in other contexts, or if different people perceive it as far more irritating.

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In general, I don’t find it any more irritating than you do. I come across far more multispecies observations than opted-out observations. Those irritate me.

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It’s my wrist that will eventually get irritated by copying / pasting usernames (one by one, impossible to paste a comma separated list of usernames, that could be yet another simple feature request) to these projects:

https://www.inaturalist.org/projects/user-has-opted-out-of-community-taxon-collection

https://www.inaturalist.org/projects/observer-only-allows-other-people-to-add-their-observations-to-projects-they-have-joined

https://www.inaturalist.org/projects/observer-does-not-allow-other-people-to-add-their-observations-to-projects

When I’m doing this, I think: it’s just nonsense that I spend my time doing this because a simple query in the database would provide the necessary information, I should just wait for iNat to make this available, by providing the filter on the observations that have these 3 kinds of restrictions.

What irritates me is that I have to do it myself by hand.

I’m conscientious, I don’t want to download observations over and over again for nothing because I don’t want (case 1) or can’t (cases 2, 3) add them to one of these projects.

I agree that it is a “niche”, but I do need it if I want to do things optimally. With regard to the opted-out (case 1), it’s my editorial choice not to include these observations in my projects, but with regard to the restrictions to add to projects (cases 2, 3) it’s a technical requirement, I can’t do anything with these observations so please “don’t show them to me” (don’t show them again and again, it is not a matter of getting them once and just ignoring them).

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I think of iNat identifying like carding wool, comb up, and down, left to right, then right to left. Till all the fibres are neatly lined up.

Each of us chooses a different direction. Mine is the one that ‘irritates ME!!’ Together we can tease out the tangles (Opted Outs are my tangles, yours might be potted plants). Thanks to @jeanphilippeb I have chewed my way back thru 10 years (and some even older, 19 footsack seems SO long ago) of Cape Peninsula Pre-Mavericks.

I rely on others, with a different mindset and skills, to comb thru by taxon.

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This is the problem that I usually entrust the “taxonomy swaps” to take care of. While there are a dime-a-dozen opinions on splitting/lumping (probably a huge argument to be had), I think iNat goes by the most recent taxonomic decision. However the genus means less to me than the species epiphet, so as long as my species name remains the same I don’t usually bat an eye.

I have already seen responses about “the most recent revision is the standard” which is technically the rule for scientific nomenclature. It works well but can also cause problems. Taxonomy is often the victim of taxonomic vandalism, which is usually the insane over-splitting and renaming of clades based on minimal criteria or 1-2 specimens where a proper comparison with relatives was never made. Unfortunately those bad taxonomy papers and their names can stand given the rules of nomenclature unless they are formally synonymized, which takes the time of poor overworked and underpaid taxonomists. Long story short, it stinks but we are stuck with the names, so we have to go along with it. Stubbornly holding onto old genera and species in defiance of the new taxonomy only introduces confusion.

For example the genus Macaria used to be split into Speranza and Macaria. The common white Speranza pustularia was well known as that name but was recently lumped into the Macaria. There is another name Semiothisa which is older, and Itame has also been used. As much as I like this moth in the old and useful Speranza separate from the Macaria, I just have to accept the new taxonomy and place all my pustularia into Macaria pustularia now. If I opted out and kept them as Speranza pustularia, and others joined me in silent objection, there would be TWO separate sets of data for one species. This doesn’t make sense.

Adopting your own custom taxonomy works fine for your own life lists, but on a public system I think we all need to be on the same page. Species splits don’t seem to bother me but the genus re-namings are a pain to keep up with.

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@aspidoscelis - it occurs to me that tags probably could do what you want without much additional difficulty depending on if/how you process your photos before making observations (and maybe even if you don’t do any prior processing).

I have a mix of observations made directly from the app and uploaded via the web interface.

For observations I add via the web interface, I do some light photo editing, but also add keywords with species names (I’m using Adobe Lightroom, but there are other straightforward ways of adding keywords to EXIF data). iNaturalist usually does pretty well at picking up the species names from the keywords and automatically applying them as my ID. It always includes all the keywords as tags on the observation.

I’ve not tried tagging things in the app, but it’s easy enough to add tags to an observation on the website after it has been uploaded. (I often do this to let myself know when I’ve updated keyworks in my photo database, but not agreed with new IDs on iNaturalist, when I don’t feel I have the knowledge to do so.) Others can see the tags you’ve put an observation, but you’re the only one who can edit them, as best I can tell.

If you want to find observations based on the ID you gave, if you can use the filter thing and add the name that you want to search for in the Description/Tags box. Of course others may have the same tag on their observations, so if you only want yours, you would want to limit the search to observations made by you.

I’m not sure if it would suit your purposes. It’s still something of a parallel taxonomy, but it might be easier than using the annotation process you described.

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There is no such rule.

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@gwark — If I were only interested in my own IDs of my own observations, tags would probably work although with a lot of duplicated effort. Entering IDs twice isn’t much effort on a per-observation level, but across thousands of observations I don’t really see working with two parallel ways of entering and storing IDs as a viable option. So, if I were going to use tags for that purpose, I would “opt out” of community ID in a different sense—I would stop entering IDs into the iNaturalist ID system.

However, what I’m really interested in is being able to see “observations identified as [taxon] by [user]” via the normal Explore & Identify UIs. Sometimes I would want to limit that to my own observations, more often not. Similarly, the user I’m interested in is often going to be me, but there are many contexts in which it won’t be.

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I see - that makes sense. I didn’t realize you were also interested in searching for observations identified as something by users other than yourself. In that case, tags wouldn’t be so much help, for sure (especially if you’re interested in observations other than your own).

I don’t know if the format works for you, but I can pull up a listing of identifications of a particular taxon (and its lower branches) made by a user using the identifications page with this url format:

https://www.inaturalist.org/identifications/?user_id=[user_name]&taxon_id=[taxon_number]

It seems to work reasonably well for ends of branches.

For example,
https://www.inaturalist.org/identifications/?user_id=gwark&taxon_id=147159

returns observations where I made an ID of ABC Island Brown Bear (Ursus arctos ssp sitkensis)

In particular, it also returns this observation: https://www.inaturalist.org/observations/18287087 where my ID is maverick, so that tells me it’s going based on my ID, not based on what the observation is showing up as.

( I found it by using the following URL:
https://www.inaturalist.org/identifications/?user_id=gwark&taxon_id=147159&category=maverick )

In cases where the taxon has branches below it, then it might not be as helpful, since lower IDs will also be picked up. That is, if you search for all the IDs I have made as Asteraceae, you will get all of those, plus all of the IDs I’ve made of any genus, species, and subspecies under Asteraceae. I don’t know if there’s a way to tell it to be strict and only include IDs I’ve made as Asteraceae but nothing more refined.

I don’t know if this is helpful for your purposes or not - certainly the format on the webpage isn’t so easy to deal with if you’re wanting to do any data analysis, but since the information is accessible there, maybe there’s a way to access it through the API.

I know you said you use R (presumably a package that accesses iNaturalist data? If so, it’s likely using the API in the background). I’m not sure if there’s a way to use the R package you mentioned using to pull this information. I’ve used R extensively before, but not to get and work with data from iNaturalist.

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not sure why you’re doing this manually.

https://forum.inaturalist.org/t/edit-project-breaks-entirely-for-project-with-undefined-user/30070/13

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There is no rule of priority… news to me. Then is you are doing a taxonomic revision in the future, how do you assign the correct, up-to-date valid name to a taxon? Don’t you have to deal with all names, synonyms or not?

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There is a rule of priority. The earliest legitimate name applied to the species concept (or family concept, or whatever) must be used for that taxon, with a few exceptions. There is no rule that the most recent name or the result of the most recent revision must be used. Whether to use the most recent name is up to the taxonomic judgement of the person using the name. Most of us use whatever seems to be the consensus of people whose judgement we respect or whatever a recent reference uses – we delegate the choosing to others. We don’t have to do that, though we can expect communication problems if we don’t.

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