How iNaturalist Counts Taxa

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A ‘taxon’ is a node on the tree of life. Consider a simplified branch of the tree with the following 7 taxa in the Amphibian family Salamandridae.


Now suppose we posted 9 observations and they were identified such that they were hanging on these taxa: 4 observations identified as Genus Nothophthalmus, 2 observations identified as Family Salamandridae, 2 observations identified as Taricha granulosa granulosa, and one observation identified as Taricha torosa.


How many taxa are represented by observations

When you’re logged into iNaturalist, click on ‘Your Observations’ in the header.

The Observation tab displays the number of Observations (e.g. 9) and the ‘Species’ tab displays the number of taxa represented by these observations (e.g. 3). But how exactly is iNaturalist counting here?

Leaf count

The default way that iNaturalist counts the taxa represented by these observations is called the ‘leaf count’. The leaf count avoids double counting (e.g. counting both Family Salamandridae and its child Genus Notophtalmus) by counting the number of distinct tips of the tree. The one caveat is that it rolls up ‘infrataxa’ (taxa with ranks finer than ‘species’ such as ‘subspecies’) to their parent species so that observed species are always included in the count.

To calculate the leaf count, iNaturalist first rolls up infratraxa. For example, the two observations on Taricha granulosa granulosa would be counted as two observations on Taricha granulosa. Then any observed taxa that ancestors of other observed taxa in the set are removed. For example, Family Salamandridae is an ancestor of taxa like Genus Notophtalmus and is thus ignored.

This means that the final count is 3 taxa: Genus Nothophthalmus represented by 4 observations, Taricha granulosa represented by 2 observations, and Taricha torosa represented by one observation.

An advantage of the leaf count is that distinct taxa that have been observed but haven’t been identified to species are included (e.g. Genus Nothopthalamus), but it avoids double counting (e.g. Family Salamandridae and Taricha torosa). A disadvantage of the leaf count is that it can be confusing to explain and is costly to compute.

You may notice that the the tab on Your Observations is labeled ‘Species’ even though ‘Taxa’ would be more correct as the count may include non-species ranks (e.g. Genus Nothophthalmus). We sometimes use the term Species rather than Taxa since its more familiar to novices.

Notice that the Filters menu on Your Observations has a ‘2’ next to it.

This is because Your Observations is identical to the Explore page with just two changes to the default Explore filters. Unlike Explore, Your Observation checks the Your Observation filter to show observations from just you. Similarly, while the Explore page defaults to checking ‘Verifiable’ observations (ie ‘Research’ and ‘Needs ID’ but not ‘Casual’ observations), Your Observations has Verifiable unchecked and thus includes Casual observations in the count.

Suppose the following Needs ID (NI), Research Grade (RG) and Casual (CA) observations. Checking ‘Verifiable’ would ignore Taricha torosa since its only represented by Casual observations.

Species count

When we display leaderboards of several counts side by side (e.g. the Observers tab on Explore or Projects), it is too computationally difficult to compute the leaf count for each.

Here, iNaturalist displays the ‘species count’ which entails rolling up infrataxa and then only counting species. In this example, the species count would be 2

If you’d prefer the species count rather than the leaf count on the Species tab in Explore, use the Rank control in the Filters menu and set High to Species

Counting taxa with Life Lists

Another place you may have noticed a Species count on iNaturalist is on your Profile. This number is generated by your primary Life List on iNaturalist. Clicking on the number will take you to your primary Life List which counts taxa a bit differently than the ways described above.

Lists are a relatively antiquated part of iNaturalist. Because they haven’t been updated for a while, lists are a bit clunky. Lists are made up of ‘listed taxa’. ‘Life Lists’ are lists that automatically create listed taxa from observations. Everyone on iNaturalist gets a primary Life List automatically and can create as many additional lists as they like.

Primary Life LIst

Your primary Life List will generate listed taxa for each taxa that you observe. Your Life List will ‘roll up’ infrataxa by also creating listed taxa for the parent species (e.g. Taricha granulosa) of an infrataxa (e.g. Taricha granulosa granulos) represented by observations even if the parent species isn’t represented by observations itself. Unlike the Explore pages described above, you can also manually add or remove any taxa from your list that you like regardless of representation by observations.

Suppose you had the same 9 observations described above and you also manually added Notophthalmus viridescens, your Life List would have 6 listed taxa on it. Each directly backed up by observations except Notophthalmus viridescens (manually added) and Taricha granulosa (e.g. rolled up from Taricha granulosa granulosa).

But primary Life Lists are configured, by default, to count observed listed taxa via the leaf count so that they match the leaf counts displayed on the Your Observations Species tab (note that lists don’t have a way of excluding listed taxa backed up by only Casual observations, so these counts are only comparable to counts on Explore where ‘Verifiable’ is unchecked).

In this hypothetical example, with these default ‘observed = yes’, ‘rank = leaves’ and ‘taxonomic status = any’ settings, of the 6 listed taxa belonging to the list, only 3 would be displayed and the count would be 3.

Similarly, if the settings were changed to be ‘rank = species’ the count would change to 2 in line with the species count described above.

If the setting were changed to ‘rank = any’ the count would change to 5 by adding in the ancestor taxon Family Salamandridae and the infraspecies Taricha granulosa granulosa. All 5 would be: Family Salamandridae, Genus Notophthalmus, Taricha torosa, Taricha granulosa and Taricha granulosa granulosa

‘Taxonomic status’ refers to whether taxa are active or inactive. When the taxonomy on iNaturalist changes (e.g. a species is split) active taxa may be inactivated and vice versa. Usually observations and listed taxa are updates, but sometimes they can’t be if the output of the change is ambiguous or if you opted out of following taxonomic changes.

Re-syncing your Life List

As mentioned previously, List functionality on iNaturalist is a bit clunky. As observations move from one taxa to another (via changing identifications etc.) listed taxa aren’t always properly created and destroyed. This can cause your list to quickly get out of sync with the list of taxa represented by your observations displayed elsewhere on the site such as Explore. Likewise, choosing to manually create or remove listed taxa from your Life List or change the ‘Rank restrictions’ setting from the default ‘allow any’ will cause your Life List to get out of sync with your observations.

To check whether an individual Listed Taxa is not backed up by an observation (either because its out of sync or you manually created the listed taxa) click ‘Edit’ to open the Listed Taxon page. The source will be an observation if the Listed Taxa thinks it was created from an observation or your username if the Listed Taxa thinks you manually added it. You can click ‘refresh’ to re-sync the listed taxa if you think it should be backed up by observations that its not recognizing

To re-sync your whole Life List, first make sure that your ‘Rank restrictions’ are at the default ‘allow any’ setting. Then under ‘Toos’ first ‘Re-apply list rules’ and then ‘Reload from observations’ (the order here is important).

Assuming you’re viewing your Life List with the default ‘Observed = yes’, ‘Rank = leaves’, ‘Taxonomic status = any’ filters, these steps should bring your Life List count in line with the count of taxa represented by your observations displayed on Explore (remember to uncheck ‘Verifiable’ on the Explore filters). The tools described above are very clunky and exert a significant strain on the system so please use them sparingly, especially if you have more than a few hundred observations.

Your other lists

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’.

For example, in the example above, all 6 listed taxa would be displayed. Note that there are other kinds of lists on iNaturalist such as place checklists that aren’t covered here and behave a bit differently.

We aren’t actively developing Lists and we are considering replacing the functionality they offer with more scalable approaches. But at the moment, they are the only way to achieve certain popular functionality such as displaying a paginated list of taxa represented by your observations as a taxonomically sorted list. The Species tab on Explore, by contrast, only displays taxa ordered by observation frequency and can only display the first 500 taxa.

Revised on October 28, 2018 05:48 AM by loarie loarie