Wikipedia talk:Automated taxobox system/Archive 4

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Linking taxobox to nomenclatural databases, e.g. WoRMS (Aphia)

Given taxonomy is dynamic, is it possible to have an auto taxobox on a species article automatically keep up to date with changes in published taxonomy by linking it with an identifier to a nomenclatural database such as the WoRMS (Aphia) database? Having the taxobox be dynamic in this fashion would allow taxon articles to avoid out-of-date taxonomies and save manually updating large numbers of taxon articles to reflect new information. Advice is very welcome. Frogs&dogs (talk) 01:03, 6 February 2020 (UTC)

Whether it's possible or not is one issue, but in my view it would be thoroughly undesirable and I would strongly oppose it.

• There are often different taxonomies in different taxonomic databases; taxonomy is a subjective matter.
• The article text needs to be kept in line with the taxobox. One of the (few) negative features of the automated taxobox system is that by changing a taxonomy template the taxobox can be changed without checking that the relevant articles have also been changed. I not infrequently come across articles where the taxobox is inconsistent with the text of the article.
• WoRMS in particular covers different groups of organisms. There are legitimate reasons for using different classifications in different areas of the tree of life.
• Two examples of inconsistent classifications in different areas: birds and dinosaur articles use different ranks for Aves; the Pteridophyte Phylogeny Group classification is used for ferns, more-or-less as used by the Checklist of Ferns and Lycophytes of the World, but not what the main general plant taxonomic database, Plants of the World Online, uses for ferns.

Choosing classifications and agreeing to changes should always require editor consensus. Peter coxhead (talk) 17:36, 6 February 2020 (UTC)

need help w/ speciesbox

Hello, I'm sorry if this question has been asked millions of times already, but I need help with editing a speciesbox. I'm trying to write a new page on a species belonging to a monotypic genus (it's currently listed under its old genus on Wikipedia). I started by just copy-pasting a taxobox from another species onto the page and editing it. But when I changed the "taxon" parameter, it gave me an error. I'm assuming it has something to do with the fact that maybe an automatic taxonomy displayer hasn't been created for the species. How would I create one?

edit: I'm writing the page in my sandbox.

Thanks, JadeSpire (talk) 17:25, 2 March 2020 (UTC)

@JadeSpire: Are you asking about Bletilla striata at User:JadeSpire/sandbox? It looks like the taxonomy template at {{Taxonomy/Bletilla}} already exists. Also, as the species page exists as well, you can just make adjustments there. Let us know if you have anything else you want to ask. --awkwafaba (📥) 18:04, 2 March 2020 (UTC)

Or is it User:JadeSpire/Practice, concerning Dendrobium speciosum, which would use {{Taxonomy/Dendrobium}}? That also has an existing page you can edit. --awkwafaba (📥) 18:11, 2 March 2020 (UTC)

(edit conflict)

@JadeSpire: Assuming you mean the page User:JadeSpire/Practice, the {{speciesbox}} for Dendrobium speciosum seems to be working (except the name is using the page name). What change to the |taxon= did you want to make? —  Jts1882 | talk  18:08, 2 March 2020 (UTC)

Hi all, thanks for the quick response. I was talking about the Practice page – sorry for not clarifying earlier. I'm trying to create a new page on Psychopsiella limminghei, so I pasted in the page being used for D. speciosum. I thought I would first change the speciesbox before editing the content. In essence, I'm trying to create a new taxonomy template for P. limminghei. Sorry for confusing you. :) JadeSpire (talk) 18:40, 2 March 2020 (UTC)

@JadeSpire: when you get a taxobox like the one here, click on the "fix" link. This will start a "taxonomy template". The minimum you need to complete is the rank, "genus" here, and the parent, whatever the next higher taxon is for this genus – presumably "Oncidiinae". Hope this helps. Peter coxhead (talk) 22:31, 2 March 2020 (UTC)

@Peter coxhead: thanks for the help. Just curious, is it likely that the taxonomy template will stay up or is there a chance that it will be "speedily deleted?" It is legitimate, but I'm not 100% familiar with Wikipedia rules. JadeSpire (talk) 03:54, 3 March 2020 (UTC)

@JadeSpire: I see you have successfully created the taxonomy template for Psychopsiella. A new taxonomy template is unlikely to be speedily deleted as it will be assumed it is created for future use and the link to your user space can be checked. Articles in the main namespace get treated differently because a poor article or an obvious early draft shouldn't be presented to readers.

Your edit notice for the template says "genus split from Psychopsis; change accepted by Kew/World Checklist". It's good practice to add the reference to the |refs= parameter of the taxonomy template. You can use the {{cite web}} or {{WCSP}} templates, e.g. <ref>{{WCSP|167054|Psychopsiella limminghei|accessdate = 3 March 2020}}<ref>. —  Jts1882 | talk  08:04, 3 March 2020 (UTC)

References

Thank you very much! :) JadeSpire (talk) 17:24, 3 March 2020 (UTC)

@JadeSpire and Jts1882: you mustn't use the ref tags in a taxonomy template, just the citation. Peter coxhead (talk) 19:45, 3 March 2020 (UTC)

@Peter coxhead: I removed them before putting them in. :) JadeSpire (talk) 21:33, 3 March 2020 (UTC)

@JadeSpire: so I realized after my post! Peter coxhead (talk) 22:26, 3 March 2020 (UTC)

Collapse functionality?

I noticed on Sarcocystis that the subdivision field is really huge. It covers about half of the page. Can't we implement an optional 'collapsed' functionality to the 'Species' part? With a show/hide button? Cheers, Manifestation (talk) 15:24, 27 March 2020 (UTC)

MOS:DONTHIDE. – Jonesey95 (talk) 15:31, 27 March 2020 (UTC)

Manifestation, you can repeat the content in the text and say "see text" in the speciesbox. If the content is repeated in the text, you could keep it in the speciesbox with Template:Collapsed infobox section begin. Or you could even create List of Sarcocystis species Enwebb (talk) 15:50, 27 March 2020 (UTC)

@Jonesey95: That's nonsense. I can think of several instances in which you might collapse chunks of content to make the article more viewer friendly.

@Enwebb: Ok thanks. I have tried Template:Collapsed infobox section begin, see here. The results are... reasonable. But can't the functionality be a default part of the box? List of Sarcocystis species might not pass the notability threshold, since only four Sarcocystis species have their own article. Cheers, Manifestation (talk) 16:08, 27 March 2020 (UTC)

I would oppose collapsed text being a default part of the infobox, per MOS. If you have an objection to the current text at MOS:DONTHIDE, which is a community guideline, please take it up on the talk page for the Manual of Style, Wikipedia talk:Manual of Style. – Jonesey95 (talk) 16:46, 27 March 2020 (UTC)

I too would strongly oppose collapsible text, per MOS:DONTHIDE. There's no reason whatsoever to have a hidden list in the taxobox. Reasonable length species lists, say up to 50, can be put in the text with a wikilink from the taxobox, longer ones can have their own list article. Since species are inherently notable, I've never seen any sustained objection to a separate list article. Peter coxhead (talk) 17:32, 27 March 2020 (UTC)

I also don't recommend the collapsible text, but the original point is valid, it's far too large for an infobox. I think the species should be moved to the body of the text (it can be in columns to save space) and just have that section of the infobox deleted. Mattximus (talk) —Preceding undated comment added at 17:48, 27 March 2020‎ (UTC)

Ok, fine. How is this? - Manifestation (talk) 18:51, 27 March 2020 (UTC)

Much better. There is some advice in the Template Data (used in Visual Editor) not to add long lists of subdivisions to a taxobox. But there are other documentation pages that don't have that advice. Plantdrew (talk) 22:25, 27 March 2020 (UTC)

• Picking up on the "don't have collapsed content in boxes" bit - I have several times added pre-collapsed synonym lists to taxoboxes when the number of entries hits a dozen or more. Seems to be a reasonably common practice, and I can't remember ever seeing a synonyms list present in the main body instead. What's the take on this? --Elmidae (talk · contribs) 16:55, 17 April 2020 (UTC)

I also routinely collapse large synonym lists in taxoboxes. Loopy30 (talk) 22:38, 17 April 2020 (UTC)

Automatic cladogram

Since we already have taxa in correct order with Template:Automatic taxobox, can we use this info to create something like {{Automatic cladogram}}? The idea is you put two parameters, name and depth and it would automatically draw a cladogram for you. For example: {{Automatic cladogram|Dinosauria|2}} would create a cladogram with Dinosaur as parent and two taxon ranks below.  Dinosaur (talk) 🌴🦕🦖 -- 20:34, 15 April 2020 (UTC)

That sounds like a good idea. Of course, this wouldn't be used for taxa with volatile classification schemes or chronospecies, like belemnite which has 4 cladograms, or Homo floresiensis where the cladogram uses the |label= parameter to denote direct ancestry   User:Dunkleosteus77 |push to talk  01:56, 16 April 2020 (UTC)

I don't think any classifications are stable enough that this would be beneficial. The automatic taxobox templates are themselves changed all the time, and they don't reflect one simple classification scheme, so a resulting cladogram would be a hodgepodge of different schemes, therefore WP:synth. FunkMonk (talk) 05:41, 16 April 2020 (UTC)

This won't work for the reason that FunkMonk gave. There used to be code that would automatically generate the child taxa of a given taxon from the taxonomy templates. However, it had to be removed because of the way taxonomy templates are used. In summary, taxonomy templates encode a particular upwards classification used in a given case; they cannot be used downwards because multiple inconsistent upwards classifications may end at the same taxon.
Let me explain in more detail. Some taxa are represented by more than one taxonomy template ("variants"). This enables the system to encode different classifications for the same taxon. The best known example is in fact in dinosaurs. The 'dinosaur' system and the 'bird' system are different. If you go to Template:Taxonomy/Aves, you'll see that the parent is "Ornithurae/skip", which works its way up to "Sauropsida", leaving gaps. This is what bird editors want. If you go to Template:Taxonomy/Ornithurae, you'll see a much fuller hierarchy, but it also works its way up to "Sauropsida". If you try to generate a cladogram downwards from "Sauropsida", you need first to find all taxa whose taxonomy templates have |parent=Sauropsida. Ignoring a sandbox version, there are five, which would give you the start of the cladogram as:

Sauropsida	Reptilia Archosauria (via Archosauria/skip) Avemetatarsalia (via Avemetatarsalia/skip) Lisboasaurus (a genus) incertae sedis

Going down from Reptilia, you would eventually find Archosauria and below it Avemetatarsalia. You'd also find Avemetatarsalia going directly down from Archosauria. I can give many other examples. Taxonomy templates do not encode a tree, but a network.
It has been suggested that to get a cladogram, you just ignore the variants and follow the main taxonomy templates (i.e. those without "/qualifier"), but this doesn't work either, because which version has a qualifier is largely historical: the first created version will be the plain one, later ones will be variants, but the later ones may be the most up-to-date. Peter coxhead (talk) 05:59, 16 April 2020 (UTC)

In short the taxonomy templates work upwards so, even if the other issues on variable taxonomy were resolved, are only suitable for a cladogram showing an article taxon as a terminal. If you want a cladogram with the article as the root the taxonomy templates don't have the relevant information in a form accessible from a template or module. Hypothetically there two ways it could be done.

1. If the |subdivisions= parameters were well-formed and had the child branches, it would be possible to extract this information with Lua in a module using the child taxa in |subdivisions= and then reiteratively getting subsequent child taxa using title objects to get the |subdivisions= content from the taxoboxes in the pages for the child taxa. Given the variety of formats in the |subdivisions= this is impractical and editing the pages to generate a standard format in |subdivisions= would be more effort than constructing a cladogram from scratch.
2. The taxonomy template information can be extracted in a downwards direction using Javascript to access the API. I already have a script that does that and can generate a list of the taxonomy. This could be used to generate a draft cladogram using the {{clade}} template, but it would likely need editing anyway, as it couldn't handle alternative taxonomies. And any method using Javascript can only be a tool or an added extra; it can't be used for the standard page output.

But that is all hypothetical. I agree with the above that getting automated cladograms from the taxonomy templates is impractical at best. I think any effort to systematize the cladograms would be better used to generate a series of standard accepted and/or consensus cladograms in templates and then reuse those in articles. —  Jts1882 | talk  10:15, 16 April 2020 (UTC)

@Jts1882 About the javascript method, what is your opinion if the code is modified so that if it finds A is the parent of B and C, and B is the parent of C then it would change its former A-C line to A-B-C? This would fix the problem that Peter coxhead raised. I agree with FunkMonk this method would be synthetic, have little scientific value and the resulting cladograms should not be included (or included but with a warning) in articles. A situation where this could be useful is when someone with limited expertise in an area just wants to have some quick general idea about where a particular taxon stands. Offical cladograms are usually small, only cover some branches, he cannot "zoom out" to see the bigger picture. If time allows it, could you modify your code to make it a gadget Jts1882?  Dinosaur (talk) 🌴🦕🦖 -- 02:58, 17 April 2020 (UTC)

@Khủng Long: just to be clear, it's not only that the taxonomic "tree" reduces to a net, it's also that incompatible classifications are encoded in the taxonomy templates. Compare upwards from Template:Taxonomy/Embryophytes/Plantae (used by every single flowering plant taxobox), which treats Plantae as a kingdom, and Template:Taxonomy/Embryophytes (used mainly in taxoboxes for "algae"), which does not include any kingdoms, replacing Plantae by Archaeplastida and Viridiplantae – roughly, Plantae sensu lato and Plantae sensu stricto respectively.

(It's sometimes thought that Wikidata could be used instead, but this makes even more explicit the fact that there are variant taxonomies, since a taxon item can have multiple parents: see, for example, Lemnaceae (Q14293890).) Peter coxhead (talk) 06:26, 17 April 2020 (UTC)

Even if this kind of template is technically feasible, I don't see any reason to use it and I don't think it's a good idea to use it anyways. Most cladograms currently in use on articles are based on the results of specific papers, not some well-resolved consensus which can be summarized easily in one universal cladogram. If this system is used, it would generate cladograms which have never appeared in the literature and therefore would not be congruent with our policies on sourcing our information and not generating original research. In addition, the automatic taxobox template does not make use of unnamed clades, while cladograms need to, a disconnect which would create artificial and unsourced polytomies in any cladogram derived from the taxobox. Fanboyphilosopher (talk) 02:32, 23 April 2020 (UTC)

Exactly right. Peter coxhead (talk) 06:30, 23 April 2020 (UTC)

Not sure where to request fix

The page Phlaeothripidae uses an automatic taxobox which appeare to be somehow malfunctioning. If I'm not signed in, the page doesn't load properly, and the preview text that accompanies the Google hit (Google search here), itself contains taxobox error message copy:

Phlaeothripidae is a family of thrips with hundreds of genera.

They are the only family of the suborder Tubulifera, and are

themselves ordered into two subfamilies, the Idolothripinae

with 80 genera, and the Phlaeothripinae with almost 400.

Family: Phlaeothripidae; Uzel, 1895

Missing taxonomy template (fix): Tubulifera

Phlaeothripidae - Wikipedia

I am not familiar enough with Automatic taxboxes to fix it myself, or even to diagnose the problem, and I'm too busy remodeling a garage to learn about it right now. I'm guessing it's an easy fix for someone who just knows how the system works, so I chose to report it here. If you read this far, thanks. :) -GTBacchus^(talk) 19:26, 28 May 2020 (UTC)

Is it just the Google snippet that's the problem? The taxobox in the article looks fine to me, even when not logged in, but I do see the error in the Google snippet. I guess Google just happened to take a snapshot of the page at an inopportune time. 19:44, 28 May 2020 (UTC)

The taxobox and google search seem in order for me. Is it still a problem for you? Sometimes there are strange caching issues. —  Jts1882 | talk  19:48, 28 May 2020 (UTC)

I think that the parent of Phlaeothripidae was changed before the parent's taxonomy template was set up, so there was a transient error in the taxobox, which got picked up by Google and also got cached. Experience shows that you need at least a null edit to force a full refresh of the hierarchy of taxonomy templates. Peter coxhead (talk) 21:45, 28 May 2020 (UTC)

Previously, the taxobox appeared normal, but other parts of the page were broken, like all the links along the top right corner of the page, and all the links on the left side of the page, were smashed together in groups. It just looked like broken HTML somewhere in the mix, but I could still read the article. Now, that's not happening, and only the Google snippet is being weird, but I'll try clearing my browser cache or something. -GTBacchus^(talk) 17:37, 29 May 2020 (UTC)

Change to handling of ichno- and oo- ranks in taxonomy templates

Following a discussion at WP:Dinosaurs, I have changed the handling of taxonomy templates so that it is no longer an error to be flagged if an ichno- or oo-taxon has a parent at the same normal rank (e.g. an oofamily has a family as the parent). This affects only a very few animal taxonomy templates and corresponding articles, but if you notice any resulting errors, please let me know (and revert the relevant edit if the error is serious). Peter coxhead (talk) 13:31, 7 June 2020 (UTC)

1 July 2020 use stats update

Project	Auto	Manual	Total taxa	Percentage auto	# auto added since 1 January 2020
Algae	1411	540	1951	72.3	121
Amphibians and Reptiles	17315	350	17665	98.0	1357
Animals	3981	3414	7395	53.8	239
Arthropods	4639	6217	10856	42.7	2764
Beetles	13641	22068	35709	38.2	828
Birds	13728	149	13877	98.9	11
Bivalves	1330	67	1397	95.2	11
Cephalopods	1327	1132	2459	54.0	21
Dinosaurs	1429	89	1518	94.1	36
Diptera	5966	5735	11701	51.0	916
Fishes	16330	5804	22134	73.8	856
Fungi	2861	9586	12447	23.0	1217
Gastropods	13267	19789	33056	40.1	880
Insects	28499	40872	69371	41.1	2655
Lepidoptera	33030	64722	97752	33.8	4063
Mammals	6770	647	7417	91.3	-51
Marine life	3816	2556	6382	59.8	225
Microbiology	1809	9407	11216	16.1	368
Palaeontology	10068	5428	15496	64.8	482
Plants	53101	12452	65553	81.0	5344
Primates	928	2	930	99.8	15
Rodents	2978	93	3071	97.0	-2
Sharks	736	37	773	95.2	4
Spiders	7353	1402	8755	84.0	167
Tree of Life	121	58	179	67.6	19
Turtles	678	1	679	99.9	27
Viruses	1477	189	1666	88.7	709
Total	221946	186512	408458	54.3	21111

Mammal subprojects with articles tagged for both mammals and subproject:

Project	Auto	Manual	Total taxa	Percentage auto
Bats	1531	4	1535	99.7
Cats	228	0	228	100
Cetaceans	411	0	411	100
Dogs	254	1	255	99.6
Equine	102	0	102	100

Since January, auto taxobox use has more than doubled for arthropods, and almost doubled for fungi. Viruses didn't quite double, but went from 47.4% to 88.7%. Insects and lepidoptera had more auto taxoboxes added in this period than any other since I started tracking these stats (barring a couple periods where a bot was creating a large number of new articles with auto taxoboxes). Diptera passed 50%. Project banners were removed from some mammal (mostly Canidae) and rodent articles, bringing the number of automatic taxoboxes down there (mammals are still down a net of 41 manual taxoboxes though). And the turtle is Bairdemys (it has a subtribe listed, but no other genera in the family have any infrafamilial classification; all should or none should). Plantdrew (talk) 01:49, 2 July 2020 (UTC)

Is there an easy way to query/list the articles associated with those stats? Shyamal (talk) 11:50, 2 July 2020 (UTC)

I believe they are done with Petscan, looking for pages with particular templates (the taxoboxes) belonging to a particular category. There are issues with the depth of category to look at, too few and you miss taxa, too many and you pick up lots of extra pages (parasites, cat attractants, etc). So for mammals I get 8827 results for a depth of 3 and 47231 results for a depth of 8 looking for automatic taxoboxes and speciesboxes. There are probably some other settings needed. I thinks the exact searches are chosen for consistency so progress in conversions can be monitored. An alternative is to use the search facility to find manual taxoboxes with a particular taxon, but this doesn't work with automated taxoboxes. —  Jts1882 | talk  14:07, 2 July 2020 (UTC)

@Shyamal:, the queries are based on WikiProject banners, which is why there are separate (non-inclusive) counts for animals/arthropods/insects/beetles. This is the search I ran for beetles with manual taxoboxes, and this is for beetles with automatic taxoboxes. The parameters are specified in the "Templates & links" tab (keep in mind Petscan is flaky and stops working from time to time). In general it is more practical to do a search with a taxon category (such as a family) instead of a WikiProject banner to find articles with manual taxoboxes (Petscan won't display more than 10,000 results, so for a large project such as beetles not all manual/automatic taxobox articles will be displayed in a single search). Plantdrew (talk) 20:48, 2 July 2020 (UTC)

@Jts1882:@Plantdrew: Thanks for the tips. Shyamal (talk) 03:09, 3 July 2020 (UTC)

Has anyone successfully exported the templates & categories of the Automated taxobox system to a remote project?

I've spent the past several days porting the ATS over to gd:Wiktionary, but I am having a heck of a time getting it to "talk" to the Taxonomy "database" at en:wikipedia:Category:Taxonomy templates. My first set of modifications failed. I haven't exhausted my efforts yet, but if someone has already invented the wheel, I'd love to see their modifications. I am working alone over at Uicleir, so, barring a successful port to use as an example, I would love some advice on how best to proceed. I'd much rather use the ATS for obvious reasons, but will use the manual Taxoboxes if necessary. Cheers.

Kibi78704 (talk) 05:18, 23 July 2020 (UTC)

The automated taxobox system relies on the taxonomy templates (<35,000 of them), which have to be on the same wikipedia so you'd have to copy all of them for it to work reliably. It doesn't use the categories but gets the parent from the relevant taxonomy template for the taxon and works up to high taxa from there. I don't know if any wikipedia project has imported all the taxonomy template.

Other than manual taxoboxes there are versions that use Wikidata (e.g. on the Hebrew and Catalan Wikipedias). There are well-documented problems with using Wikidata, which is why the English Wikipedia doesn't use it, but for smaller Wikipedia projects it has advantages. —  Jts1882 | talk  08:26, 23 July 2020 (UTC)

@Kibi78704: it's been ported to the Simple English Wikipedia; see the taxobox at simple:Panthera for example. However, as Jts1882 notes, because the system relies on transcluding taxonomy templates, they have to be on the same wikipedia, because transclusion doesn't work across wikipedias. So although, e.g., simple:Template:Taxonomy/Panthera exists, you can't use something like {{:simple:Template:Taxonomy/Panthera}} to transclude it, any more than the Simple English Wikipedia can use {{:en:Template:Taxonomy/Panthera}} to transclude the one here. I'm not aware of a way round this, although there may be one.

For reasons not to use Wikidata, see the first section of the essay at User:Peter coxhead/Wikidata issues. Peter coxhead (talk) 09:17, 23 July 2020 (UTC)

Thank you @Jts1882 and Peter coxhead: for saving me a great deal of frustration, though I am very disappointed to hear about these limitations (of which I was unaware). It seems there is no good solution to this issue for a tiny Wiki. There is only the one of me; maintaining whichever taxonomic implementation appears to be a daunting task, especially knowing how often updates occur these days. I had so hoped to be able to connect to a central repository of data that was maintained by those more connected to the taxonomic field. Móran taing (Thank you very much) Kibi78704 (talk) 15:21, 23 July 2020 (UTC)

@Peter coxhead: I read your essay on Wikidata issues. Well done. Thank you for pointing it to me.

I am not quite sure whether Wikispecies is driven by Wikidata, or if it is entirely separate, but I have noticed many issues with Wikispecies, as well. It is a shame that this issue, i.e. the issue of having a single, well-designed, well-maintained central repository of data was not better implemented. I suppose that is the nature of Wikiland. Kibi78704 (talk) 15:36, 23 July 2020 (UTC)

@Kibi78704: to be fair, the problem is partly with the nature of taxonomy and classification. Non-biologists and beginning biologists often think there is an agreed coherent system. In reality, taxonomists are highly disputatious and regularly disagree as to how to classify organisms, so there are sometimes wildly different approaches. (E.g. in one view of the fern genus Blechnum it has about 30 species, in another view about 250.) Wikidata could do better in my view, but it wouldn't be easy. Peter coxhead (talk) 16:55, 23 July 2020 (UTC)

@Peter coxhead: I understand both the nature of taxonomy/classification and the Wikidata issue. I have been an amateur botanist and an aficionado of archaeology for decades and have witnessed the massive upheavals in taxonomy since I was a child and am very conversant with taxonomic synonyms. I also appreciate the problems with Wikidata, not only as a project largely run by volunteers of varying degrees of proficiency, but also as a 30+-year veteran software developer. Perhaps modelling taxonomy in Wikidata wasn't the best idea, not only because of the issues you discuss in your essay but simply because taxon classification is so fluid these days; however, it is what it is and better than nothing at all, I suppose.

I am now beginning to lean toward porting the Taxonomy templates to gd:Wiktionary; I'll ruminate over it for a few more days before I act. I realized this morning that I don't have to port the whole set and may do it piecemeal as I go; there will most likely only be a few thousand taxa. I hope. I wish there were a way to link a change alert from the original Taxonomy templates to the remote copies, but if wishes were horses, I'd have a stable. I'll do what I always do and add a link to the documentation pages.

Thank you for all of your assistance. It's been fun and informative discussing this topic with you. Best wishes on Simple English. Kibi78704 (talk) 21:21, 23 July 2020 (UTC)

re: "I don't know if any wikipedia project has imported all the taxonomy template." I get tons of notifications from taxonomy templates I've created being linked on Wikidata after being copied to zh.wiki. I'm surprised to find that zh doesn't have the most taxonomy templates after en. Category:Taxonomy_templates has 69k members. vi:Thể_loại:Bản_mẫu_Taxonomy has 66k. zh:Category:分类学模板 has 23k, and ru:Категория:Шаблоны:Таксономия has 17k. As far as I'm aware, Vietnamese still mostly uses manual taxoboxes in spite of having most of the taxonomy templates (Vietnamese is on of the languages with a large number of bot created articles on organisms). sco:Category:Taxonomy_templates has 1,677 members; with 57k articles, Scots almost certainly the highest ratio of taxonomy templates to articles. There are some other languages thatwhere I often get notifications of Wikidata template links, but which don't seem to have a category for taxonomy templates (Malayalam and Farsi for two). Plantdrew (talk) 00:04, 25 July 2020 (UTC)

Off topic, but the Vietnamese wikipedia is an object lesson in the problems of bot-created articles: it has a huge number of multiple articles on the same taxon under synonymous titles. Peter coxhead (talk) 18:57, 25 July 2020 (UTC)

Updates to Ichnobox and Oobox templates

I had been aware for some time that the way in which {{Ichnobox}} and {{Oobox}} handled automatic italicization was faulty. There were workarounds, but these were particularly tricky for disambiguated genera, like Sauropus (ichnogenus), and were prone to causing DISPLAYTITLE errors. I started fixing these templates, but then realized that it would be much easier to extend the Lua code used to implement {{Automatic taxobox}} to handle ichno- and ootaxa, which would then deal with italicization in a completely consistent way. (Species articles are rare, and there never have been ichno- or oo- equivalents of {{Speciesbox}}.)

I've released the Lua versions of {{Ichnobox}} and {{Oobox}}. Tests suggest that they work fine, and the changes haven't affected pages using {{Automatic taxobox}}, but if anyone notices errors, please report them and/or revert the change to the template.

One side-effect is that ichno- and ootaxoboxes relying on the page title rather than an explicit |taxon= are now tracked in Category:Automatic taxoboxes relying on page title. It's not actually an error, but they can be fixed over time. Peter coxhead (talk) 10:49, 1 October 2020 (UTC)

Colour of Ichnoboxes

Having spent some time working on Ichnoboxes, I feel that their colour is not quite right: it's too green, too suggestive of the colours we use for plants and green algae. I'd like to change the colour to something less saturated, but still distinct from other taxobox colours. My suggestion (and now Lythronaxargestes' as well) and comparisons with somewhat similar taxobox colours:

Plantae

Current Ichnos colour

Proposed Ichnos colour 1

Proposed Ichnos colour 2

Proposed Ichnos colour 3

Animalia

Bacteria

Views, please. Peter coxhead (talk) 15:49, 1 October 2020 (UTC)

Hm. I personally think an orange-adjacent colour would be clearer (not the beige of Animalia), something like this or this?

I would like to have a colour-blind person weigh in, though. Lythronaxargestes (talk | contribs) 20:06, 1 October 2020 (UTC)

@Lythronaxargestes: yes, accessibility is important. The set of colours at {{Taxobox colour scheme}} was, I recall, checked and modified for accessibility. One issue is the contrast between the black text and the background. Your first possibility above may be too bright; also an orange tone is used for incertae sedis. It's difficult to find another distinctive colour, but your second one seems fine to me. Peter coxhead (talk) 21:15, 1 October 2020 (UTC)

@Lythronaxargestes: I added your second suggestion to the table above. I prefer it to mine. Or perhaps the third colour above, which is the same hue but slightly lighter, increasing the contrast with the text. Peter coxhead (talk) 07:07, 3 October 2020 (UTC)

I like the third. It matches the other colours well. Lythronaxargestes (talk | contribs) 15:07, 3 October 2020 (UTC)

Agreed. Unless there is an accessibility issue, I'd choose the third option. —  Jts1882 | talk  15:16, 3 October 2020 (UTC)

Ok, well, no-one else seems interested, and we agree, so I'll implement the third option. Peter coxhead (talk) 08:02, 6 October 2020 (UTC)

Royle's pika

I ran across a species article that didn't have a speciesbox, so I tried to add a box. However, I'm pretty sure I managed to completely mess up... Help!--SilverTiger12 (talk) 22:17, 17 October 2020 (UTC)

No, not a complete mess, only a minor error which I fixed. (Errors in taxoboxes show up in a number of error-tracking categories, which I and others monitor most days, so they usually get fixed fairly quickly.) Peter coxhead (talk) 09:20, 18 October 2020 (UTC)

Domain: Eukaryota

I've only noticed it over the past couple of weeks, but it looks like since March of this year at Template:Taxonomy/Eukaryota/displayed, every plant, animal, fungus, etc. has been displaying "Domain: Eukaryota". I think I remember back from {{Taxobox}} that we were supposed to top out at kingdom. Was there discussion before that change was made? Does everybody think it's a good idea? Should I be adding "Domain: Eukaryota" to Taxobox templates? Thank you. SchreiberBike | ⌨  08:06, 17 November 2020 (UTC)

The issue is not that Template:Taxonomy/Eukaryota/displayed forces the display of this rank; it should. The issue is that Jts1882 in this edit on 18 October 2020 changed the child to point to Eukaryota/displayed rather than Eukaryota. I agree there's no consensus for this, so I've reverted it pending discussion (not here: this is a Wikiproject TOL issue). Peter coxhead (talk) 09:03, 17 November 2020 (UTC)

My mistake. Similarly, the animals and fungi were caused by this edit, which I've now reverted. As the edit summary says, we want to display eukaryote when not an animal, plant or fungi, which I understand is the consensus. Many other eukaryotes groups are now not showing Eurkayota at the top and I intended to fix this. I'm not sure how I missed the behaviour for animals, plants and fungi (possibly a caching issue?).

The edit was made in response to a problem (Automatic_taxobox_glitches) raised on your talk page by User:SMcCandlish for taxa like Aconchulinida. Some taxoboxes deal with this using |display_parents= in the taxobox but this fails (and needs incrementing) when additional higher taxa are added to the chain, which is happening quite often with the likes of CRuMs and TSAR.

Given the exceptions to showing Eukaryote are limited to the three traditional kingdoms, it makes sense to handle these, rather the larger number and often changing other eukaryote groups. One possibility is to create chains of alternative taxonomy templates, but I think it might be best handled in Module:Automated taxobox. It should be possible to check for the three kingdoms where we don't want to show higher taxa and stop the hierarchical chain output there. —  Jts1882 | talk  14:38, 17 November 2020 (UTC)

I'm glad youse are on top of this. I don't know enough about the guts of this particular set of complex templates to go wading into them; I just noticed some confusing results like the Aconchulinida thing. PS: I don't think it's a bad thing that "Eukaryota" was appearing at the top of the "three traditional kingdoms". I actually had a lot of fun the other day digging around in Eukaryota and where else it led. It wasn't something I'd looked at in probably a decade or longer, and I was surprised at some of the reclassifications of various microscopic life. I would think that various people from old folks to kids would have a big "whoa!" moment with some of that stuff, like learning what a eukaryote is and that various things that seem more related to each other for being micro-organisms are actually more related to us than to various other minute life forms. I'll defer to WP:TOL on it, of course, but I'll !vote for showing the full taxo tree.  — SMcCandlish ☏ ¢ 😼  15:33, 17 November 2020 (UTC)

In order to get Eukaryota displayed for Amoebozoa, I created Template:Taxonomy/Unikonta/displayed. However, I don't think Unikonta is something that should actually be displayed down to species level (so I didn't set |always_display=). Is "/displayed" an appropriate way to name a variant template for a taxon that isn't displayed (but where the template is need to complete the chain up to something that is displayed)? Any thoughts on a better way to name it? Plantdrew (talk) 22:28, 20 November 2020 (UTC)

The name is counter intuitive. Perhaps Template:Taxonomy/Unikonta/showdomain would be clearer. —  Jts1882 | talk  08:22, 21 November 2020 (UTC)

I think it might be best handled in Module:Automated taxobox – I'm very much against putting processing of this kind in the code rather than the data; it would prevent editors creating special cases via variant taxonomy templates and it's against the principles of modularity. The automated taxobox code should process the data in the configuration settings and the taxonomy templates, rather than make decisions independently.

The name is counter intuitive – I agree; it's best to keep "/displayed" for the variant taxonomy template that differs only in having |always_display=yes. Using "/showdomain" seems better to me. Peter coxhead (talk) 17:03, 21 November 2020 (UTC)

Assistance with incertae sedis

I'm trying to convert the fungus family Aphanopsidaceae to a automatic taxobox. It's in the Ascomycota, but is incertae sedis with respect to class and ordinal placement. I've created the template here, using Ascomycota as the "parent", but am not sure how to make the template show incertae sedis for the class and order. If someone could edit that template to show me how to make it do that, I would be grateful (or point me to the documentation for this – I wasn't able to find it myself). Esculenta (talk) 16:42, 25 December 2020 (UTC)

@Esculenta: I think setting the parent of Aphanopsidaceae in {{Taxonomy/Aphanopsidaceae}} to Ascomycota, as you have done, is adequate. What is to be gained by adding the incertae sedis entries? It can be done, though, by creating appropriate taxonomy templates. There is a brief description at WP:Automated_taxobox_system/advanced_taxonomy#Incertae_sedis_taxonomy_templates showing how to set up {{Taxonomy/Incertae sedis/Ascomycota}}.

If you want to show both class and order as incertae sedis it could be done with something like {{Taxonomy/Ascomycota/class incertae sedis}}, with |parent=Ascomycota and |rank=classis, and {{Taxonomy/Ascomycota/order incertae sedis}}, with |parent=Ascomycota/class incertae sedis and |rank=ordo. If this done it is important to provide a source |refs= to show that this is part of a taxonomic assessment. —  Jts1882 | talk  08:33, 26 December 2020 (UTC)

@Esculenta: I agree with Jts1882 – there's no need nowadays to show incertae sedis at lots of intermediate ranks. In the past, when strict Linnaean taxonomy ruled, it was expected that all the principal ranks would be filled out, but with modern phylogenetic classifications often employing multiple clades of indeterminate rank, I don't think it's necessary. And as Jts1882 rightly says, you need source(s) that specifically say "incertae sedis" for the ranks. Peter coxhead (talk) 11:13, 26 December 2020 (UTC)

• Thanks for the assistance. It still took more half an hour to get it figured out, but I think it's working now. To answer the question "What is to be gained by adding the incertae sedis entries?", if these ranks aren't in the taxobox, people will think they are missing. If reliable sources says a certain rank is incertae sedis, this should be reflected also in the taxobox, which is a summary of what we know (or don't know) of the organism's classification. Regarding "modern phylogenetic classifications often employing multiple clades of indeterminate rank", that doesn't happen very much with the Fungi. Esculenta (talk) 19:43, 26 December 2020 (UTC)

6 January 2021 stats update

6 January 2021 update

Project	Auto	Manual	Total taxa	Percentage auto	# auto added since 1 July 2020
Algae	1445	537	1982	72.9	34
Amphibians and Reptiles	17679	349	18028	98.1	364
Animals	4400	3347	7747	56.8	419
Arthropods	5044	5928	10972	46.0	405
Beetles	15244	20595	35839	42.5	1603
Birds	13868	128	13996	99.1	140
Bivalves	1343	65	1408	95.4	13
Cephalopods	1344	1127	2471	54.4	17
Dinosaurs	1452	89	1541	94.2	23
Diptera	6197	5614	11811	52.5	231
Fishes	17122	5218	22340	76.6	792
Fungi	3270	9256	12526	26.1	409
Gastropods	14466	18682	33148	43.6	1199
Insects	31182	38734	69916	44.6	2683
Lepidoptera	35641	61923	97564	36.5	2611
Mammals	7010	618	7628	91.9	240
Marine life	4155	2472	6627	62.7	339
Microbiology	2000	9348	11348	17.6	191
Palaeontology	10490	5439	15929	65.9	422
Plants	56562	12094	68656	82.4	3461
Primates	933	3	936	99.7	5
Rodents	2993	80	3073	97.4	15
Sharks	764	64	828	92.3	28
Spiders	8757	78	8835	99.1	1404
Tree of Life	129	58	187	69.0	8
Turtles	685	17	702	97.6	7
Viruses	1528	152	1680	90.9	51
Total	269429	176785	446214	60.4	47483

Mammal subprojects with articles tagged for both mammals and subproject:

Project	Auto	Manual	Total taxa	Percentage auto
Bats	1537	5	1542	99.7
Cats	215	0	215	100
Cetaceans	417	2	419	99.5
Dogs	248	1	249	99.6
Equine	104	0	104	100

PETSCAN has been flaky, so I'm getting these numbers out a little later than I'd prefer. Since July 2020, Spiders have gone from 84% to 99% use of automatic taxoboxes. Insects, Beetles, Lepidoptera, and Gastropods have added 1000+ automatic taxoboxes; these projects still have more than 50% manual taxoboxes, but are moving forward. Progress on most other projects has been pretty low (new articles likely account for most of the new automatic taxoboxes). Of note, there is a big difference between the "Total" (calculated from the template transclusion count), and the sum of counts calculated from PETSCAN searches by WikiProject banners and taxobox templates. "Total" gain is 47k articles, but summed count by WikiProject Banners is 17k articles (and that is an overestimate as some article have banners for multiple WikiProjects). I'm pretty sure what is driving that difference is the addition of a large number of pages in draft space with taxobox templates and no banners. Plantdrew (talk) 22:49, 6 January 2021 (UTC)

These are interesting stats, thanks for compiling. Although not directly related to the quantification of automated taxoboxes, I think it could be useful to have a column showing estimated global total #of described taxa, and % of completion. For the Fungi, the estimated # of species is 148,000 (2020 source: doi:10.1002/ppp3.10148), meaning 8.45% of known fungi have Wikipedia articles. Esculenta (talk) 00:01, 7 January 2021 (UTC)

@Plantdrew: thanks for the update. A warning to all: I took the relatively small proportion of spider articles that still have manual taxoboxes as a challenge. What's interesting so far is that a high proportion of them are problematic: either higher level groups that are no longer recognized or synonyms (sometimes with an article already at the accepted name). I suspect that a lot of the articles with manual taxoboxes in groups that mostly have automated ones are either old or created by less active and hence perhaps less knowledgeable editors. So they need to be checked carefully before being converted to automated taxoboxes. Peter coxhead (talk) 11:19, 7 January 2021 (UTC)

Is there an app for that?

I vaguely recall on my watchlist some time ago someone changing manual to automatic taxoboxes (or maybe species boxes) using some sort of app ... am I imagining this or is it really a thing, and if so, where can I find it? Esculenta (talk) 15:54, 27 January 2021 (UTC)

Possibly this (User:William Avery/taxoboxalyzer). It's a bit experimental. William Avery (talk) 16:29, 27 January 2021 (UTC)

That's the one, thanks! I'll give it a try. Esculenta (talk) 16:41, 27 January 2021 (UTC)

Need help with tardigrade taxobox

Hello, I started a page for Limmenius, a genus of tardigrade under Milnesiidae. However, there is an error with the template, and I'm not sure how to fix. Thanks! EponineBunnyKickQueen (talk) 05:27, 6 February 2021 (UTC)

The error is because there wasn't a taxonomy template for Limmenius. To fix these errors you need to follow the link "fix" which will take you to a page to create the template. You need to fill in |rank=genus and |parent=Milnesiidae and add a suitable reference. I have done this for you and created {{Taxonomy/Limmenius}}. —  Jts1882 | talk  07:42, 6 February 2021 (UTC)

Thanks! EponineBunnyKickQueen (talk) 06:30, 7 February 2021 (UTC)

bat sub-orders

This is certainly correct about the steep learning curve, I've given up. Is it possible to force a certain taxonomy level to be displayed, either on a page by page basis or for a particular taxon? I want the pages on bat species and other bat taxa to display the sub-order. Irtapil (talk) 09:57, 28 March 2021 (UTC)

If there was a consensus to display the suborder for bats (please discuss first at WT:MAMMALS or WT:WikiProject Mammals/Bats Task Force), then at for example Template:Taxonomy/Yinpterochiroptera you would add the line |always_display=yes. Peter coxhead (talk) 10:06, 28 March 2021 (UTC)

Species groups/subgroups

Hello! I'm currently working on improving coverage of Drosophila flies; part of this entails moving things over to automatic taxoboxes. It doesn't look like the automatic taxobox system supports species groups or subgroups. While I understand enough to get them to work, I don't understand the internals very well. Does anybody know how species groups and subgroups could be added? Thank you! Tol | talk | contribs 22:37, 14 June 2021 (UTC)

See Drosophila quinaria species group and Template:Taxonomy/Quinaria. |rank=species_group is supported in taxonomy templates. If the name of the species group isn't unique (e.g. it's used as a genus name elsewhere), the taxonomy template could be called something like "Template:Taxonomy/Drosophila species group Quinaria". If you need any more help, do ask here or on my talk page. Peter coxhead (talk) 06:39, 15 June 2021 (UTC)

Supported (i.e. recognized) 'ranks' include species_complex, species_group and species_subgroup; the underscore can be replaced by a space, but I think is clearer in the taxonomy template. If you need others, they could be added to Template:Anglicise rank, but it would need a good case to be made. We don't want to proliferate minor informal ranks; you can always use clade. Peter coxhead (talk) 06:48, 15 June 2021 (UTC)

@Peter coxhead: Peter, how do you feel about "superspecies", which is bit more Latin? I added this in here a while ago, but happy to replace. Superspecies redirects to species complex. YorkshireExpat (talk) 17:25, 15 June 2021 (UTC)

@YorkshireExpat: who uses the rank "superspecies"? Can you give an example of its use in a reliable source? Peter coxhead (talk) 18:55, 15 June 2021 (UTC)

Ornithologists use it; incoming links to superspecies are overwhelming from bird articles. Here's a recent reference. Plantdrew (talk) 19:04, 15 June 2021 (UTC)

@Plantdrew: well, it can certainly be added to {{Anglicise rank}} if it's likely to be used in a taxobox – is it? Presumably it goes between subgenus and species, though to check its ordering it would have to be ordered with respect to section and subsection. Ah, for the good old days of simple Linnaean ranks! Peter coxhead (talk) 19:33, 15 June 2021 (UTC)

We've gotten by without so far, so I'm not sure it needs to be added, but I'll check with WPBIRDS and see if there is any interest. Plantdrew (talk) 20:14, 15 June 2021 (UTC)

Can we have supergenus while we're at it :)? YorkshireExpat (talk) 20:38, 15 June 2021 (UTC)

@Peter coxhead: On superspecies, the herring/lesser black-backed gulls are a classic example. See here with a hyphen (super-species). YorkshireExpat (talk) 20:52, 15 June 2021 (UTC)

@Peter coxhead: Thank you so much; it's not listed at Wikipedia:Automated taxobox system/taxonomy templates#rank, so I didn't realise it just worked like that. Tol | talk | contribs 17:05, 15 June 2021 (UTC)

@Tol: all taxoboxes, manual and automated, 'understand' the rank names in Template:Anglicise rank in the sense that they map them to a standard English form – any other rank name is just capitalized (and if used in a taxonomy template will put it in an error-tracking category). A subset of ranks are checked for consistency by the automated taxobox system – it's these that are shown at Wikipedia:Automated taxobox system/taxonomy templates#rank. Maybe the documentation needs tweaking to clarify this. Peter coxhead (talk) 18:55, 15 June 2021 (UTC)

Ah; that makes sense. Thank you again! Tol | talk | contribs 19:05, 15 June 2021 (UTC)

@Tol: I have now revised Wikipedia:Automated taxobox system/taxonomy templates#rank. I hope this will help editors in future. The documentation of the automated taxobox system needs constant review. Peter coxhead (talk) 19:20, 15 June 2021 (UTC)

@Peter coxhead: Thank you so much for your help. Tol | talk | contribs 19:22, 15 June 2021 (UTC)

Template-protected edit request on 15 June 2021

Please add a new line as follows:

From:	To:
|genus|ichnogenus|oogenus|subgenus|ichnosubgenus|oosubgenus	|genus|ichnogenus|oogenus|subgenus|ichnosubgenus|oosubgenus
	|species_group|species_subgroup|species_complex
|supersectio|sectio|subsectio|series|subseries|species|ichnospecies|oospecies	|supersectio|sectio|subsectio|series|subseries|species|ichnospecies|oospecies

Thank you, Tol | talk | contribs 21:23, 15 June 2021 (UTC)

 Done I have sometimes considered whether it would be better to combine in one place the rank configuration set up in {{Anglicise rank}}, {{Is italic taxon}} (which should more logically be "Is italic rank") and function getRankTable in Module:Autotaxobox, but their usage differs between manual and automated taxoboxes, and not all template editors know Lua, so keeping the first two in the template code has advantages. However, they can become inconsistent, as you noticed! Peter coxhead (talk) 06:40, 16 June 2021 (UTC)

Yes; well — I want to learn Lua at some point, but I presume it wouldn't be hard to understand a simple function which checks if some input is in some array of strings. (And, it would be easy to add another string on.) But, I suppose it's fine the way it is. Tol | talk | contribs 16:43, 16 June 2021 (UTC)

@Tol: one issue is that typically a Lua module is equivalent to an entire 'program', containing many functions, whereas typically templates are kept relatively small in separate pages. The way forward, I think, would be to create an "Autotaxobox/conf" module which just contained small configuration functions – this would be a safer module to edit.

Re Lua: I find it an attractive language, and easy to learn and use – but I spent so many years teaching and working with Java and Javascript that it's hard to stop my fingers inserting {}, even though before then I also taught and wrote Pascal in various versions. Peter coxhead (talk) 07:53, 18 June 2021 (UTC)

30 June 2021 use stats update

30 June 2021 update

Project	Auto	Manual	Total taxa	Percent auto	# auto added since 6 January 2021	# manual subtracted
Algae	1732	538	2270	76.3	287	-1
Amphibians and Reptiles	18838	321	19159	98.3	1159	28
Animals	6195	3061	9256	66.9	1795	286
Arthropods	6809	4925	11734	58.0	1765	1003
Beetles	16443	19930	36373	45.2	1199	665
Birds	13909	122	14031	99.1	41	6
Bivalves	1437	65	1502	95.7	94	0
Cephalopods	1386	1107	2493	55.6	42	20
Dinosaurs	1534	21	1555	98.6	82	61
Diptera	8839	4816	13655	64.7	2642	798
Fishes	19044	3724	22768	83.6	1922	1494
Fungi	5752	7452	13204	43.6	2482	1804
Gastropods	17171	16258	33429	51.4	2705	2424
Insects	37915	35311	73226	51.8	6733	3423
Lepidoptera	39072	58742	97544	40.1	3431	3181
Mammals	7128	534	7662	93.0	118	84
Marine life	5138	2038	7176	71.6	983	434
Microbiology	2103	9920	12023	17.5	103	-572
Palaeontology	11115	5058	16173	68.7	625	381
Plants	63969	8421	72390	88.4	7407	3673
Primates	935	3	938	99.7	2	0
Rodents	2999	76	3075	97.5	6	4
Sharks	773	60	833	92.8	9	4
Spiders	9130	0	9130	100.0	373	78
Tree of Life	129	59	188	68.6	0	-1
Turtles	710	5	715	99.3	25	12
Viruses	1594	140	1734	91.9	66	12
Total	268553	159352	427905	62.8	-876	17433

Mammal subprojects with articles tagged for both mammals and subproject:

Project	Auto	Manual	Total taxa	Percentage auto
Bats	1540	5	1545	99.7
Cats	206	0	206	100.0
Cetaceans	419	2	421	99.5
Dogs	237	3	240	98.8
Equine	104	0	140	100.0

I compiled these numbers two days ago, posting today. I've added a column for reduction in the number of manual taxoboxes; as many projects are now largely using automatic taxoboxes, the number of additional articles with automatic taxoboxes increasingly reflects the creation of new articles under these projects rather than progress in converting manual taxoboxes to automatic.

I noted in my last update that there was a large increase in the number of articles returned by my search method for the "total" row that wasn't reflected in the rows for the individual projects. Starzoner had created a very large number of drafts with automatic taxoboxes. Starzoner was blocked, and their drafts were deleted. Even though 17,000 articles were converted from manual taxoboxes to automatic in the last six months, there are still 876 fewer articles with automatic taxoboxes after Starzoner's drafts were deleted.

Method: For the most part I use Petscan to search for articles with a talk page banner for a particular Wikiproject and either {{Taxobox}}, or any of {{Automatic taxobox}}+{{Speciesbox}}+({{Infraspeciesbox}} and/or {{Subspeciesbox}} (depending on whether botanical/zoological code is relevant)), and record the results. Example search for algae with automatic taxoboxes (search terms are in the Templates&Links tab in Petscan). For viruses, I search for {{Virusbox}} rather than the other automatic taxobox templates. For plants, I sum the results for the Plants, Banksia, Carnivorous plants and Hypericaceae projects. "Total" is derived from the Template Transclusion Count tool ([https://templatecount.toolforge.org/index.php?lang=en&namespace=10&name=Speciesbox#bottom e.g. results for Speciesbox), and is not actually sum of the results for individual projects (some articles have talk page banners for multiple Wikiprojects, and would be counted twice if rows were summed). I started compiling these stats in April 2017, and have been updating roughly every six months since December 2017. I've kept my method consistent; perhaps I should have included all of the automatic taxobox templates (Hybridbox, Ichnobox, etc.), but I didn't do so at the beginning, and the other templates aren't used in very many articles.

Caveat: The remaining manual taxoboxes in projects with a high percentage of automatic taxoboxes mostly have some kind of "problem". I have periodically reviewed all the manual taxobox articles in projects with less than 141 manual taxoboxes, and chose not to convert them to automatic taxoboxes at that time (however, it has been awhile since my last review, so there probably a few recently included articles I haven't reviewed). "Problems" may include:

• Fossil taxa; fossil classifications may be derived from multiple sources and present classification on Wikipedia may include mutually incompatible hypotheses. Fossil taxa are often not be linked from extant parent taxa.
• Synonymy; there is some obvious synonymy issue; e.g., a species is in a genus which redirects (as a synonym) to another genus; maybe the species article needs to be moved or maybe the genus should be reinstated
• Common names; articles with common name titles may not correspond to taxa, but still have manual taxoboxes. In some cases {{Paraphyletic group}} may be appropriate, in others the taxobox should be removed
• Parasite and pathogens; article on parasites and pathogens may be tagged for the WikiProject of the organisms they infect. Higher level taxonomy templates for the parasites may not yet exist, and the classification presented in manual taxoboxes may not be up to date.

I haven't reviewed every article in Amphians and Reptiles, Mammals, and Cephalopods, but most of the remaining manual taxoboxes under these projects are fossil taxa, with a smattering of other "problems". I'd certainly encourage people to work on groups with a small number of manual taxoboxes, but do pay attention to detail. Plantdrew (talk) 00:47, 3 July 2021 (UTC)

It's interesting to see that Spiders has 100% auto, considering that it is bugs, which tend to be speciose. And the total percentage auto has gone up by 2% or so since last time - progress!

I'm also curious what the last few bats, dogs, and cetaceans are that have manual taxoboxes. The Dogs project is active enough that one of them might be able to deal with a confused article, at least. --SilverTiger12 (talk) 17:34, 3 July 2021 (UTC)

Bats: Hassianycteris (fossil, parent is a redlink, and parent not mentioned in grandparent); Matthesia (fossil, both Archaeonycteridae and Palaeochiropterygidae claim this as an included genus); Nothoaspis reddelli (tick parasitizing bats); Polyctenidae (bugs parasitizing bats); Pseudogymnoascus destructans (pathogenic fungus; family and genus lack taxonomy templates, and order shown as incertae sedis, but may be Thelebolales (fungal classification needs updating))

Cetaceans: Andrewsiphiinae; fossil taxon, not mentioned in parent (I just took care of the other cetacean with a manual taxobox, which was also a fossil (but was mentioned in parent))

Dogs: Capnocytophaga canimorsus, Ehrlichia canis, Neorickettsia helminthoeca; all bacterial pathogens that lack taxonomy templates for genus and family

It's a good set of examples illustrating potential "problems". The three bacteria infecting dogs are straightforward, it's just that bacteria have the lowest rate of adoption of automatic taxoboxes. Two insects parasitizing bats also seem straightforward, but insects still have a low rate of automatic taxoboxes. Three fossils not mentioned in parents (or with multiple parents). One fungus affecting bats with higher fungal classification needing to be updated somehow. Plantdrew (talk) 20:02, 3 July 2021 (UTC)

I had a look-see and found that the last cetacean article is a subfamily that does, according to at least one recent paper, exist, so I went and added mention of it to the parent article and replaced the manual taxobox with an autotaxobox. --SilverTiger12 (talk) 20:45, 3 July 2021 (UTC)

I completed a five-month review of all amphibian and reptile related project taxoboxes in Feb, 2020. The only manual taxoboxes remaining at that time were fossil taxa without full taxonomic sources. I consider Amphibians and Reptiles to be "done". Loopy30 (talk) 22:24, 3 July 2021 (UTC)

Good work. I guess I can now say that projects with less than 322 (rather than 141) manual taxoboxes have had all those articles individually reviewed. Lepospondyls and temnospondyls are inconsistently tagged for WikiProject Animals and WikiProject Amphibians and Reptiles, and often lack a WikiProject Palaeontology banner. I'm not sure whether these groups should be considered amphibians are not (but this isn't the best forum to discuss that). Plantdrew (talk) 18:35, 4 July 2021 (UTC)

As well as Amphibia (Feb 2020), I have also reviewed all individual taxoboxes for the following taxa within WikiProject Marine Life:

• Porifera (Sep 2019)
• Ctenophora (Mar 2019)
• Trilobozoa (Mar 2019)
• Placozoa (Sep 2018)
• Cnidaria (Oct 2018)
• Kimberella (Sep 2019)
• Proarticulata (Feb 2020)

I have also started (but not yet completed) both Xenacoelomorpha and Holothuroidea. Loopy30 (talk) 22:33, 4 July 2021 (UTC)

The Viruses category is not "done" as I skimmed through it and found some articles that can have the manual taxobox replaced with a virusbox, so I will work on these articles. Velayinosu (talk) 01:24, 5 July 2021 (UTC)

Bug?

Just found a bug editing Pleistocene coyote. When setting extinct=yes the subspecies field gets the marker but the trinomial does not, however this is done automatically for the binomial of species. YorkshireExpat (talk) 22:03, 3 July 2021 (UTC)

@YorkshireExpat: well spotted! Jts1882 got there before I did, and it's fixed. Peter coxhead (talk) 06:57, 4 July 2021 (UTC)

In the examples I checked I noticed an issue when looking at Caspian tiger, which is recently extinct (with the year given in the |extinct= parameter). This is no longer recognised as a distinct subspecies, being part of the continent species. We want the extinct year with the conservation status, but not with the trinomial as the whole subspecies is not extinct. I think we need an |extinct_year= to add the year to the conservation status without adding the dagger. This illustrates the problem with the dual use parameters that has been discussed before. —  Jts1882 | talk  07:00, 4 July 2021 (UTC)

@Jts1882: although I agree re the dual use of |extinct=, there's a different problem with the taxobox at Caspian tiger: it should have a level below the subspecies for the population which is extinct. This can't be done with {{Subspeciesbox}} (and in view of the rarity of the case, shouldn't be added). I've used a manual taxobox to solve this problem – there will always be edge cases where manual taxoboxes are best. Peter coxhead (talk) 08:22, 4 July 2021 (UTC)

Articles on populations of various Carnivora that were formerly recognized as subspecies (and using common name titles) was precisely the case I had in mind when I said "in others the taxobox should be removed" in my comments on the use stats thread. Leaving them with manual taxoboxes (rather than trying to make automatic taxoboxes handle these cases) is another option. — Preceding unsigned comment added by Plantdrew (talk • contribs) 19:23, 4 July 2021 (UTC)

@Jts1882: and @Peter coxhead: Can I be a pain and suggest the dagger might not be bold? YorkshireExpat (talk) 10:43, 4 July 2021 (UTC)

Sorted. YorkshireExpat (talk) 17:27, 4 July 2021 (UTC)

Strange issue

For whatever reason, the Template:Taxonomy/Paraves and all subsidiary templates are shown as being members of Mammalia. This does not appear to be the result of recent vandalism to Template:Taxonomy/Paraves, as it has been unmodified since 2017. All the higher temples, such as Template:Taxonomy/Pennaraptora, appear to be fine. Hemiauchenia (talk) 11:22, 4 July 2021 (UTC)

It was caused by this edit, which was reverted yesterday but was still cached somehow. A null edit on Template:Taxonomy/Paraves seems to have fixed it. There might be other cases going by User_talk:Sulaimat —  Jts1882 | talk  11:48, 4 July 2021 (UTC)

Looks like DrawingDinosaurs has reverted the other cases. —  Jts1882 | talk  11:52, 4 July 2021 (UTC)

It's perhaps worth reminding editors that changes to a template, including a taxonomy template, don't immediately show up in any page that transcludes that template, including other templates, or in any category that is affected by changes to the template. How long it takes for the database to update depends on the load; recently it seems that it usually takes more than a day or less.

It's helpful not to save a page, article or template, with a missing taxonomy template: use preview and create the missing template(s) before saving. This prevents non-errors polluting the error-tracking categories while the database updates. I'm sure I'm not the only editor who wastes time checking pages which are actually o.k. (Null edits usually fix the problem, but occasionally a purge is also needed.) Peter coxhead (talk) 21:27, 4 July 2021 (UTC)

Parvavis

Why does the taxobox on the Parvavis page italicize the species name, but not the genus? I would like to note that in March an IP tried to fix it by adding italic marks to the genus parameter (which made the taxobox unable to recognize it) and adding "Parvavis" to the species parameter (which created a "Parvavis Parvavis chuxiongensis" Miracusaurs (talk) 07:48, 12 July 2021 (UTC)

The |genus= and |species= parameters shouldn't be formatted with Wikitext. This interferes with the automatic italicisation. I've removed the italics code from |species= and it looks OK now. —  Jts1882 | talk  08:16, 12 July 2021 (UTC)

Talk pages for taxonomy templates

I'm sure I'm not alone in having my watchlist flooded with new talk pages for the taxonomy templates. Are these really necessary? Given they will be watched by so few, wouldn't it be better to have a special talk page for the taxonomy templates or to redirect them here? —  Jts1882 | talk  12:01, 4 July 2021 (UTC)

Making large volumes of pointless edits, such as talk pages for files is Ser Amantio di Nicolao's modus operandi, which is why he is the #1 Wikipedia editor by number of edits. Hemiauchenia (talk) 12:17, 4 July 2021 (UTC)

Ouch. YorkshireExpat (talk) 16:42, 4 July 2021 (UTC)

These are actually, in my view anyway, harmful rather than pointless edits. I never watch taxonomy templates I create or edit, because if they are vandalized it will almost always show up in the error-tracking categories which I monitor. Having individual talk pages could encourage a new editor to leave a comment there where no-one will see it. I agree with Jts1882 that redirecting to one centralized talk page would be better. If this were agreed in an RfC, a bot could make the necessary changes. Anyone else have a view? Peter coxhead (talk) 21:09, 4 July 2021 (UTC)

Personally, I'd say delete them all, because talk pages for individual taxonomy templates sounds like the most useless thing ever, and most people aren't ever going to be aware that they exist because, well, most people have to go use WP:Autotaxobox system/intro to make one in the first place. --SilverTiger12 (talk) 21:14, 4 July 2021 (UTC)

I consider them pointless (been observing with bemusement as my watchlist was flooded). Discussions about the classification or templating of a given taxon are supposed to be had at the talk page of the taxon article, and discussions about template-related issues are going to be rare enough that they are much better off at the suggested central venue (which I would back in an RfC). --Elmidae (talk · contribs) 23:28, 4 July 2021 (UTC)

I agree with all of you and would support an RfC to delete these taxonomy template talk pages. (My watchlist is flooded as well...) Loopy30 (talk) 23:36, 4 July 2021 (UTC)

Well, do let Ser Amantio di Nicolao know you're unhappy by making him aware of this discussion. He's usually responsive to complaints. – wbm1058 (talk) 21:17, 5 July 2021 (UTC)

Given the concerns, I'll stop. I was unaware there would be complaints, as a number of talkpages had previously been created - mostly, as I recall, for gastropods, fungi, and coleoptera.

And please, please, if this is troublesome to you, do let me know on my talkpage. I try not to be unresponsive to concerns. --Ser Amantio di Nicolao^{Che dicono a Signa?}_{Lo dicono a Signa.} 22:29, 5 July 2021 (UTC)

@Ser Amantio di Nicolao: I think we all dropped the ball here by not notifying you - sorry. --Elmidae (talk · contribs) 00:02, 6 July 2021 (UTC)

@Elmidae: Quite alright - it happens. I've stopped for now, which is the main thing. --Ser Amantio di Nicolao^{Che dicono a Signa?}_{Lo dicono a Signa.} 00:14, 6 July 2021 (UTC)

I found an example of what Peter coxhead mentioned here. Velayinosu (talk) 00:55, 14 July 2021 (UTC)

Template-protected edit request on 21 July 2021

{{Don't edit this line {{{machine code|}}}
|rank=superordo
|parent=Dracohors
|link=Dinosaur|Dinosauria
|always_display=true
}}

Are you requesting to change the Dinosaur template rank to superordo? YorkshireExpat (talk) 21:59, 21 July 2021 (UTC)

"orphaned" taxonomy templates?

Is there an error/tracking category for taxonomy templates lacking a |parent= parameter? I deleted the whole line by accident, and when I caught it on preview it didn't have any big red error warnings. I can't remember how to do regex to get a list of how many templates may be affected, but was still curious. --awkwafaba (📥) 22:28, 7 September 2021 (UTC)

A search for taxonomy templates without |parent= finds 335 results. All these use |same as= (335 results with "same as" or no results without "same as") so are not errors. —  Jts1882 | talk  06:52, 8 September 2021 (UTC)

A different way to slice up progress on automated taxoboxes

I'm not trying to disparage the great statistical updates that @Plantdrew: provides (thanks for those, BTW). I like to divide up the mountain of unconverted taxoboxes different ways, partially to feel a little accomplished to complete mini-goals like getting all the taxoboxes in pages included in WikiProject Poland. Anyhoo, I came up with a couple of more useful lists, GAs with manual taxoboxes (156) and FAs with manual taxoboxes (27). It's a little depressing that these are not empty lists, as Good and Featured Articles are supposed to be of high quality, and usually that means an automated taxobox and not a manual one. I'll be hacking away at these, but just thought I'd mention it here if anyone is interested. --awkwafaba (📥) 23:18, 20 September 2021 (UTC)

@Awkwafaba: a very high proportion of the GA and especially the FA articles are fungi. Fungus taxonomy has been changing even more rapidly than many other groups (at least in my experience of trying to maintain a checklist website). Just as one example, Verpa bohemica has the accepted name Ptychoverpa bohemica in Mycobank. So it's not just a case of converting existing manual taxoboxes, but also of researching the taxonomy. Peter coxhead (talk) 07:52, 21 September 2021 (UTC)

Researching and updating taxonomy doesn't necessarily have to be part of the process of converting manual taxoboxes, but in practice, I treat it that way; if I notice the taxonomy is outdated, I often leave manual taxoboxes in place with the idea of coming back to them later.

I have some notes at User:Plantdrew/Animal automatic taxobox progress and User:Plantdrew/Plant automatic taxobox progress on groups with remaining manual taxoboxes.

I have previously done a little work (but not much) following akwafaba's approach of searching for FAs and GAs with manual taxoboxes. Another high impact approach would be searching for articles linked from a popular pages report; e.g. beetle have 297 manual taxoboxes among the 1000 most viewed articles (which shows that highly viewed articles are more likely to have an automatic taxobox than a beetle article chosen at random). Plantdrew (talk) 15:48, 21 September 2021 (UTC)

unusual ranks in taxonomy templates

{{Taxonomy/Dalbergioids}} and its parent, {{Taxonomy/Meso-Papilionoideae}} both have |rank= set as unranked_tribus. {{Taxonomy/ADA clade}} has rank as "cladus" ("clade" is more frequent). @Jts1882:'s taxonomy browser fails to pull up a taxonomy tree for these, apparently because of the unusual ranks. Is there any reason to support unranked ranks in taxonomy templates? This seems to be bleed-through from {{Anglicise rank}}'s support for unranked ranks in manual taxoboxes. And cladus/clade aren't being handled in the same way? Plantdrew (talk) 03:25, 26 August 2021 (UTC)

I would certainly change "unranked_tribus" to something else; probably "clade"/"cladus" is appropriate.

Within the automated taxobox system, as far as I know, "clade" and "cladus" are output in the same way. I guess that originally "cladus" was provided as an alternative because most ranks are Latin and it was consistent. However, whenever there's string matching involved, they will be handled differently. So, for example:

• {{#invoke:Autotaxobox|find |Xanthocercis |cladus}} → ADA clade
• {{#invoke:Autotaxobox|find |Xanthocercis |clade}} → Fabids

This may be what affects Jts1882's taxonomy browser.

It would certainly have been better to have standardized on one or the other, but is it worth doing now? Peter coxhead (talk) 07:13, 26 August 2021 (UTC)

(edit conflict)

The taxonomy browser defaults to strict mode (i.e. strict pattern matching in the searchs). If you select "All", {{Taxonomy/Meso-Papilionoideae}} has three children: tribes {{Taxonomy/Exostyleae}} and {{Taxonomy/Baphieae}} (both of which have child genera), and {{Taxonomy/Dalbergioids}} (which is empty). {{Taxonomy/ADA clade}} also has three children: {{Taxonomy/Angylocalyceae}}, {{Taxonomy/Amburaneae}} and {{Taxonomy/Dipterygeae}} (all with children). I suspect the hyphen and space in the taxon name are the problem (but can't remember the details of the script).

As for the question, the support is historical to indicate place in the hierarchy for unranked taxa for manual taxoboxes and presumably continued support made automatic taxobox conversion easier. There are only a few such taxonomy templates still using |rank=unranked-xxx (search insource:/rank *= *unranked_/). Many more use |rank=unranked (search insource:/rank *= *unranked/). —  Jts1882 | talk  07:20, 26 August 2021 (UTC)

Well, as a first step, converting all the "unranked ..." to just "unranked" seems sensible; it's all that will be displayed anyway. Done now; I found a couple of "unranked clade" that I converted to "clade". Peter coxhead (talk) 08:21, 26 August 2021 (UTC)

Returning to the question of "clade" vs. "cladus", I found 600+ vs. 93. Is it worth converting the 93? It could be done by a bot. Peter coxhead (talk) 08:27, 26 August 2021 (UTC)

I like consistency, but I'm not sure if it's more consistent to have cladus Latinized like the ranks, or leave it un-Latinized like the other supported values that aren't Linnaean ranks. I'm not sure about the value of having both "unranked" and "clad(e/us)" as options. Are there any unranked taxa at present that are not clades (there are certainly ranked taxa that aren't monophyletic clades). Plantdrew (talk) 00:12, 27 August 2021 (UTC)

@Benboy250: picking up your comment at Template talk:Taxonomy#Unranked vs Clade, the reason for both is the need to follow sources. If there's a source that says that a taxon is an unranked clade, then use "clade" (or "cladus") in the taxonomy template. If the source doesn't say it's a clade, then just use "unranked". I would expect the latter to be rare. Peter coxhead (talk) 16:07, 28 September 2021 (UTC)

I think that the distinction is useful. While we could used unranked for all, using clade carries additional information. This isn't necessary in a taxobox, but isn't likely to cause any confusion. —  Jts1882 | talk  06:32, 29 September 2021 (UTC)

Nil error handling

I made this change which fixes the script error when the mw.title.new('Taxonomy/'..taxon, 'Template') is nil. This should have zero impact on any non-script error transclusions. But, please revert and let me know if this causes a problem. Thanks! Plastikspork _―Œ^(talk) 15:35, 9 October 2021 (UTC)

@Plastikspork: Might have caused an error in test cases here? YorkshireExpat (talk) 19:29, 9 October 2021 (UTC)

@YorkshireExpat: no, that was caused by you moving two taxonomy templates to Category:Unnecessary taxonomy templates. Please check "What links here" before you do this; if you had you would have seen the use by the test case. I will look into changing the test case later. Peter coxhead (talk) 06:49, 10 October 2021 (UTC)

@Peter coxhead: Interesting, which moves caused this? Apart from the moth tribe I haven't moved anything lately (couple of weeks). Does this take a while to update? I always forget the "What links here"; a most useful thing! YorkshireExpat (talk) 07:38, 10 October 2021 (UTC)

@YorkshireExpat:Template:Taxonomy/Norovirus GII.4 Sydney and Template:Taxonomy/Norwalk virus, changed on 25 August! Yes, changes to taxonomy templates can take a very long while to propagate through Wikipedia; it was may have been prompted by Plastikspork accessing the test cases page – I suspect that such pages are given a very low priority for updating. Peter coxhead (talk) 08:32, 10 October 2021 (UTC)