User talk:Peter coxhead

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Plant article naming convention[edit]

Hi Peter coxhead. There is a plant article naming convention request at the Help Desk. I saw your name listed at Naming_conventions_(flora) contributions and am hoping you would post your thoughts at How long does speedy deletion usually take?.[1] I asked Pmanderson on the Pmanderson talk page, but not sure if she/he will see the request. Thanks. --

tetrahedronX7[edit]

Hey thank you for editing . My friend

Are clades ranks or not[edit]

Hi Peter, could you please have a look at this discussion. Dwergenpaartje (talk) 17:15, 26 October 2016 (UTC)

Good answer there. I had not seen that discussion, but the question was on my mind for MOS:ORGANISMS purposes. I would still like to advance that to guideline. The only likely hitch is the breed capitalisation thing; I am thinking of going with the "capitalise formal breed names" version and excising the "lower-case it all" version, since the former represents current practice here, for the most part, and MOS:LIFE was carefully written to avoid the issue entirely. Maybe labeling the former a de facto consensus that has seen some controversy, and leave it at that, pending anyone actually launching an RfC about the matter. After the bird-caps fiasco, I've discouraged people from doing this (heading off RfCs about it twice). If one arose now, I would not resist it because enough time has probably passed that the "life forms and capitalisation" issue fatigue has worn off; but I would not relish it. Anyway, that guideline draft is well-researched, and has sat around for years with nearly zero controversy otherwise.
That said, I suppose the nit-pick question is still potentially open: Could a formal clade name (which the examples in that discussion were not) be used as a subgeneric taxon, in Genus_name clade_name order? I would think yes. Would that make the latter a subgeneric rank subject to italicization? I suspect not. I think it would be non-italicized, like a cultivar name and various other non-ranks. Maybe there's an abbreviation that is used in front of it? This isn't a point I've looked into. Clades may be the only missing item in MOS:ORGANISMS WP needs to care about.  — SMcCandlish ¢ ≽ʌⱷ҅ʌ≼  09:26, 28 November 2016 (UTC)
@SMcCandlish: well, under the nomenclature codes, only the allowed ranks can be used, so a name like Genus_name clade_name would be totally outside their purview. If the PhyloCode ever became widely accepted, which seems no more likely now than it has since it appeared, it italicizes all clade names, and suggests (in Article 21) various ways of distinguishing between species names under the codes and species names under the PhyloCode, e.g. Discodorididae|Diaulula|sandiegensis shows that the species [R]Diaulula sandiegensis belongs to the clades Discodorididae, Diaulula and sandiegensis (the [R] being one way of showing that a rank-based name is being used). So if Genus_name clade_name is meant to show two clades, then it could be written Genus_name|clade_name; however, almost no-one actually does this in reliable sources, so it would be wrong here. If Genus_name clade_name meant to show an informal (i.e. not rank-based) group within a rank-based genus, then it's outside any code, and I would recommend what I wrote before, namely not italicizing the clade name, as we consistently don't for clades at whatever level, but italicizing the genus name, i.e. Genus_name clade_name. I think we agree on this.
There are various problems coming up as clade-based approaches spread, since there is a need to make clear when a name is meant as a formal rank and when it's a clade name, not least because the ending of the name has a meaning in the former case but not in the latter. This recently arose over "Euphyllophyta". If this is a name under the ICN, then it has to be a division/phylum. If you want to lower the position of the group but still use an ICN name, then the ending has to change, e.g. "Euphyllophytina" for a subdivision/subphylum. But many authors seem to be using either name as a clade name, with no rank implication. The most neutral position at present, given that there's no consensus in the literature over whether to use a clade or a rank name, or the rank to be used in latter case, seemed to be to use the informal, "English" name "euphyllophyte".
The nomenclature of higher-level taxa is a complete muddle in reliable sources at present, which makes it hard to know what to do. Recently we've seen a new editor going around trying to impose one particular recent view of the higher levels of plant taxonomy, but this is clearly a POV. Giving every single possible clade a name, as the dinosaur people seem to do, (a) is unhelpful to readers – who can remember what all the clades are? (b) screws up the automated taxobox system by making the hierarchy too deep. Sigh... Peter coxhead (talk) 11:35, 28 November 2016 (UTC)
Big worm-can then. Your "not italicizing the clade name, as we consistently don't for clades at whatever level, but italicizing the genus name" seems reasonable. We could include a footnote that PhyloCode would italicize all clade names, but has not been widely adopted, and WP does not follow it since most RS don't, and the usage will be confusing to readers.  — SMcCandlish ¢ ≽ʌⱷ҅ʌ≼  22:46, 28 November 2016 (UTC)

Excavata colours[edit]

Speaking of hardcoded colours...the taxoboxes that contain unranked_regnum = [[Excavata]] are all hardcoded with RGB(250,250,100), because automatic colour selection doesn't work with that clade. I'm afraid I inserted a lot of those codes myself, because it seemed better than retaining the spurious Kingdom Excavata. If you were to adapt Template:Taxobox colour to seek colours for unranked_regnum = [[Excavata]] I could pull out all those hardcoded yellows, if you like. Unfortunately, Excavata's monophyly is in doubt, so perhaps it makes sense to wait, before going to the trouble?  Deuterostome  (Talk) 19:16, 1 November 2016 (UTC)

@Deuterostome: I just removed the hard-coded colour at Euglenozoa, and it still works fine. Can you tell me where |unranked_regnum=[[Excavata]] doesn't work? Of course, it's possible that some of the changes I've been making over the last couple of days have fixed something that wasn't working before. The entire taxobox colour template code is a maintenance nightmare! Peter coxhead (talk) 19:32, 1 November 2016 (UTC)
You're right! I tried it on a half dozen pages, and it worked perfectly. I definitely tested it a couple of days ago, before making a few dozen edits; so, either I made a mistake when testing, or the template has mysteriously healed itself. :D I'll extract the Excavata codes, when I have time (probably tomorrow). I'll take care of the "greenyellow" infestation in SAR pages, too, but that'll take a bit longer. There are well over a thousand articles to review.  Deuterostome  (Talk) 20:54, 1 November 2016 (UTC)
Considering the time I've spent on it, I doubt that it "healed itself"! :-) Anyway, we seem to be making progress. Let me know if you find any taxoboxes that should generate the right colour, but don't. Peter coxhead (talk) 21:00, 1 November 2016 (UTC)
Huh, I thought those rattling, whistling, wheel-and-chain-driven templates sort of maintained themselves. :p I pulled out the Excavata colors, and nothing spooky happened. Excavata itself might be going out of business, but that's a problem for another day.  Deuterostome  (Talk) 12:10, 2 November 2016 (UTC)

Liriope (genus)[edit]

Could you please move Liriope (genus) to Liriope (plant)? There's also a genus Liriope (jellyfish), so (genus) isn't sufficient disambiguation.

Yes check.svg Done Peter coxhead (talk) 08:53, 2 November 2016 (UTC)

There's a little complication with it being the exemplar at {{Speciesbox/doc}} of a taxonomy template that doesn't need to be disambiguated even though the parent article requires it. I'm not quite sure what should happen {{Taxonomy/Liriope}}; move and take the redirect RfD? Delete by moving without leaving a redirect (is that kosher?)?

I'd suggest Cancer (genus) as the new exemplar for the speciesbox documentation, if it's desirable to have an exemplar that uses "(genus)" as a dab term. Cancer (crab) is potentially ambiguous with astronomy/astrology topics, so I doubt that there's any chance the genus will ever take a different dab term. The only problem is, it's not using an autotaxobox. I'm not aware of any great candidate exemplars that do currently use an automatic taxobox (Asparagus (genus) is the best I can think of, but would require a little rewording of the speciesbox documention). Plantdrew (talk) 02:51, 2 November 2016 (UTC)

I took out the example at {{Speciesbox/doc}} for the present.
The question, I think, is whether both the taxonomy templates for the plant and jellyfish genera need disambiguation.
  • There's no problem with having an article at "X (plant)" and the taxonomy template at "Template:Taxonomy/X" if the need to differentiate X arises from non-genera, as was the case with Liriope.
  • There's no need to differentiate all uses of X in articles; if one is clearly the main use, it goes at "X", and the rest have disambiguation terms added to their titles.
So if one use of X as a genus name is clearly main, I don't see why the taxonomy templates shouldn't be at "Template:Taxonomy/X" for the main genus use and "Template:Taxonomy/X (y)" for the secondary genus use. It's certainly the case for Liriope that plant is well-known in gardens and the jellyfish genus has only one species, so as a genus name, "Liriope" has its main use for the plant. Hence I would keep Template:Taxonomy/Liriope for the plant, and use Template:Taxonomy/Liriope (jellyfish) for the other. Peter coxhead (talk) 09:27, 2 November 2016 (UTC)
OK, sounds reasonable about the template. Is that also your reasoning for leaving Lirope (genus) pointing to the plant and not the dab page? To me, that undermines the point of moving in the first place (especially when the other dab rcat template says that the redirect is not an incomplete disambiguation). Plantdrew (talk) 16:43, 2 November 2016 (UTC)
No, that was an mistake: it's become too automatic after an article/redirect swap to change the redirect to point to the article. Corrected now. Please check that the Rcat is correct. Peter coxhead (talk) 17:07, 2 November 2016 (UTC)

Cryptists & Archaeplastida[edit]

Curious to know your source (am I falling behind? ;)). Burki et al, 2016 drops them into the middle Archaeplastida, sister to green algae & land plants, with rhodophytes basal to both groups. Deuterostome  (Talk) 10:34, 3 November 2016 (UTC)

Yes, I realize that my edit summaries weren't quite right, although I'm doubtful that we can take Burki et al. (2016) as definitive, given that other papers since 2014 reach different conclusions. But by all means put them elsewhere if you think it's justified. The real point as that they aren't "incertae sedis" and shouldn't be treated as such, since at the very least they are eukaryotes. Peter coxhead (talk) 10:42, 3 November 2016 (UTC)
@Deuterostome: to be clear, I'm taking a conservative view: unless the article clearly has another 'colour determining taxon' in the taxobox, I'm just treating it as a eukaryote. Other editors are free to assign more specific colours; hopefully later this will all be automated. Peter coxhead (talk) 11:00, 3 November 2016 (UTC)
I agree with that approach, and consider it wise not to shuffle taxa about every time a new phylogeny is proposed. I have no problem with restricting use of incertae sedis, and using Eukaryota as the colour. In coming years, we're going to see lots of new eukaryotes of uncertain affinity (a friend has a lab full of undescribed kingdom-level critters, just waiting to mess up Wiki's templates!), and we'll need somewhere to stick them until taxonomy can catch its breath. :D  Deuterostome  (Talk) 11:27, 3 November 2016 (UTC)
I guess the deeper question is "What are the taxobox colours for?" The answer has to involve readers, rather than editors. I strongly suspect that readers would have been better served by treating all single-celled eukaryotes ("protists") as a grade with a single taxobox colour (at most separating out green algae); only experts are going to be interested in the subgroups of this grade, and they don't need colours anyway, since they will recognize the names (well, they will if they read every latest paper!). However, we are where we are, and I think that the approach I've taken works adequately and seems to be supported by those who have commented so far. It certainly accommodates extra "kingdoms" without resorting to incertae sedis. Peter coxhead (talk) 11:36, 3 November 2016 (UTC)
Re. "what are the taxobox colours for," it's a good question. To be honest, I don't have an answer. German Wikipedia gets along without them (and the taxonomy there is generally pretty good). Other countries use the colours in a variety of ways, and the results are generally quite inconsistent. French Wikipedia, to take one example, uses colour to differentiate "algae" from "protists", but criteria are unclear, and the application is capricious (the heterotrophic Astasia is considered "algae," for instance; the photosynthetic rhizarian chlorarachniophytes are also considered algae, but Rhizaria itself has the protist colour, etc). Any colour system is inevitably going to divide clades at some place in the tree.  Deuterostome  (Talk) 13:07, 5 November 2016 (UTC)

Veratrum[edit]

Hello --

I don't want an edit war but I challenge your simply deleting an edit I made on Veratrum instead of improving on it. I see how I might further clarify my addition but not if you are just going to again delete it.

Veratrum is in the article described as being a member of the "corn lily" family. My addition "The corn lily family -- distantly related to true lilies -- also includes Beargrass and Deathcamas." is both descriptive and correct. I made this change because the earlier version with its comment about them not resembling lilies is confusing. They do not much look like true lilies, true, and they don't much look like hellebores. But they very much look like other corn lilies, some of which also are toxic.

Before I made this change I added a lengthy explanation in Talk:Veratrum to which you could have (and did not) respond to. If it matters, I have worked in hort and landscaping for over 25 years. I have my own web pages but opt to not publish that on my Wikipedia page -- it would not be that useful in this discussion anyway.

Thanks GeeBee60 (talk) 17:07, 10 November 2016 (UTC)

Sorry for not commenting on the talk page – I've been very busy working in another area of Wikipedia. I still can't see that the addition is helpful in an article about the genus – sure, explain why the genus has its English names, but why mention beargrass and deathcamas? Peter coxhead (talk) 22:35, 10 November 2016 (UTC)

Flower[edit]

Why is there a taxobox on the Flower article? --EncycloPetey (talk) 16:18, 18 November 2016 (UTC)

I agree there shouldn't be; I was just fixing the one that was there. I've made major changes to the taxobox code recently (see Template talk:Automatic taxobox#Major rewrite of the colour setting system and Template talk:Taxobox#Update to taxobox colour setting), which have had the side-effect of making strange taxoboxes show up in error-tracking categories. Mostly I've just been rapidly fixing taxoboxes so they don't generate errors, rather than, in most cases, having the time to stop and look more carefully into the issues. Glad you did! Peter coxhead (talk) 16:30, 18 November 2016 (UTC)

A barnstar for you[edit]

Blueprint Barnstar 2.PNG The Template Barnstar
For all your work improving taxobox templates Plantdrew (talk) 18:25, 19 November 2016 (UTC)
Well deserved! Thanks for all the work, Peter.  Deuterostome  (Talk) 20:24, 19 November 2016 (UTC)

@Plantdrew and Deuterostome: I was reluctant to accept thanks for this work until I knew that it could actually be finished, i.e. extended to all the automated taxonomy templates. Since the less-used ones, like {{Infraspeciesbox}}, actually do more processing, it wasn't guaranteed that they would work with the changed approach to setting taxobox colour. However, I updated the last one today, and they all seem to work. So thanks for your appreciation! Peter coxhead (talk) 18:13, 23 November 2016 (UTC)

<clap clap> Looks like it was quite a chore.  — SMcCandlish ¢ ≽ʌⱷ҅ʌ≼  07:16, 28 November 2016 (UTC)
@SMcCandlish: thanks for the appreciation. Yes, it was a chore, although there was a considerable sense of achievement once I'd got it to work. I need to write up what I've learnt about using the template language in a way that minimizes expansion depth in relation to the number of levels of the taxonomic hierarchy that can be traversed. I still don't totally understand how the Wikimedia software counts expansion depth (the explanation given at m:Help:Expansion depth is not exactly well written), but I do now know, partly by understanding and partly by experiment, how to optimize the coding. However, the whole automated taxobox system is very fragile; many pages (like Pteranodon) are at the absolute limit of expansion depth. Peter coxhead (talk) 07:44, 28 November 2016 (UTC)

ArbCom Elections 2016: Voting now open![edit]

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World spider catalog[edit]

Sorry, i have no idea how to correctly communicate to another user through wiki!

You undid a change i made on a spider page (genus Davus) saying they were 'accepted' in the world spider catalog. That site doesn't not 'accept' or 'deny' anything for taxonomy, it's merely a listing of proposed changes that have been published. Another person/group could equally make another catalog with a different set of proposed taxa listed, differing if they choose to ignore/omit some proposals. Neither of these catalogs would be a definitive 'accepted' version. — Preceding unsigned comment added by Sjl197 (talkcontribs) 01:26, 22 November 2016 (UTC)

@Sjl197: sorry, I didn't notice your post at first because of its placement. There's a lot to learn here! Put comments to users on their talk page, at the bottom.
I agree that choosing the word to use is tricky. However, 'list' clearly isn't right, because the WSC lists all sorts of names: it lists synonyms, for example. The WSC doesn't just list proposals as you say. Its editors make judgements: see e.g. here and the entries for the species involved, e.g. Selenocosmia arndsti. For another example, see Malaridae where there is the comment "Synonymy of the type genus Malkara with Perissopmeros (Murphy & Roberts, 2015: viii) not sufficiently justified and is not accepted here". So the entries in the WSC clearly do involve some degree of 'acceptance'. Peter coxhead (talk) 21:22, 22 November 2016 (UTC)
@Peter coxhead: Absolutely, i'm just learning how to work with Wiki once in a while, so apologies when i get editing stuff wrong! On the issues, i understand your points, and agree their editors at times make judgments, such as those examples. Firstly, though they're not judging per se on the 'taxonomic reality' (i.e. natural groupings), they largely seem to 'judge' on whether a published proposal is sufficiently justified or not for them to warrant updating it in their catalog (or not). Perhaps you're using the term 'accepted' as equivalent to 'preferred current usage'. If so, i think many would agree with you, but i would not. In one of those links, the WSC says "(T to and resurrection of Chilocosmia as opinion, not accepted here)". The critical part of wording I see as vital to consider is the word 'here'. The WSC is what is says it is, a catalog. There have been plenty of other catalogs before them too, i.e. Brignoli, Roewer, Petrunkevitch etc. None of these were authoritative statements on what is 'accepted' per-se in the sense that i worry you might be using, or more importantly perhaps as wiki readers might interpret. Each catalog indeed has/had judgments, each indeed has/had some proposals 'accepted' or not into each catalog. But my point being that none of them are/were in any way definitive (i.e. = 'preferred current usage'). What i was was trying to say before was that other authors or editors can equally make another listing, and it would be no more of ' 'preferred current usage' than WSC is. And this indeed happened with past catalogs which contradict one another. Another way to see that WSC is not definitive I expect could be shown in future by Dr. Gunter Schmidt, if he does 'publish' again on those (heaven forbid, as some of his works are dire), when i expect he'd write the name combination again as Chilocosima arndsti. This would equally ignore/conflict against the 'opinion' of those editors at the WSC! So, in essence, what i'm saying it that - i can 'accept' that technically you can be correct in saying 'accepted by the WSC' (or in exact wording you put with "the World Spider Catalog accepted the following species") but i'd strongly prefer it if you'd avoid the term 'accepted' altogether. So instead to say something like "is LISTED by them" to entirely avoid misunderstanding between 'accepted by them (and perhaps only them)' versus 'widely accepted =preferred current usage'. The essence being that the WSC editors are NOT a taxonomic authority, but editors of a catalog which lists names (inc. synonyms, which are also valid names). It gets to a wider problem that i'm a bit concerned you're trying to make Wiki pages FIT with the WSC as THE definitive source/reference.
@Sjl197: if we wrote "the accepted species are:" or "the species are:" this would be absolutely wrong, for the reasons you give. That's why we write "The World Spider Catalog accepts:" or (for plants) "The World Checklist of Selected Plant Families accepts:". It's their opinion, their judgement. If there are other opinions in reliable sources, other judgements, then they should of course be covered in the article; Wikipedia adopts a neutral point of view.
The places where we just have to pick one point of view are (1) the article title (2) the taxobox. Articles can only have one title; taxoboxes, by their nature, can only show one particular taxonomy. So in those I would virtually always use the WSC – not because it's especially authoritative but because it's virtually complete, and therefore consistent. If we tried to use names/classifications from different sources in article titles and taxoboxes we'd end up with a hopeless muddle. But the text must always show other opinions, so long as these are found in reliable sources of a comparable age (i.e. are not out-of-date).
I can only repeat that "list" is wrong: the WSC doesn't just "list" all names neutrally, regardless of their status. It treats some as its accepted names and others as (junior) synonyms: as soon as you list a name as a synonym you make a judgement as to the 'correct' name. The WSC makes judgements.
The problem with concepts like "widely accepted" or "preferred current usage" is it's difficult or impossible to source them. All we can do is to say what names are accepted by what sources, which is what we should do.
It's also worth pointing out that the purpose of a list of species in a genus article is to provide links to Wikipedia articles; purely by itself the list itself is not encyclopedic. Peter coxhead (talk) 22:44, 22 November 2016 (UTC)

Sarcopterygii in automatic taxoboxes[edit]

At Kenichthys (among other Tetrapodomorpha articles) where Sarcopterygii ought to display as a class, it's absent, since it's been skipped in the taxonomy template hierarchy. I understand why that's done, but I don't understand why the result is different than with other paraphyletic groups treated as classes (reptiles). I'm guessing maybe the bird and reptile hierachies maybe fork at some point (perhaps with a parent in the reptile hierarchy that's not included in the bird hierarchy). Is there an easy way to get Sarcopterygii displaying as a class for basal tetrapodomorphs? Plantdrew (talk) 02:03, 5 December 2016 (UTC)

The problem is with knowing what the side-effects would be. As I'm sure you understand, there are two reasons why skip templates have been inserted. The first reason is to shorten taxonomic hierarchies to avoid expansion depth problems. If this is the reason, we can just move the skip a level higher. There are possible longer term solutions, including perhaps recoding parts in Lua. The second reason is to avoid two classes showing up because of very different approaches to classification, as happened with birds. If this is the reason, then it needs quite a bit of investigation. Here the deep underlying reason is that any automated taxobox system has to assume a single agreed classification to work properly, and for vertebrates, there just isn't one. The only real solution I can see would be to have taxonomy templates of the form "Template:Taxonomy/taxon/system", and then different WikiProjects could adopt different systems.
I have limited access/time for the next couple of days, but I'll try to get back to this. Peter coxhead (talk) 08:05, 5 December 2016 (UTC)
@Plantdrew: motivated by the work that Jts1882 has been doing in converting {{Clade}} and {{Cladex}} to Lua, I looked at re-writing some of the core parts of the automated taxobox system in Lua. It took me about 20 minutes to knock up a Lua version of what took me 30-40 hours in the template language – and this was the first time I'd programmed in Lua. As far as I can see, there's no problem in traversing at least 100 levels of the taxonomic hierarchy in Lua. So, my first step is to complete some of this work and include it in the automated taxobox system. Then those skip templates and hard-coded levels needed at present to deal with the expansion depth problem can go, I believe. That should make it much easier to see what skips are actually needed to deal with different classifications. Peter coxhead (talk) 22:48, 7 December 2016 (UTC)
Fantastic news! Plantdrew (talk) 22:54, 7 December 2016 (UTC)
@Plantdrew: I've now deployed the first bit of Lua coding in {{Automatic taxobox}}. It reduces the expansion depth of Pteranodon (the worst case I know of) from the absolute maximum of 40 down to 33. More to come. I hope this won't be a green light for dinosaur editors to add yet more clades! Peter coxhead (talk) 08:53, 8 December 2016 (UTC)
Great. I did ask if there was an "easy way to get Sarcopterygii displaying". Rewriting the taxobox in Lua wasn't exactly what I had in mind as "easy", but if you want to take that on, more power to you. Plantdrew (talk) 17:06, 8 December 2016 (UTC)
@Plantdrew: actually I'm feeling stupid that I didn't do this before (I'm only going to convert those key parts of the automated taxobox system that traverse the taxonomic hierarchy, which is where the problems arise). Not all done yet, so avoiding skip templates would still cause problems. The relevance to your original question can be seen by comparing Template:Taxonomy/Rhipidistia/skip and Template:Taxonomy/Rhipidistia. I think that Sarcopterygii disappears because it was necessary to link to the former rather than the latter to reduce expansion depth. If the expansion depth issue can be fixed, and I now think it can, then we can remove all the skip templates except those necessary to avoid duplicate class ranks, etc.
If a short-term fix is important, it should be ok to go Tetrapodomorpha → Rhipidistia → Sarcopterygii/skip → Vertebrata instead of Tetrapodomorpha → Rhipidistia/skip → Vertebrata, but it's always a matter of trying it and seeing what happens.
The automated taxobox system traverses the taxonomic hierarchy in three distinct places. I've coded one of them in Lua (determining taxobox colour, which is happens first). On to the next two, but it will take several days to code and test. Peter coxhead (talk) 17:41, 8 December 2016 (UTC)