A day in the life of Planet

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Jools
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Re: A day in the life of Planet

Post by Jools »

Thank you!

The last couple of weeks have been full on at work. I work at a group level and oversee five companies, one of them is not doing very well so I will step in to lead a recovery team for the next 10 months. I typically work on Planet in the early morning, but this new role means I've been travelling at that time. However, this week I only have a day trip to Manchester, so some progress has been made.

In the few hours I got to work on the site since last I posted in this thread and now, I've been working on the data submission and vetting pages. What used to happen is a authorised user would submit new data for a species, then, at the point I vetted it, the latitude and longitude co-ordinates of the type locality would be calculated.

This was done without any oversight, it just happened in the background and has led to a number of odd occurrences of species usually due to an incorrectly written set of co-ordinates in the source material. To address this, I've moved the calculation "up" a level so that it is done at the submission stage, furthermore, a map if available to me on the vetting page so I can readily "see" errors.

The mapping code is complex, needing a decent grasp of PHP, SQL and JavaScript, it's now working but I think will need a few things to be changed. Perhaps having a map on the data submission page would be a good idea.

I also think that, soon, I will replace the "click on the map icon" layout of the species pages and just show the map, or at least a small one, by default.

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Re: A day in the life of Planet

Post by Jools »

While the co-ords fix is quite high on the "TODO" list that is my inbox, when a bug comes along that removes data, it goes right to the top of the list. How many of you are familiar with the "variants" function on the species page? The classic example is in the and in catfish terms the "species" with the most is . If variants exist, you get a dropdown box to the right of the species name.

What had happened was whenever an adm,in re-ordered or edited the images on a particular species, then all variant info for all those images was lost. Offski. Nuked. Gone. Forever.

The bug was introduced when we added some refactored a lot of the admin code. So, after about a weeks work (mostly testing and investigation), the issue is fixed and also I've tidied up that admin page and the admin function that moves or renames a species too.

You, dear end user, will not notice much difference unless some kind admin like @Bekateen or @MatsP actually goes back in and adds back the data. But, at least, we've stopped the rot.

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Re: A day in the life of Planet

Post by bekateen »

Thanks Jools. I had no idea the "variants" were even working with images yet. I've tried multiple times in past to associate existing photos of albino BN with the variant page, but nothing happened with I pressed the "Do It" button. Likewise for the black . Does your fix mean that now we can assign existing photos from a species CLOG page to a variant and the photos will move too? (Why am I asking... I'll just go give it a try with the C. schultzei. LOL)

Thanks again, as always.
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Re: A day in the life of Planet

Post by bekateen »

Okay, I tested it with melanized . I have a few observations and a question:
  1. The function now works - I moved a few photos of melanized C. schultzei into the "black" variant category and they now load with the variant page. YAY! \:d/ :-BD ^:)^
    AND
  2. If you (as a member or guest) visit the species CLOG page and select the variant, all the variant photos appear on the variant's sub-page (I'm not sure what else to call it... the variant-specific CLOG page?).
    BUT
  3. If you click on any one of the photos of the variant from the variant page, and then click the "Next Image" link, you are not transferred to the next photo of the specific variant; but rather, you are transferred to the next photo of the species as displayed on its home CLOG page (not the variant page), regardless of whether that next photo is of the same variant or of the wild-type or a different variant.
    AND
  4. When using the EDIT OR RE-ORDER PHOTOS link as an admin, the editing page has no institutional memory of which photos have previously been assigned to a particular variant. So for example, what if I move 4 schultzei photos to the black variant page and then realize that I missed another photo that should also get moved? If I go back to edit the photos and assign the missed picture to the variant, then I also have to re-assign all the other variant photos too, or else they will be "forgotten" and moved back to the main CLOG page for the species.
    FINALLY, a question:
  5. I didn't want to mess things up, so I did not attempt to assign any pictures labeled "DON'T REPLACE OR MOVE PLEASE!;" but I wondered if they can be safely assigned to a variant without screwing up or losing their association with articles in Shane's World or in COTM.
Sorry, Jools. X_X :YMHUG:

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Re: A day in the life of Planet

Post by MatsP »

It should be safe to assign variants to all pictures. The "do not move this image" relates to articles that link to the image - the image link is not changed by the variant information, it is just used to select which images to show when selecting a specific variant (and if you "don't set it") the image will just show up in "no variant selected" view [which is the default when you go to a species page].

Article links use the image number within the species, so something like /Ancistrus/cf_cirrhosus/3.jpg [this is not EXACTLY how it works, but sufficient for this discussion]. So say that this picture is showing the mouth of a regular brown Ancistrus, and I move it around, because I think picture three would be better showing a picture of the dorsal fin of an albino instead. Then the picture in the article will also now show the dorsal on an albino, which perhaps doesn't match the text about "in the picture we can see the scraping plates in the mouth that Ancistrus use to collect aufwuchs from rocks and stones".

The actual problem is that there isn't a good association between article images and the species pages they occur on - there's just a field saying "used in some article" in the database.

--
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Re: A day in the life of Planet

Post by bekateen »

Thanks for that explanation, Mats.

Cheers, Eric
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Re: A day in the life of Planet

Post by Jools »

It might not seem like it would take this much but after about 16 hours of work, I've got all the "free to view" Catfish Study Group back issues of the Journal online at the CSG site and also linked here in a Shane's World article. Link below:

https://www.planetcatfish.com/shaneswor ... p+Journals

That's a LOT of catfish info now online (https!), searchable (by google and internally) and preserved for as long as Planet or the CSG lasts. The time was taken extracting all articles and authors, getting them into chronologycal order and getting the front cover pics online. Been meaning to do this for three year. :-)

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Re: A day in the life of Planet

Post by lfinley58 »

Hi Jools,
Thanks for the large amount of work on this project! There is plenty of outstanding reading for all concerned and is a great plus for PC (and the CSG, no doubt, as some will want to get access to the issues that are not free for view. This is definitely a top of the line world class publication).
One observation (not a complaint): the first four issues displayed on PC (and the same ones on the CSG site) have a pop-up asking for a password. Just for interest I tried my PC password and it didn't work on any of the four.

Thanks again for the heavy shouldering of this project.
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Re: A day in the life of Planet

Post by Jools »

Hi Lee,

Great spot! The last few journals (they are big files) had not uploaded cleanly (so the old password ones were still in effect) and indeed the last few indexed issues did not have the authors added. All done now so they should be fully up-to-date! I quite enjoy this sort of thing - just wish I had more time to do more.

Cheers,

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Re: A day in the life of Planet

Post by Jools »

I've been pushing on with the wishlist and catfish spotter features of late but I thought I should quickly mention that the occurrence maps have now been updated to use the latest google maps API and they render in "terrain" mode now which I think is a little more useful for the fishkeeper.

Cheers,

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Re: A day in the life of Planet

Post by Jools »

Sadly I no longer have access to the digital versions of the CSG Journal, so I guess I'll just ensure that what's there historically remains available but a lot of it is out of my control now (if it ever was in my control! :) ).

Since last posting I've been gnawing over what to do about the CotM feature. Now I probably have enough time to write about one species per month I have the twin challenges of (a) I'm running out of species I've kept and (b) what to do with the not inconsiderable gap. My OCD tells me I've got to fill the missing articles but I recognise that if I just start it up again then there a not that many that it'll really matter to (expect me).

I have been doing a lot of finishing of things left half done. For example, the "wishlist" and "spotter" features are fully functional and working. No bugs that I can see and they seem to be used well.

Over the summer I've done a LOT of behind the scenes upgrade stuff. Everything from our database, the forum software, and the other operating system / deeper technologies have been upgraded to latest production versions. The internet is a wonderful place, but these days you can't leave your front door unlocked and ensure everything is on latest versions and so forth at least means you're not the easiest target on the street. This has been done across ARN, so Planet, aquaticrepublic.com and zebrapleco.com all upgraded.

During and after an unusually long and very pleasant summer holiday I've been looking at a bunch of taxa that were out-of-date. There were a few duplicated species (where we had species entries for both what is now a junior synonym and a the valid species itself). I spent a lot of time learning new cichlid and cyprinid genera! We are now left with a few catfish species which I am finding it "emotionally" difficult to change.

These are:
Valid name=Corydoras britskii, clog name=Brochis britskii.
Valid name=Corydoras multiradiatus, clog name=Brochis multiradiatus.
Valid name=Corydoras splendens, clog name=Brochis splendens.
Valid name=Pterygoplichthys punctatus, clog name=Ancistrus punctatus.
Valid name=Synodontis batensoda, clog name=Brachysynodontis batensoda.
Valid name=Wallago micropogon, clog name=Wallagonia micropogon.
Valid name=Dolichancistrus cobrensis, clog name=Dolichancistrus pediculatus.
Valid name=Parauchenoglanis monkei, clog name=Parauchenoglanis guttatus.
Valid name=Pterygoplichthys disjunctivus, clog name=Pterygoplichthys anisitsi.
Valid name=Rhamdia voulezi, clog name=Rhamdia argentina.
Valid name=Synodontis xiphias, clog name=Synodontis gambiensis.
Valid name=Synodontis membranaceus, clog name=Hemisynodontis membranacea.
Valid name=Wallago micropogon, clog name=Wallagonia leerii.

Each one needs a little or a lot of research, some I've simply not changed as I'm irrationally attached to the genus (Brochis, Hemisynodontis) and others I don't understand (e.g. Wallago). So, going to work through these in the near future.

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Re: A day in the life of Planet

Post by bekateen »

Jools, where would this site be without your ongoing diligence. Thank you for all you do.
Jools wrote: 28 Aug 2019, 16:28Since last posting I've been gnawing over what to do about the CotM feature. Now I probably have enough time to write about one species per month I have the twin challenges of (a) I'm running out of species I've kept and (b) what to do with the not inconsiderable gap. My OCD tells me I've got to fill the missing articles but I recognise that if I just start it up again then there a not that many that it'll really matter to (expect me).
My two cents (which is worth less than the metal in the coins) is to (for now) let the empty dates slide. If you can keep an ongoing COTM, use the current months for now and back date only when you have cause. From reviewing old COTMs, it's evident you used to have a lot of help from other contributors. I can speak for myself and acknowledge that I too have a few half done, but with work see no immediate completion date on the horizon. Just do what you can and don't let OCD get you off focus.
Jools wrote: 28 Aug 2019, 16:28During and after an unusually long and very pleasant summer holiday I've been looking at a bunch of taxa that were out-of-date. There were a few duplicated species (where we had species entries for both what is now a junior synonym and a the valid species itself). I spent a lot of time learning new cichlid and cyprinid genera! We are now left with a few catfish species which I am finding it "emotionally" difficult to change.

These are:
Valid name=Corydoras britskii, clog name=Brochis britskii.
Valid name=Corydoras multiradiatus, clog name=Brochis multiradiatus.
Valid name=Corydoras splendens, clog name=Brochis splendens.
Valid name=Pterygoplichthys punctatus, clog name=Ancistrus punctatus.
Valid name=Synodontis batensoda, clog name=Brachysynodontis batensoda.
Valid name=Wallago micropogon, clog name=Wallagonia micropogon.
Valid name=Dolichancistrus cobrensis, clog name=Dolichancistrus pediculatus.
Valid name=Parauchenoglanis monkei, clog name=Parauchenoglanis guttatus.
Valid name=Pterygoplichthys disjunctivus, clog name=Pterygoplichthys anisitsi.
Valid name=Rhamdia voulezi, clog name=Rhamdia argentina.
Valid name=Synodontis xiphias, clog name=Synodontis gambiensis.
Valid name=Synodontis membranaceus, clog name=Hemisynodontis membranacea.
Valid name=Wallago micropogon, clog name=Wallagonia leerii.

Each one needs a little or a lot of research, some I've simply not changed as I'm irrationally attached to the genus (Brochis, Hemisynodontis) and others I don't understand (e.g. Wallago). So, going to work through these in the near future.
  • Valid name=Corydoras britskii, clog name=Brochis britskii.
  • Valid name=Corydoras multiradiatus, clog name=Brochis multiradiatus.
  • Valid name=Corydoras splendens, clog name=Brochis splendens.
    • From the writings of Alexandrou and others a few years ago, I imagine the entire Corydoradinae will be blown up to 9 genera. So for now, I'd advise leaving Brochis as is. If you add Corydoras (and the species names) as synonyms, I'd think you're fine for now. People will find them either way.
  • Valid name=Pterygoplichthys punctatus, clog name=Ancistrus punctatus.
    • According to Eschmeyer's CoF, these are distinct. P. punctatus is valid. A. punctatus is a synonym of . But as with , and , there may be details hobbyists notice that scientists either overlook or disregard. So whether indeed A. punctatus = A. hoplogenys, I'm not fit to determine, having never kept either. But A. punctatus is not to be synonymized with P. punctatus.
  • Valid name=Synodontis batensoda, clog name=Brachysynodontis batensoda.
  • Valid name=Synodontis membranaceus, clog name=Hemisynodontis membranacea. (I moved this entry in your list to align with my follow-up):
    • Not sure if this helps, but there's this old post from the forum:
      Borbi wrote: 23 Jul 2010, 12:47 Pinton, A., Otero, O., The bony anatomy of Chadian Synodontis (Osteichthyes, Teleostei, Siluriformes, Mochokidae): interspecific variations and specific characters, Zoosystema, 2010, 32(2), 173-231.

      Abstract:
      The genus Synodontis Cuvier, 1816 (Siluriformes, Mochokidae) numbers about 120 species and is exclusive to the freshwater of Africa except Maghreb and Cape Province. It is one of the most widespread catfi sh of African freshwater. The Synodontis fossil record covers the last 18 Myr and most of the Synodontis fossil bones are found in a disarticulated state. Th e identification of the fossils at a specific level is so far impossible, because we lack an osteological study of the species. Here, we present the study of the osteology of eleven Synodontis species living in Chad: S. batensoda Rüppell, 1832, S. clarias (Linnaeus, 1758), S. courteti Pellegrin, 1906, S. eupterus Boulenger, 1901, S. filamentosus Boulenger, 1901, S. membranaceus (Geoffroy Saint-Hilaire, 1809), S. nigrita Valenciennes, 1840, S. ocellifer Boulenger, 1900, S. schall (Bloch & Schneider, 1801), S. sorex Günther, 1864 and S. violaceus Pellegrin, 1919. Each species is characterized based on its bony anatomy. The morphological variability within and between the species is discussed. The entire skeleton is described, bone by bone. A total of 61 osteological characters, both qualitative and quantitative are established. We emphasize the bones that are well preserved in the fossil, i.e. the mesethmoid, the lateral ethmoid, the frontal, the supraoccipital, the cleithrum, the pectoral spine, the middle nucal plate and the dorsal spine. As a first result, the Chadian Synodontis species can be recognized on the basis of bony characters only. Second, we are also able to attribute isolated bones to nominative species or to a group of species. At last, we note that no osteological character legitimates the distinction of the genera Hemisynodontis Bleeker, 1862 and Brachysynodontis Bleeker, 1862.
      Red ink emphasis added by me. Would also explain synonymization of if reliable.
  • Valid name=Dolichancistrus cobrensis, clog name=Dolichancistrus pediculatus.
    • Sorry to muddy the water here, but Eschmeyer's CoF has D. pediculatus as a synonym of . The CoF synonym makes more sense (than does D. cobrensis) if you are looking at distribution and watersheds.
  • Valid name=Pterygoplichthys disjunctivus, clog name=Pterygoplichthys anisitsi.
    • Another muddy pond - Eschmeyer's CoF has P. anisitsi as a synonym of . The CoF synonym makes more sense (than does P. disjunctivus) if you are looking at distribution and watersheds.
  • Valid name=Wallago micropogon, clog name=Wallagonia micropogon.
  • Valid name=Wallago micropogon, clog name=Wallagonia leerii
    • Eschmeyer's CoF has W. leerii valid as leerii (but in Wallago), not as W. micropogon.
    • If it's any help there's this. In the absence of a molecular genetic analysis, then if jaw length is a reliable trait, then both W. micropgon and W. leerii should stay in Wallagonia (Red ink emphasis added by me):
      Silurus wrote: 06 May 2014, 05:55 Roberts, TR, 2014. Wallago Bleeker, 1851 and Wallagonia Myers, 1938 (Ostariophysi, Siluridae), distinct genera of tropical Asian catfishes, with description of †Wallago maemohensis from the Miocene of Thailand. Bulletin of the Peabody Museum of Natural History 55: 35-47.

      Abstract
      The Southeast Asian silurid catfish genus Wallagonia Myers, 1938, although regarded as a junior synonym of Wallago Bleeker, 1851 by recent authors following Myers (1948), differs fundamentally from it in many external and osteological characters. The genera evidently have been distinct since at least the middle Miocene and apparently are not closely related to each other. Wallagonia seems most similar to the silurid genus Ompok. Wallago differs most strikingly from all other silurids in having a much longer gape, extending ventroposteriorly well beyond the eyes. The extremely elongate upper jaw has a unique bony composition and suspension. It consists of three bones: the toothed premaxillary bone anteriorly, and the toothless suborbital and first postorbital bones posteriorly. The premaxillary bone is partially suspended from the cranium by the infraorbital bone. The closest relatives of Wallago have not been identified. Wallagonia and Wallago have no previously reported fossil records. Fossils of the family Siluridae have been identified as representatives of the Eurasian temperate genus Silurus (Kobayakawa, 1989). Here an extinct species of Wallago is described, W. maemohensis, on the basis of a complete cranium with attached, fully toothed left premaxillary in an unusually fine state of preservation from a Miocene deposit near Lampang in northern Thailand. Fossil catfishes previously reported from Thailand belong to the families Bagridae and Pangasiidae and are from Pliocene deposits (Roberts and Junmongthai 1999).
  • Valid name=Rhamdia voulezi, clog name=Rhamdia argentina.
    • Eschmeyer's CoF has R. argentina as "status uncertain." Based on distribution (R. argentina in the Rio Magdalena of Colombia, R. voulezi along the Parana in Brazil), if R. argentina is valid, it certainly isn't the same species as R. voulezi.
  • Valid name=Synodontis xiphias, clog name=Synodontis gambiensis.
    • More muddy water: Eschmeyer's CoF has S. gambiensis as a synonym of .
  • Valid name=Parauchenoglanis monkei, clog name=Parauchenoglanis guttatus.
    • Sorry, I've got nothing here. In the forum, there are multiple posts where you all discuss the validity of the species and the reorganization of the genus... out of my wheelhouse.
Hopefully something there helps.

Cheers, Eric
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Re: A day in the life of Planet

Post by Jools »

Around late autumn/fall last year I went through all of these taxonomic weirdos and managed to sort them all out. Some are bad interpretation of good data, some are contentious and some are technically correct but hard to accept. Finally, I set-up a robot to go check these each month and see what changes, report it to me and I'll move things around should the need arise.

Meanwhile, also in 2019, something happened on Planet that has never happended before. Consistently, more folks accessed the site using their phone than their computer. As websites go, Planet was pretty slow to this party, and it still has a much larger than usual ratio of computer (big screen) users versus the mobile/cell phone folks - but that line has been crossed and it's never reverted.

What your intrepid web designer will tell you need to deal with this is a so-called "responsive design", this means that you design the website in such a way as it delivers the same info, or experience to the user no matter what device they use to view it. Given bits of Planet are more than 20 years old, some of this was going to be tricky.

However, I had a go. Firstly, maps now show nicely on a phone screen and scale well to larger screens. The first page I have spent a lot of time on modernising is the family page.

Here is one: https://www.planetcatfish.com/aspredinidae

To see what I mean, look at this link on your phone's browser. Then turn your phone through 90 degress to look at it landscape. Then, look at it on your computer screen. Then, if you can, put it onto your smart TV. Good luch turning that though 90 degrees. :-)

So, the modernisation continues, but I quite like how this page now works. Sub families next!

Cheers,


Jools
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Re: A day in the life of Planet

Post by TwoTankAmin »

If I ever own a smart phone, I will try that. The linked page looks great on my big screen. :-)
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bekateen
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Re: A day in the life of Planet

Post by bekateen »

Hi Jools,

It does look nice on my Samsung phone, and the phone rotation does work too.

Two quirks I see on my desktop (using Chrome 79.0.3945.130 browser on Win 7) are
  • on family pages and CLOG pages I don't see the map, but rather a thin bold line where the map should be (as if the map is missing but an empty shadowed border is displayed), and
  • on other pages, I get a popup error message related to the maps, although it pops up only intermittently. The message is "multimap.js:Exception e:ReferenceError:google is not defined."
Of note, the maps display normally in Firefox 72.0.2 and in MS Internet Explorer 11.0.9600.19596. So perhaps the problem in Chrome is more about my Chrome than it is about the website code. I appreciate the fact that my PC is several years old and is not running the latest software in some cases.

On an unrelated but also possibly related matter, on the Family page for Loricariidae, the map has not been displaying for some time now. This occurs in all three browsers and on my Samsung phone. I think this issue is old enough that it is not tied to your changes, but maybe they are related?

Cheers, Eric
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Re: A day in the life of Planet

Post by Jools »

I think all the map issues are resolved now, but if not raise a bug or drop me a pm/email with the specifics.
At the time of writing, we are now at 58% mobile (smartphone) users and the bulk of the remainder are laptop/desktop computers.

The work continues to amend areas of the site to work better on the devices the majority are using to access the site. This then leads us to articles. There are several categories of articles on the site, CotM, book reviews, general info (help, about etc) and, of course, Shane’s World. In total there are about 560 articles. Each one takes about 5 minutes to edit to the new layout, somewhere there are lots of images or a complex layout take longer, up to half an hour or a few (for example, Wolfgang Ros’ excellent big cat articles or Janne Ekstrom’s breeding pleco articles) take longer. So, maybe 10 minutes on average.

10 minutes times 560 articles = 93 hours. As I can work on the site about 30 minutes each day, that means I should have used COVID-19 lockdown to get this done! However, lockdown for me has meant twice as much paid work (sadly twice the work, same pay), supporting schooling three kids at home and all the other stuff many of you will have faced too like remotely assisting older relatives etc. So, it’s about 50% done but some of the “biggies” have been tackled. On the plus side, I've got the process down to a fine art!

Some ways into it however I realised if I was just making articles display well on smaller screens, I’d do nothing very noticeable to the site for ages and not add new content, pictures or features. So, I built a robot to tell me, gradually, which pages had the combination of the worst layout and were most read. I’ve been steadily working through these and I think I’m getting to some of the less read / “darker corners” of the site and flushing out decades-old cobwebs. Thus, I think I will have all the articles completed by late fall (autumn) and be able to carry on with other initiatives such as adding @HaakonH ‘s awesome pleco photo back catalogue.

Meantime, several folks have provided great new content, such as @Erlend D Bertelsen ’s great series of new CotMs, many taxon updates from @bekateen and bits and bobs from my emails of old - @lfinley58 in particular.
So, onwards and upwards! Hope you’re all well and staying safe, sane and fishy!

Jools
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Re: A day in the life of Planet

Post by bekateen »

Thanks for your hard work, Jools!

Cheers, Eric
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Re: A day in the life of Planet

Post by Jools »

You're welcome Eric.

Today, I've launched the refreshed family and subfamily pages.

Family example: https://www.planetcatfish.com/common/fa ... der=chrono
Subfamily example: https://www.planetcatfish.com/common/fa ... mily_id=82

Main improvements are it works better on small screens, the information shown on each is the same (previously some information was on one of the other) and also added the ability to sort the species list in a number of ways. It's quite fun to see what order some families developed in and what were the earliest species.

Cheers,

Jools
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bekateen
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Re: A day in the life of Planet

Post by bekateen »

Works well after looking at a couple of taxa.

Also, once I check out the "chronological listings" of species, it's easy to spot CLOG data errors where data is filled in for year of description and author of description for fish that are not yet described (C/CW/L/LDA/sp.`XYZ`). I've already submitted a few revisions to delete such data, but so far I haven't touched any "cf" and "aff" species entries (although probably they're should be revised too, since they aren't confirmed as the actual species).

Cheers,
Eric
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Jools
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Re: A day in the life of Planet

Post by Jools »

Excellent, I see those corrections coming in and will sort them out, thanks!

Actually, it was after re-reading "Chronological enumeration of nominal species and subspecies of Corydoras" for another project on the arc-striped corys that I had the idea that visualising the data in this way might be useful. And so I am glad it was.

Cheers,

Jools
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