More Callichthyinae than I can imagine? (But no loricariids)

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bekateen
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More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Hi Jools,

Today I noticed that the distribution map for the subfamily Callichthyinae shows an inordinately high number of drop pins. I suspect it's showing corys too. At the same time, for a while now the Loricariidae don't even plot a a map.

Cheers, Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

You know, subfamilies could never have worked, but all the code was in place to support it - was just missing the final piece. So, after a bit of sleuthing, a relatively simple thing to fix.

Will look at the Loricaridae map next...

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Jools wrote: 28 Sep 2020, 20:51You know, subfamilies could never have worked, but all the code was in place to support it
If I'm reading you correctly, :)) :)) :))

Thanks. And Cheers,
Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

I am too literal. :-) So, families are fixed up now too but the mega family that is the Loricariidae still won't work. I think it's something in the data. The document tree is 211363 characters, it will take me some time to check it...

Here's a sample:

Code: Select all

<div id="xmlparser">
<geodata>
<marker>
<latitude>-0.28333333333333</latitude>
<longitude>-76.45</longitude>
<type>type-locality</type>
<name>Panaque titan</name>
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<marker>
<latitude>-3.6644444444444</latitude>
<longitude>-61.481388888889</longitude>
<type>type-locality</type>
<name>Panaque bathyphilus</name>
</marker>
<marker>
<latitude>-9.4519444444444</latitude>
<longitude>-56.512777777778</longitude>
<type>type-locality</type>
<name>Panaque armbrusteri</name>
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<latitude>-8.4975</latitude>
<longitude>-75.56</longitude>
<type>type-locality</type>
<name>Panaque schaeferi</name>
</marker>
<marker>
<latitude>4.6097222222222</latitude>
<longitude>-53.359166666667</longitude>
<type>type-locality</type>
<name>Harttiella intermedia</name>
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<latitude>3.9544444444444</latitude>
<longitude>-54.180555555556</longitude>
<type>type-locality</type>
<name>Harttiella janmoli</name>
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<marker>
<latitude>4.6030555555556</latitude>
<longitude>-53.417777777778</longitude>
<type>type-locality</type>
<name>Harttiella longicauda</name>
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<marker>
<latitude>4.79575</latitude>
<longitude>-53.930388888889</longitude>
<type>type-locality</type>
<name>Harttiella lucifer</name>
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<latitude>-13.1316</latitude>
<longitude>-70.3943</longitude>
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<name>Inambari Ancistrus heterorhynchus Ancistrus marcapatae Ancistrus maldonadoi</name>
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<latitude>-14.439</latitude>
<longitude>-46.2573</longitude>
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<name>Jatai Ancistrus jataiensis</name>
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<type>occurrence</type>
<name>Tulumayo Ancistrus jelskii</name>
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<latitude>-3.38474</latitude>
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<name>Ampiyacu Ancistrus malacops Ancistrus variolus Ancistrus sericeus</name>
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<name>Zulia Ancistrus martini</name>
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<name>Bobonaza Ancistrus occidentalis Pterygoplichthys weberi Lamontichthys stibaros Panaqolus albomaculatus</name>
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<name>Hueque Ancistrus falconensis</name>
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<name>Ricoa Ancistrus falconensis</name>
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<longitude>-51.9812</longitude>
<type>occurrence</type>
<name>Jordão Ancistrus agostinhoi</name>
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<latitude>3.27626</latitude>
<longitude>-75.2317</longitude>
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<name>Upper Magdalena Ancistrus tolima Spatuloricaria gymnogaster Sturisomatichthys leightoni</name>
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<latitude>-7.0099</latitude>
<longitude>-60.1325</longitude>
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<longitude>-69.6347</longitude>
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<name>Las Piedras Ancistrus sp(l513)</name>
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<longitude>-59.0707</longitude>
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<longitude>-53.0548</longitude>
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<longitude>-79.0814</longitude>
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<name>Chota (Chotano) Spatuloricaria puganensis</name>
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<latitude>5.96166</latitude>
<longitude>-76.7485</longitude>
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<name>Atrato Spatuloricaria atratoensis Lasiancistrus caucanus Leptoancistrus sp`atrato` Dasyloricaria latiura</name>
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<marker>
<latitude>8.03492</latitude>
<longitude>-77.5844</longitude>
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<name>Tuira Spatuloricaria fimbriata Lasiancistrus caucanus Lasiancistrus planiceps Sturisomatichthys citurensis Sturisomatichthys dariensis Dasyloricaria capetensis Dasyloricaria latiura Dasyloricaria tuyrensis</name>
</marker>
<marker>
<latitude>5.38104</latitude>
<longitude>-76.6277</longitude>
<type>occurrence</type>
<name>Certegui Spatuloricaria fimbriata</name>
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<marker>
<latitude>10.3582</latitude>
<longitude>-66.3208</longitude>
<type>occurrence</type>
<name>Venezuela Caribbean Waters Farlowella martini</name>
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<marker>
<latitude>-0.28015</latitude>
<longitude>-76.1877</longitude>
<type>occurrence</type>
<name>Aguarico Farlowella odontotumulus</name>
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<latitude>2.35959</latitude>
<longitude>-65.1245</longitude>
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<name>Mavaca Farlowella odontotumulus</name>
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<longitude>-61.9716</longitude>
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<name>Middle Madeira Farlowella smithi</name>
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<longitude>-71.1219</longitude>
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<name>Guaripiche Farlowella venezuelensis</name>
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<longitude>-52.8972</longitude>
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<name>Sinnamary Harttia guianensis Metaloricaria paucidens</name>
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<longitude>-56.0923</longitude>
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<longitude>-37.3767</longitude>
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<latitude>0.433956</latitude>
<longitude>-54.0131</longitude>
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<latitude>5.01752</latitude>
<longitude>-59.6576</longitude>
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<name>Kuribrong Corymbophanes ameliae</name>
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<longitude>-65.1158</longitude>
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<name>Matacuni Exastilithoxus fimbriatus</name>
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<marker>
<latitude>6.29687</latitude>
<longitude>-62.9442</longitude>
<type>occurrence</type>
<name>Caroni Exastilithoxus fimbriatus Pseudancistrus reus</name>
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<marker>
<latitude>0.036736</latitude>
<longitude>-65.0635</longitude>
<type>occurrence</type>
<name>Marauiá Exastilithoxus hoedemani</name>
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<marker>
<latitude>-3.2</latitude>
<longitude>-60.0538</longitude>
<type>occurrence</type>
<name>Lago Janauari (Lake Hyanuary) Oxyropsis wrightiana Loricariichthys acutus</name>
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<marker>
<latitude>9.1738</latitude>
<longitude>-79.0765</longitude>
<type>occurrence</type>
<name>Mamoni Crossoloricaria variegata</name>
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<marker>
<latitude>-23.0434</latitude>
<longitude>-44.6889</longitude>
<type>occurrence</type>
<name>Taquari (Rio de Janeiro State) Hemipsilichthys nimius</name>
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<marker>
<latitude>-23.2271</latitude>
<longitude>-44.7804</longitude>
<type>occurrence</type>
<name>Perequê-Açu Hemipsilichthys nimius</name>
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<marker>
<latitude>-22.0624</latitude>
<longitude>-43.766</longitude>
<type>occurrence</type>
<name>Prêto (Minas Gerais) Hemipsilichthys papillatus Curculionichthys insperatus</name>
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<marker>
<latitude>1.91133</latitude>
<longitude>-54.3489</longitude>
<type>occurrence</type>
<name>Mapaoni Guyanancistrus tenuis</name>
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<marker>
<latitude>-12.4688</latitude>
<longitude>-64.2502</longitude>
<type>occurrence</type>
<name>Guaporé Pterygoplichthys lituratus Hypoptopoma baileyi</name>
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<marker>
<latitude>-22.433</latitude>
<longitude>-64.533</longitude>
<type>occurrence</type>
<name>Lipeo Pterygoplichthys disjunctivus</name>
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<marker>
<latitude>-17.735</latitude>
<longitude>-40.5756</longitude>
<type>occurrence</type>
<name>Mucuri Delturus angulicauda Pogonopoma wertheimeri</name>
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<marker>
<latitude>-16.4005</latitude>
<longitude>-41.1679</longitude>
<type>occurrence</type>
<name>Jequitinhonha Delturus brevis</name>
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<marker>
<latitude>7.92868</latitude>
<longitude>-73.2825</longitude>
<type>occurrence</type>
<name>Colombia Caribbean Rivers Sturisomatichthys panamensis</name>
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<marker>
<latitude>-1.27431</latitude>
<longitude>-80.2954</longitude>
<type>occurrence</type>
<name>Ecuador Pacific Coast Rivers Sturisomatichthys panamensis Sturisomatichthys frenatus Isorineloricaria spinosissima</name>
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<marker>
<latitude>4.76326</latitude>
<longitude>-60.8737</longitude>
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<name>Kukenan Neblinichthys yaravi</name>
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<latitude>5.06974</latitude>
<longitude>-62.4897</longitude>
<type>occurrence</type>
<name>Upper Caroni Neblinichthys roraima</name>
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<marker>
<latitude>5.84828</latitude>
<longitude>-59.7892</longitude>
<type>occurrence</type>
<name>Mazaruni Neblinichthys echinasus Neblinichthys brevibracchium Paralithoxus cf_raso Hypostominae sp(l376)</name>
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<marker>
<latitude>-0.775886</latitude>
<longitude>-77.1833</longitude>
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<latitude>-3.7449</latitude>
<longitude>-77.3497</longitude>
<type>occurrence</type>
<name>Morona Aphanotorulus horridus</name>
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<latitude>-8.8092</latitude>
<longitude>-54.9323</longitude>
<type>occurrence</type>
<name>Upper Curuá Spectracanthicus sp(l391)</name>
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<latitude>-10.8849</latitude>
<longitude>-49.9603</longitude>
<type>occurrence</type>
<name>Javaés Spectracanthicus javae</name>
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<name>Biguaçu Epactionotus advenus</name>
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<longitude>-49.9766</longitude>
<type>occurrence</type>
<name>Mampituba Epactionotus itaimbezinho</name>
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<marker>
<latitude>5.60129</latitude>
<longitude>-76.4536</longitude>
<type>occurrence</type>
<name>Upper Atrato Dolichancistrus atratoensis</name>
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<marker>
<latitude>6.83917</latitude>
<longitude>-64.8045</longitude>
<type>occurrence</type>
<name>Aro Pseudolithoxus anthrax</name>
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</div>
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

The loricariidae have been broken for some time now, but didn't used to be (obviously). I don't recall it breaking after an update, but who knows about that. Rather, I was wondering if it could be a single flawed data point for one of the newer species added a few months back. Could a data point break the whole map? Or does it necessarily have to reside in the code?

Could it be a max size limit for number of points to plot? Something like that?

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

An interesting aside as you talk about the subfamilies not working before your fix today:

Here is my original report of the Loricariidae map being broken (viewtopic.php?f=36&t=48478) in May 2020. In that report, I mention that the Loricariinae map IS working but the Hypostominae map is broken. Go figure.

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

Then, in your second post, you say the Loricariinae map is broken? So, I think maybe the page was in flux at that time - anyway, is now sorted.

Cheers,

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Jools wrote: 28 Sep 2020, 22:26Then, in your second post, you say the Loricariinae map is broken? So, I think maybe the page was in flux at that time - anyway, is now sorted.
Did I mistype? Please allow me to start over, so that we don't need to refer to the posts above:

Yesterday I discovered that the Callichthyinae subfamily was mapping too many points- I speculate that it was mapping either the entire Callichthyidae family or possibly it was mapping the Corydoradinae subfamily; I couldn't distinguish between the two options because I was viewing the pages on my phone (the pins don't show species when viewed on a phone).

Today I added the info that the whole family Loricariidae is broken since at least last May, but even back then, the subfamily Loricariinae was working, and it still is (along with all the other Loricariid subfamilies EXCEPT Hypostominae).

Today, in response to your comment that the program wasn't set up for subfamilies, I was saying that it is then all the more weird that the Callichthyinae subfamily was broken yesterday, when you then recognize that most of the Loricariid subfamilies were mapping fine yesterday, and in fact even back in May those subfamilies worked. That's what I meant to communicate.

The Callichthyinae seems to be fixed now, as you reported.

However, when I check the Loricariidae family page, the map doesn't populate. Likewise, the Hypostominae subfamily map doesn't populate either, even though all the other subfamilies of the Loricariidae do work, and they've worked since last May. So I suspect that the problem might rest in the Hypostominae.

Does that make more sense?

Sorry for the confusion.

Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

Yes, that does, it's as you say, there is a data issue (or the software is not robust enough to deal with it) in the subfamily .

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

Ok, so I've fixed the problem. It was caused by the text "bearing 269°" in the type locality for . It was the 329th entry in the list....

So the maps works. However, and I know this now shows other "bad data" with plecos in parts of the world they should not be. This is a separate issue which I have been aware of for a long time. The map makes South America look very busy and I will, in the future, consider pin clustering as per the undernoted:

https://developers.google.com/maps/docu ... javascript

However, for now, this beast is slain.

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Awesome fix! Thanks, Jools.

FWIW, I don't mind the map of So. America looking very busy, as zooming in is sufficient to clarify. I routinely use the maps here and at GBIF to attempt to identify species for myself and for others. The graphical presentation of the maps are invaluable, since I don't have the locations of the rivers memorized in any helpful way. I'm a visual thinker and visual learner.

Whether you choose to pursue the cleaning up of the pins is up to you. But just know I personally don't see it as an improvement. In fact, if pins are pooled together, it would initially mask information until the pins are untangled fully with (potentially) strong zoom: Even a little zoom can start to spread nearby pins apart, so their placement begins to clarify with event the slightest zoom. But by contrast, as I practice with the sample provided in your link, some of the pins don't disentangle until you've zoomed way in on the map, which then automatically hides other areas of the map because of the intensity of the zoom. Since both conditions are disentangled by zooming, and since the current state of maps starts to disentangle with even minor zooming, I see no benefit myself to the clustering of pins... but that's just my two cents.

Thanks again.

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

OK, that's useful feedback. More important is finding these "errant" species that are all over the globe and working why our parsing of the lat/long info isn't correct in those instances. I think there are several bug reports for this, so will get on to them soon.

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

I'd be happy to help with the repair of the errant type locality data, except that I'm not empowered to make those changes. But what I can do is assemble a spreadsheet of the species, their inaccurate coordinates and what the likely coordinates should be. You could then simply apply them without having to use your time to track down the info.

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

We can work out a way to empower you. :-) How about we start with a wrong one and figure it out. Any candidates?

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »



The coordinates listed on the CLOG are:
  • -40.183611, -10.413611
I suspect the two numbers are simply reversed and should be:
  • -10.413611, -40.183611
FWIW, the inaccurate pairing is present both in the data fields for type locality Lat/Long and also in the text field of the type locality
Rio Itapicuru, on Federal highway BR 407, 8 kilometers north of Senhor do Bonfim to Juazeiro, Bahia State, Brazil, 40°11'01"S, 10°24'49"W.
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

Yes, got it in one and this is the main issue. Here, the problem is simply our software interprets the type locality and maps it onto the species page. That the authors have messed up the locality is not something a computer is going to understand without a lot more support (although it might be able to swap them if S/N is before W/E, not sure needs research). So, what I need to do is be able to edit the co-ords even if the type locality is wrong. This is where we can empower a data submission/admin to help...

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Jools wrote: 30 Sep 2020, 20:57So, what I need to do is be able to edit the co-ords even if the type locality is wrong. This is where we can empower a data submission/admin to help...
Currently, on the CLOG edit page, there are two boxes on the right side displaying the Lat/Long on record for type locality. I've learned in the past (when I tried to change the record for Pseudacanthicus leopardus, if I recall correctly) that these two fields are NOT interactive, but merely for information purposes only - they display the coordinates on record in the database, but they do not have an input/edit functionality. Would you be able to change that, so I could type in revised Lat/Long data into those fields? Or do you think that's too unregulated a power?
Uncle Ben Parker wrote:With great power comes great responsibility.

Changing the subject slightly, ... thinking beyond PlanetCatfish - When we identify data errors like this, is there a mechanism on the source end for us to submit our corrections to the place that's providing the original (erroneous) data?

Cheers, Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

Hi Eric,

Yes, there needs to be some way to interact with the lat/long data through the data submission / vetting process. That's what I plan to look at initially.

So, the source can come from different places. However, these ones are from the description, so the best I suspect you could do is go to the lead author and say, "Hey, next time you do one of these, how about doing it this way...". I don't know how that would be received or ultimately how useful it would be. There are some where is source is CoF. I'm in touch with them (Richard) from time to time, maybe 2 or 3 times a year with corrections as I find them. They appear to be appreciative of the input.

I have written a geodata checker which find all species with suspect data. I can share that with you too if that'd provide background? Might save you some work on your list?

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Hi Jools,

Sure if it's not too much trouble, I'd be willing to try the geodata tracker.

Thanks, Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

To redirect slightly, finding the problems is easy and quick - Just view the family maps and hover over the pins that aren't over the right continent. The work is figuring out what the corrected data values should be. Sometimes it's obvious; sometimes not.

Cheers, Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

I've been doing some research on how all this works. It's been over a decade since I last worked on this and a lot of the math/conversion work for it was ably done by @MatsP (always grateful).

So, at the point you do a data submission, the type locality is parsed for something that looks like a set of co-ords. These are then put in the read-only ("computed") fields. Note to self, would be helpful if they were mapped at this stage. This seems an odd design (I should know, I did it) because either you give the admin who is the data submitter the ability to submit this data or you do it later when a SuperUser vets the data submission. Need to think about that.

The only other part of this is the geocode checker which only points out invalid text that looks a bit like a lat long but isn't or is truly invalid. So now, we need to understand what the parser actually does.

It is sent some text (for this is " Rio Itapicuru, on Federal highway, BR 407, 8 kilometres north of Senhor do Bonfim to Juazeiro, Bahia State, Brazil, 40°11'01"S, 10°24'49"W.") and then it should return the lat and long in decimal degrees (because that's the simplest form for a computer to store).

Thus, 40°11'01"S, 10°24'49"W is our starting point. If you have a look at online converters, they always ask for this data in the component fields - because it's hard to split it all up to use for conversion into decimal degrees. Also, S and W could be N or E, is the seconds symbol a double quote (") or two single quotes (''). Which quote (',` or a hex or HTML entity representation of any of these symbols are used. In short, it's messy.

Out of time for now, more soon.

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

So, have checked this one and it seems like the text in the description is just plain wrong.

The descriptions says 40°11'01.0"S 10°24'49.0"W (-40.183611, -10.413611) and the actual location is around 10°24'49.6"S 40°11'01.3"W (-10.413771, -40.183703). Once you do the research, you see the author just put the S and W on the wrong co-ords!

Becuase the computed values are "hard wired" into the data, the trusty data submitter/admin can't fix this even if they overtype the type locality data with a correct value. I am writing this all out as I probably knew this at one point, didn't write it down and now have to go through it all again! Plus, if I am wrong in my assertions, I am sure someone will correct it up.

So, problem 1 is that where the data is valid but wrong, an admin needs to be able to edit. Needs some thought but nearly there...

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Thanks for the explanation, Jools.

I've tried to determine who is responsible for this type locality. It's not the original discovery (too old) I presume it's a redescription at some point in time, but do far I've not found the right paper with full text to confirm.

Cheers, Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

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bekateen wrote: 03 Oct 2020, 16:11 Thanks for the explanation, Jools.

I've tried to determine who is responsible for this type locality. It's not the original discovery (too old) I presume it's a redescription at some point in time, but do far I've not found the right paper with full text to confirm.

Cheers, Eric
It could have been CoF in this case.

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

I've sent an email to Fishbase already
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

I've changed the data submission/vetting process. Could you try one out? In other words, try to correct an erroneous entry?

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Okay will do
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

bekateen wrote: 03 Oct 2020, 16:55 Okay will do
:thumbsup:

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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by bekateen »

Okay, has an error.

The type locality reads:
Goiás, município de Barro Alto, upper rio Tocantins basin, ribeirão Pouso Alegre, tributary of rio dos Patos, 15°01’26"S, 8°49’51"W, Brazil.
The longitude should be -48°49’51"W

I tried to change the longitude from something starting with -8 to the same number but starting with -48.

I found that I am unable to edit this from my phone. For some reason, every time I make the edit on my phone and then press the "Submit" button, there was some kind of glitch, wherein the page would refresh as the editor and my changes had been removed.

On my laptop, I find it's also difficult to make the change in only one step because (I suspect) the lat and long fields are filled out to their size limit of characters. So I have to delete the existing entry and type my own fresh (as opposed to simply deleting the erroneous character and substituting the right numbers, while leaving the rest of the values unchanged).

No matter, I think I had a successful submission. I'll look forward to discovering that it worked.

Cheers, Eric
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Re: More Callichthyinae than I can imagine? (But no loricariids)

Post by Jools »

I think it did. :-)

Jools
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