RFI: How to efficiently update mammal lists
Hi all,
Sorry for another RFI post… but this time rather than the promise of a trip to join, I’ll happily share any resulting code I write for automated updating with anyone who wants it.
So, dad and I both have our current mammal lists organised using Jon’s “Mammal Watching Master List @ January 2017” (details below) and we’re looking to update it to use the
“Mammal Watching Master List @ January 2024” (again, details below). Of course, this is because this newer version is obviously better, and not just because it has an extra 1000 or so species from which to count.
There are quite a number of changes driven by the switch from the IUCN listing to the American Society of Mammalogists’ listing. Anyway, I am now looking for a way to do this that saves at least some time through automation. This is obviously fairly trivial to do for species which have not changed between the two lists. You might think this would be indicated by having the same scientific name. However, it may well be the case that there are some species which appear to be the same (ie both called “species 1”) where actually the species from the 2017 list is split into two species in the 2024 list, called “species 1” and “species 2” and without checking where we’d seen “species 1” of the 2017 list we wouldn’t know which species in the 2024 list we’d actually seen (and potentially both). So that might create some challenges (I think this can be got around by only automating the process for genera in which the whole genus is present in both lists, and for genera with missing species in either list to do it by hand). The second sort of species which I think could cause unecessary issues are where the genus name is different between the two listings, but the species names are the same. These would be easy to sort so long as I knew “old genus” = “new genus”.
So, my questions are kind of two fold. (1) Has anyone else tried to do this, and if so how? (2) Does anyone know of a resource which could help with this process? (This could either be someone else’s code that does the updating, or it could be some written information about the mapping of species in list 1 to list 2). Any help is much appreciated, and once I get some code working on this (written in R) I’ll happily share it with anyone that wants it.
Thanks in advance!
Ben (& Andrew)
Mammal Watching Master List @ January 2017 – filename = “Global mammal checklist at January 2017”. Description in the file = “This is a work in progress, will be updated regularly, and is based on the IUCN’s Red list with a few exceptions for ‘new’ species that I believe are in the pipeline and also to include feral populations of domestic species. Differences to the IUCN list are listed on the other worksheet (and highlighted here). Some common names have come from other sources (when not present on the Redlist).”
Mammal Watching Master List @ January 2024 – filename = “Mammal Taxonomy Jan 14 2024”. Description in the file = “This is a work in progress, will be updated regularly, and is now based primarily on the American Society of Mammalogists’ Mammal Diversity Database https://www.mammaldiversity.org/ (MDD). It includes a handful of exceptions, primarily from the IUCN’s latest primate taxonomy. The taxonomic order largely follows Wilson & Reeder’s Mammals of the World (2005, Johns Hopkins University Press).”
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3 Comments
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benbalmford
Thanks Valentin. When you say the “changes are recorded version to version” do you mean in posts that Jon has put up on this site, or is there a more systematic listing you know of? (I was thinking of coding it as 2017->18, highlighting “by hand” species, then correct ’18-19 etc, which would also mean that anyone with a version in something 2017 or later could run with the same code v easily). And yep, cheers for flagging Scythebill – we’ll use that, too, once we have the updated lists
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Jon Hall
Sorry that I don’t have much to add to this. It is a bit of a mess and going forward I am just going to use the mammaldiversity database (though may use separate sources for the standalone primate, cat and cetacean league tables … I am still thinking through that). But for the overall global list the MDD do a good job in tracking changes etc so going forward it would be quite easy. I am inclined to think that if you have not update the taxonomy since 2017 you might be better off doing it all by hand. It probably wouldn’t take as long as you imagine if you cross reference where you saw your species with the country ranges of the species (as now understood) on the spreadsheet. That should highlight most splits that you may have missed. There have been many changes in primates but most other larger mammals have been more stable and what seems like a huge task might only take a couple of hours I suspect. I also strongly encourage using scythebill as it makes the task a lot easier going forward. I use both excel and scythebill (of course I do .. because I am a nerd!).
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vmoser
Hello Ben,
Good thoughts! If you figure something out, I’d be interested in the code. It seems challenging, though. Maybe Jon has some input. The changes are recorded from version to version so you could program that. A challange might be when a species changes status twice between your last version and the newest of Jon, so you would need to go from version to version. Still, this does not fix that you have to put in your new hand chair ticks (new splits) by hand.
Consider switching to one of the online lists. I think Scythebill uses Jon’s list. It will be a lot of work to transfer, but you should save this time in the future (given Scythebill’s stability in the future).