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ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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Database release version - plans to update? #209

Closed MichaelJSchram closed 3 years ago

MichaelJSchram commented 3 years ago

Hello,

I am currently working on a project which incorporates trait data, thus I am working on a number of R queries to collect and aggregate trait (e.g., trophic level, max length) values for ~200 reef fishes. I notice that the most recent available release is 1904, whereas the site is operating on what appears to be 2102(?). Through some admittedly brief searches (e.g., Issue #163) it sounds like a version release for use in the package is rather involved, but at nearly 2 years old the 1904 release seems fairly out of date.

Just wondering if there are plans for a database release in the near(ish) future?

Thanks!

cboettig commented 3 years ago

apologies, some things happened in the past year or so, still working through a backlog. The Fishbase team recently provided us the most recent database dumps, I will hopefully update the rfishbase cache soon?

gfgalbraith commented 3 years ago

Hi there,

Great to hear that the cache is set to be updated soon. I have also been working on pulling traits for reef fishes and have come across numerous species which have length-weight constants on the summary webpage but return NA in a length_weight query. Guessing this will also be the sort of thing the update will resolve?

Cheers! Gemma

jaseeverett commented 3 years ago

Thanks @cboettig . I assume this will also update Sealifebase db's? I'm also getting a lot of different results compared to the website version. An update would be fantastic.

Thanks so much for your work on this software. It's brilliant.

cboettig commented 3 years ago

Again sorry for the long delay. These should be up now.

There's an unrelated issue of an expired tokens impacting use at the moment, see #216 for a workaround. There's also a patched version in the CRAN queue (rfishbase 3.1.9) that will resolve it so that setting your own GITHUB_PAT won't be necessary.