What is Taxonomy?
Taxonomy in its most general sense is the practice and science of classification. It can refer to many things. You may have heard or used the word taxonomy used to indicate any sort of classification of things, whether it be companies or widgets. Here, we’re talking about biological taxonomy, the science of defining and naming groups of biological organisms.
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Read the rest at https://ropensci.org/blog/blog/2017/07/27/taxonomy-suite
Greetings, is this suite still actively developed?
It seems like some functionality has been lost over the years, and recently packages have been archived by CRAN. Could you let me know what the plan is for the Taxonoy Suite?
Hi William,
The initial development of most of these tools was superbly handled by @sckott, he moved position and as such most of the packages he used to maintain (and actively develop) got transfered to new maintainers (for example Zachary Foster is now the maintainer of taxize).
Most of the feature development of these packages got slowed down by this process.
But maybe it could to have a list of taxonomy packages that got archived by CRAN and see what the community could do about it.
I’m sure the packages are still available on R-universe though.
Some are still heavily maintained like rfishbase with a release just last week by @cboettig.
Are you interested in any particular package @wjmatthaeus ? Or just in general?
There’s also the taxonomy task view GitHub - ropensci/taxonomy: taxonomy R packages that may be helpful, though hasn’t been updated in 5 years
Thanks to you both for your very quick responses.
At the moment I’m just looking up higher taxonomic information from a large list of genera. I managed it using curl and their API.
Every year or two I come back around to that taxonomy view when i’m trying to do something taxonomic… Last time I looked I noticed that some (one?) of the functions in taxize didn’t work anymore, can’t remember exactly what. Also noticed that the view hadn’t been updated in awhile, and now that the packages been archived I thought I’d speak up.
If community support is needed to keep these things going, I’d be happy to pitch in.
Just noticed that taxize is archived on cran. I don’t know exactly what the issue is. If you are willing to help you can chime in on the thread here taxize has been kicked off CRAN · Issue #938 · ropensci/taxize · GitHub I’ll see if there’s anything I can do to help on taxize though my time is limited.
In general if you are interested in contributing to taxonomy packages I’m sure your help would be greatly appreciated.