List of papers with R code available

[AQueff]

Hi there,
I was udating a powerpoint for a presentation on Open Science and I was looking for a new versino of the super graph showing the increasing use and sharing of R code in archaeological papers. The last one I found on the twitter and Mastodon bots are from June 2023 on Twitter.
I guess everyone has so many other things to do but I was wondering whether it was planed to continue this project?
If so, I only find the list of papers in the readme.md of the github page. Is it in this readme that one should add papers? This seems strange to me but I am no GitHub specialist. The archaepaperswithcode repo apparently says the same that it takes from this list.

Or maybe there is another way now that I am not aware of to get updated version of this nice graphic with 2023 and 2024 data? :)

[bbartholdy]

Yes, the README is the list of papers, and relies on contributions from the community to add new papers. To my knowledge there is no other way to do this.

Maybe this paper by @joeroe and @zackbatist could be useful?

[AQueff]

Thank you Bjorn,
so if we add more papers to this list, the bot should create and publish a new version of the figure? But If I add just a 2025 paper, it will make a strange figure...

[benmarwick]

Hi Alain et al., Yes, this is the repo to add papers. I took a look in https://github.com/benmarwick/archaepaperswithcode (which has stagnated since twitter removed the free API service I was using to automate posting, and I no longer use twitter myself since it changed ownership) and found that the code there is fine, but the list here had some inconsistencies that cause the code not to work. For example, if a reference is spread out over multiple lines, or has the date in it twice. I've updated the list here to make the formatting consistent, and added a little note to remind contributors in 2c8ee6c

Here's the plot of the current data that I made by running lines 96ff of archaepaperswithcode.R I think the main conclusion to take from this is that I haven't updated it much since I started doing the reproducibility reviewing for JAS and AAP on 2024. Doing those reviews is hugely time consuming and takes up all the time I used to use for reading new papers and adding them to this list 😅 I do warmly welcome contributions from everyone and would be happy to have a co-maintainer.

[AQueff]

OMG people have stopped using R in Archaeology! :) :) :)
Yes I get it is time consuming ! I don't think I have time to do that either. Probably if everyone add 2-3 papers every month it would work but yes... collaborative work is not easy!

[bbartholdy]

@benmarwick maybe this is something we could separate from the CTV repo to something that is more structured? This could perhaps make it easier to contribute. Something like https://github.com/SPAAM-community/AncientMetagenomeDir which would also make it more machine-useable.

[benmarwick]

@bbartholdy yes I think that could work well, good idea. That project you link to is very nice and would suit the list we have here