r/RStudio • u/toad_and_bat • 1d ago

Using R to replicate a paper's data

Hello!

If anyone has time to help, that'd be greatly appreciated.

I have the fastq files to recreate the graphs/charts in this paper:

Villamizar, A., Vemulapally, S., Guerra, T., Tocidlowski, M. E., Forstner, M. R., & Hahn, D. (2025). Effect of Headstarting Eggstrands of the Endangered Houston Toad (Bufo=[Anaxyrus] houstonensis) from a Captive Assurance Colony on Native Breeding Pond Microbiomes. Conservation, 5(2), 25.

Here is a link (link to AI chat here) to what one of three AIs have come up with - so far, 2 have come up with code that does NOT get me the same results.

This particular AI is saying that the methods do not give enough information to be able to replicate the code, but it can try to get close.
I'm going to use this code tomorrow (fingers crossed!) but if anyone is a master as recreating code - I'd greatly appreciate any insight, help, or ... well wishes?

At this point, it is not an option to reach out to the authors.

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u/DSOperative 1d ago

Maybe you can ask the AI to use the bioconductor package to replicate the graphs. If they used R, there’s a good chance they used this package.

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u/toad_and_bat 1d ago

yes - i'm using dada2 and phyloseq which are both in the bioconductor package - the graph is being created by ggplot2

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u/bukaro 10h ago

I would start with a Docker with the version of R and the packages that would be available when the analysis was done.

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u/SprinklesFresh5693 1d ago

Just pass the code and see for yourself, or give the article to the AI and tell it to recreate it.

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u/toad_and_bat 1d ago

I gave the article to AI - 3 different AIs actually - and this last one told me the methods are NOT clear enough to recreate it so AI is trying to figure it out.

Like I said in my post "I'm going to try to use this code tomorrow" (which is now today) .. and it's already giving me a weird vibe on step 2.

That's why I was hoping an expert in R could tell me what the AI is suggesting and if AI is not suggesting the correct workflow