Closed msmcfarlin closed 2 years ago
Hi Mike,
I apologize for the delay in my response. It looks like this is actually an issue that we started to patch and the pull request just didn't get merged, so I'll nip that in the bud shortly.
Your code looks good to me – do you get reasonable results?
Thanks!
Best, David
Just updating to say that simplifyBeta should now accept Aitchison distances.
Hi David,
Thanks for the update! The results with my code seemed reasonable though I'll check with the updated simplifyBeta() function.
Thanks, Mike
Hello,
I would like to use
simplifyBeta()
to extract Aitchison distance estimates for PCoA plotting. When I try running the function it returns an error that states ! Can't subset columns that don't exist. ColumnsA014
,A021
,A025
,A051
,A053
, etc. don't exist.simplifyBeta
works with my metadata when extracting euclidean and bray-curtis estimates so I don't think it's an error with the sample names. I noticed in the beta diversity divnet object I am using that there isn't an aitchison distance metric. I also saw in thetestBetaDiversity()
code that it uses the 'fitted_z' object to calculate aitchison distance. So I was thinking of calculating the aitchison distance using some of that code, adding it to the beta divnet object, then usingsimplifyBeta
to extract the estimates.Does that sounds like it would work? Or maybe I'm missing a step in properly calculating the aitchison distance?
Here is the code I used...
Thank you for your assistance!