Dist.shared vs summary.shared commands for beta diversity

1

Hi Everyone,

Can anyone give me a conceptual explanation of how dist.shared and summary.shared commands are different, for example, if used to calculate the bray-curtis dissimilarity index? I get different numbers for these two commands. I understand that dist.shared likely calculates the distance. But I’m not really sure how to think about summary.shared…Thoughts?

Here are the commands:
dist.shared(shared=FILE.norm.shared,calc=braycurtis…
summary.shared(shared=FILE.norm.shared,calc=braycurtis…

Thank you! :smiley:

2

If you use default arguments (i.e. if your ... is ) ) then you should get the same output, but in different formats. We strongly encourage people to use dist.shared with the rarefaction arguments.

Pat

3

Thank you, Pat. I ran all the calculators with the summary.shared command. I am seeing the same values for the odum and braycurtis calculators. I see that these equations are almost the same except BrayCurtis=1-2(odum)

Here is my code:
summary.shared(shared=MyFile.norm.shared,calc=braycurtis-thetayc-sorclass-jabund-jclass-hamming-anderberg-spearman-memchord-structchord-jest-sharedchao-structpearson-canberra-gower-hellinger-manhattan-morisitahorn-odum-soergel-sorabund-speciesprofile-structchi2-structeuclidean-structkulczynski-thetan-thetayc-whittaker-ochiai-mempearson-memeuclidean-memchi2-lennon-kulczynskicody-kulczynski-sharedsobs-sharedace)

I also see the same numbers when I run it with dist.shared

I am using mothur version 1.41.1

Thank you for your help!

4

Sorry - I don’t understand your question. What are you asking?

5

Hi Pat,

I ran all those calculators on the same data. I get the same numbers for the bray curtis calculator as odum (and also the structkulczynski). The way it is showing the output is by pairs of samples like the colum output that can be used with dist.seqs.

I assume maybe these calculatos can give equivalent values under certain circumstances? I can share my input and output files with you if needed.

Thank you for your help! Also it’s very cool to get an email from you, I love mothur!

6

I’d assume that they give the same values under some conditions