Output from summary.shared

mothur bugs
1

I have some output from summary.shared that I either don’t understand or indicates there is something wrong with my data or Mothur. I ran the following command and everything looked fine on the surface.

summary.shared(shared=final.an.shared, calc=thetayc)

Upon closer inspection, there were several thetayc values that were not bracketed by the corresponding confidence interval - e.g. the first two lines of the output read:

label comparison thetayc thetayc_lci thetayc_hci
0.03 Abidjan.534R Aleppo.534R 0.724870 0.263177 0.287082

I am wondering how the confidence interval for the estimate, 0.72, can be (0.26, 0.29). Am I misinterpreting the headers, or does this indicate some problem with my data? Any insights would be appreciated. I can work up a small, reproducible example if that would help.

I’m running version 1.28.0

Thanks!

2

Thanks for bringing this to our attention. In version 1.20, we changed the output of the calculators to be distances instead of similarities. The lci and uci values did not get changed. This will be fixed in our next release. In the meantime, you can find the values as follows:

0.03 Abidjan.534R Aleppo.534R 0.724870 0.263177 0.287082

0.03 Abidjan.534R Aleppo.534R 0.724870 (1.0 - 0.287082) (1.0 - 0.263177)

or

0.03 Abidjan.534R Aleppo.534R 0.724870 0.712918 0.736823

3

That makes sense. Thanks for the quick response!