Hello everyone! I am having trouble understanding some of my output results. This in an example of one of them:
Response temp_ celsius:
Df Sum Sq Mean Sq F value Pr(>F)
Can I correctly assume that my Shannon H is F value=4.9044 and that my p value is Pr(>F)=0.03167? If so, are these both needed to take in consideration when establishing possible interpretation of results?
Welcome to the forum, @Albert!
It’s not clear to me what these results are, or what you’re asking. Would you mind posting the command you ran, and maybe a screenshot or Artifact so it’s clearer what you’re looking at?
Best,
Chris 
Hi Chris!
I am observing how diversity can be possibly affected by temperature. So I plotted richness against temperature using:
Estimate_richness(physeq1, measures=c(“Shannon”,”Simpson”)) thengeom_smooth()using formula “y ~ x’
My output results are those mentioned in the previous post. Therefore, my question is the F value=Shannon H? And Pr(>F)= p value?
I provided a visualization in case that helps.
Hi @Albert,
It looks like you are using phyloseq, not QIIME 2, so I have reclassified this topic to "other bioinformatics tools" and altered the title for clarity. Some other users on the QIIME 2 forum are familiar with phyloseq and may be able to offer help, but otherwise I recommend reading the phyloseq documentation and using its support forum (github issues?) to get more direct help.
No, this looks like an F-statistic — you should check the phyloseq documentation for a better description of what test is being run by "Estimate_richness" and how to interpret.
Yes
Good luck!
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