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biocore / my-microbes

A set of tools for delivering personal microbiome results to individuals participating in microbiome sequencing studies.
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Include explanations for chao1 and shannon? #70

Closed jairideout closed 11 years ago

jairideout commented 11 years ago

@antgonza brought up a good point:

For the alpha rarefaction/boxplots text, should the text include explanations for chao1 and shannon (in addition to observed species and PD)? These are the four alpha diversity metrics that are included with the full dataset.

The alternative would be to exclude chao1 and shannon from the results.

gregcaporaso commented 11 years ago

I think we should exclude Chao1 from the results, and I'll write text for shannon.

gregcaporaso commented 11 years ago

After thinking about this more, I'm going to present this as richness (so observed species) and evenness (so shannon evenness). I think this makes sense in the context of Holly's comments about simplifying this.

rob-knight commented 11 years ago

Remember Shannon combines richness and evenness (consider H for even distribution of 2 vs 100 species); you could use a pure evenness metric which there are some of in qiime if I recall correctly or be more careful with explanation.

On Jan 25, 2013, at 3:55 PM, "Greg Caporaso" notifications@github.com<mailto:notifications@github.com> wrote:

After thinking about this more, I'm going to present this as richness (so observed species) and evenness (so shannon evenness). I think this makes sense in the context of Holly's comments about simplifying this.

— Reply to this email directly or view it on GitHubhttps://github.com/qiime/my-microbes/issues/70#issuecomment-12724918.

gregcaporaso commented 11 years ago

I think I'm going to just remove Shannon to keep this as simple as possible.