Indicator Species Analysis!

[Sami Khanal]

I did a cluster analysis on a species composition data which basically reflects the abundance of the species (i.e., 23 species) in thousands of plots using Sorensen approach. After analyzing different number of clusters, I feel like cluster of 11 (i.e., 11 different groups) would be suitable to represent 23 species. However, I want to test whether these groups are distinct and different from each other than the differences within groups. For the purpose, I am using approaches like Indicator Species Analysis (ISA), MRPP and PerMANOVA. While doing  ISA, it says "Excluding species with all presences" and shows relative abundance, relative frequency and Indicator values for only 5 species. I think I understood other parts of the output table except this message "Excluding species with all presences". I would appreciate if anyone can point out what this means. I want to see relative abundance, relative frequencey and indicator values for all species not just 5 species. Thanks for your help. 

[Bruce McCune]

Sami, what this means is that you're using v.6 without the updates. The "excluding species with all presences" should only happen with the Tichy and Chytry method -- There was a fix early on in v. 6 that corrected this for the regular ISA method. Hopefully this will fix your problem if you download the free fixes.
Bruce McCune

At 04:36 PM 1/16/2014, you wrote:

I did a cluster analysis on a species composition data which basically reflects the abundance of the species (i.e., 23 species) in thousands of plots using Sorensen approach. After analyzing different number of clusters, I feel like cluster of 11 (i.e., 11 different groups) would be suitable to represent 23 species. However, I want to test whether these groups are distinct and different from each other than the differences within groups. For the purpose, I am using approaches like Indicator Species Analysis (ISA), MRPP and PerMANOVA. While doing  ISA, it says "Excluding species with all presences" and shows relative abundance, relative frequency and Indicator values for only 5 species. I think I understood other parts of the output table except this message "Excluding species with all presences". I would appreciate if anyone can point out what this means. I want to see relative abundance, relative frequencey and indicator values for all species not just 5 species. Thanks for your help.

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