Distance matrices and analysis


I am comparing disease-state/healthy-state samples over time and I am using NMDS/AMOVA to describe community structure.

However, I am undecided on how to compile the distance matrix/matrices to go forward with this. The options that I have considered are (A) compiling a distance matrix with all samples using dist.shared or (B) compiling seperate distance matrices for each time point using dist.shared.

Biologically (and statistically), I am unsure on which option would be most suitable.

Thanks in advance for any advice,


Hi Jo,

We’ve done this in: http://www.ncbi.nlm.nih.gov/pubmed/25362056

Basically, we made one large distance matrix and then analyzed it using the adonis command from within vegan.


Thanks a lot, Pat!