I'm using two way crossed ANOSIM with Time and Treatment to analyze similarities in and between groups. I chose 4999 permutations but that was an arbitrary decision. I'd like to know how to define the correct amount of permutations and even though I've read some of Clarke's papers (Clarke, 1993. Non-parametric multivariate analysis of changes in community structure) and the PRIMER v.6 manual, I'm afraid I have not reached a clear answer, possibly because of lack of understanding or need of simpler language. I'd appreciate any help.
There are two things to consider. The first is the number of possible unique permutations. This is a function of the experimental design (number of replicates per group,. number of groups, balance in the design, etc.). If this number is small it can limit the power of the test to achieve p
Paul Somerfield, thank you for your detailed answer. I'm reading the appendix you attached and finding it insightful, as well as your answer. I appreciate you took time to help me with this!
I agree with Paul Somerfield and as a general rule (valid for N > 30), the statistical error halves, if the sample size is increased 4fold. I would say, that in randomization tests you get a rough estimate with 250, a reasonable result with 1000 and you are on the safe side with 4000. More than 10000 is rarely necessary. As the default number of permutations of anosim in in R is 999 (+1, the observed case), you don't make anything wrong with 4999 - except if you are limited by the number of permutations.
- Badges
- Science topic
- Similar topics
- Medicine
- Physiology
- Biosignals
- Biomedical Signal Processing
- Statistical Analysis