Search code examples
rstatisticsvegan

Different results using ANOSIM and SIMPER in R

I have run ANOSIM and SIMPER to analyse community similarity at two treatments.

When I run ANOSIM the output is:

ANOSIM statistic R: -0.04465 Significance: 0.749

meaning they are similar to each other?

but the I run SIMPER it says the composition at two treatments are 62% different to each other?

not sure how to interpret the outputs of the two tests... why are they saying different things?

Solution

  • I looked up the documentation.

    1. Are they similar to each other? Yes:

    The divisor is chosen so that R will be in the interval -1 … +1, value 0 indicating completely random grouping.

    1. Does 62% mean the groups are different from each other? No, greater than 70% is required.

      The function displays most important species for each pair of groups. These species contribute at least to 70 % of the differences between groups.

    2. There is also this note:

    The results of simper can be very difficult to interpret. The method very badly confounds the mean between group differences and within group variation, and seems to single out variable species instead of distinctive species (Warton et al. 2012). Even if you make groups that are copies of each other, the method will single out species with high contribution, but these are not contributions to non-existing between-group differences but to within-group variation in species abundance.