I am new to statistical analysis and R. I have data of relative abundance (in percentage) of 5 taxa in 8 ponds. The number of samples in the 8 ponds ranges from 7 to 12 (making the design unbalanced). Can I use PERMANOVA (vegan::adonis2) and PERMDISP to test if the composition of the 5 taxa is different in the 8 ponds?
Thank you!
I have tried as follows:
matrix<-as.matrix(Data[,c(5:9)]) # columns 5:9 refers to relative abundance of the 5 taxa in percentage
dist<-vegdist(matrix, method="robust.aitchison", na.rm = F)
adonis2(dist~ Pond, data=Data)
anova(betadisper(dist,Data$Pond))
Does the result mean that there are no difference between the ponds as a whole? And how can I analyse the differences of individual taxon among the ponds?
Thank you!
Yeah, that's fine. But you don't want the anova() method for betadisper() objects; you should use permutest() on the betadisper() object to get the permutation test of heterogeneous dispersions.
The results of the PERMANOVA mean you fail to reject the null hypothesis that the variation explained by Pond is consistent with the Null hypothesis of no effect. The results do not indicate there is no difference between ponds; there are differences (otherwise the SumOfSqs would be 0), but they are just small.
Analysing the per taxon differences would just be a univariate model so not really something you would do with adonis2()...
