I'm not a statistician and kinda working through this blindly, but why does my NMDS plot of bray-curtis measures show clear groupings for status (blue and pink) but adonis says that time point is significantly different?
distance_calc <- phyloseq::distance(rarified2, "bray")
sampledf <- data.frame(sample_data(rarified2))
adonisresult<- adonis2(formula = distance_calc ~ Status * Time.Point, data = sampledf, type = "bray")
> adonisresult
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999
adonis2(formula = adonisf, data = sampledf, type = "bray")
Df SumOfSqs R2 F Pr(>F)
Status 1 0.2534 0.05397 1.2969 0.198
Time.Point 1 0.4277 0.09111 2.1893 0.016 *
Status:Time.Point 1 0.1061 0.02259 0.5429 0.901
Residual 20 3.9072 0.83232
Total 23 4.6943 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
