How to include repeated measures in adonis function (vegan package)?

General
2

Hi, and welcome.

A reproducible example, called a reprex would be a huge help in parsing your question. Could you post one?

The examples on the adonis2 help page suggest to me as a non-specialist that FL.div model has one fixed and one interaction term, unless the fixed term is expressly excluded.

library(vegan)
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.5-6
data(dune)
data(dune.env)
# default test by terms
adonis2(dune ~ Management*A1, data = dune.env)
#> Permutation test for adonis under reduced model
#> Terms added sequentially (first to last)
#> Permutation: free
#> Number of permutations: 999
#> 
#> adonis2(formula = dune ~ Management * A1, data = dune.env)
#>               Df SumOfSqs      R2      F Pr(>F)    
#> Management     3   1.4686 0.34161 3.2629  0.001 ***
#> A1             1   0.4409 0.10256 2.9387  0.019 *  
#> Management:A1  3   0.5892 0.13705 1.3090  0.190    
#> Residual      12   1.8004 0.41878                  
#> Total         19   4.2990 1.00000                  
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# overall tests
adonis2(dune ~ Management*A1, data = dune.env, by = NULL)
#> Permutation test for adonis under reduced model
#> Permutation: free
#> Number of permutations: 999
#> 
#> adonis2(formula = dune ~ Management * A1, data = dune.env, by = NULL)
#>          Df SumOfSqs      R2      F Pr(>F)    
#> Model     7   2.4987 0.58122 2.3792  0.001 ***
#> Residual 12   1.8004 0.41878                  
#> Total    19   4.2990 1.00000                  
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Created on 2019-11-11 by the reprex package (v0.3.0)

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