[R-sig-eco] PERMANOVA and adonis: trying to clear my confusion

[Pedro Neves]

On 08/01/19 09:59, Pedro Neves wrote:
>
> Assuming that my species data is Spec_data and the factors data is 
> Env_data, my formulation is:
>
> adonis(Spec_data ~ Season * Habitat/Location, strata=Habitat, 
> data=Env_data, method="bray")
>
> Is this formulation correct, according to my experimental design?
>
Hi again:

In trying to respond to my own question, I compared the results of the 
PERMANOVA obtained with R:vegan and using the original FORTRAN program 
from Marti Anderson and Primer 6+.

The results from R are different from the ones obtained with the other 
two programs and the difference on the degrees of freedom with R, 
clearly indicate that the formula is incorrect:


Results from R (using adonis2(formula = Spec_data ~ Season * 
Habitat/Location, data = Env_data, method = "bray", by = "terms", strata 
= Habitat):

                        Df SumOfSqs      R2       F Pr(>F)
------------------------------------------------------------------------------------------ 

Season                 1   1.4465 0.07112  50.360  0.001 ***
Habitat                 1   5.9292 0.29150 206.425  0.001 ***
Season:Habitat         1   0.7575 0.03724  26.373  0.001 ***
Season:Habitat:Local   4   4.3942 0.21604  38.246  0.001 ***
Residual              272   7.8127 0.38410
Total                 279  20.3401 1.00000
------------------------------------------------------------------------------------------- 



Results from PERMANOVA (original FORTRAN code):

  Source             df        SS           MS          F P(perm) P(MC)
  -----------------------------------------------------------------------------
   Se                  1     14029.6135   14029.6135    1.5637 0.2592  
0.2358
   Ha                  1     56723.5220   56723.5220    4.2938 0.0002  
0.0188
   Lo(Ha)              2     26421.0270   13210.5135   28.1272 0.0002  
0.0002
   SexHa               1      7504.5849    7504.5849    0.8364 0.3864  
0.5542
   SexLo(Ha)           2     17944.4582    8972.2291   19.1032 0.0002  
0.0002
   Residual          272    127750.3725     469.6705
   Total             279    250373.5780
  -----------------------------------------------------------------------------

Results from PRIMER:

PERMANOVA table of results
                                                        Unique
Source     df         SS        MS    Pseudo-F    P(perm)  perms     P(MC)
------------------------------------------------------------------------------------------------------------------------
Se      1      14465     14465      1,8194     0,3153        51 0,2024
Ha      1      12752     12752     0,34679     0,6594         3 0,8376
Lo(Ha)      2      73540     36770      128,01     0,0002 4982    0,0002
SexHa      1     8616,6    8616,6      1,0838     0,3414 51    0,4186
SexLo(Ha)      2      15901    7950,4      27,679     0,0002 4980    0,0002
Res    272      78127    287,23
Total    279    2,034E5
-------------------------------------------------------------------------------------------------------------------------- 


What am I missing in R formulation?

Thanks in advance:


Pedro