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

[Steve Brewer]

I’ve generated a function called “centroidmatrix” that might be helpful to you. I think this could allow you to test the season and habitat and their interaction effects using the correct error term.

#' centroidmatrix
#' This function allows you to generate a matrix of centroids from a non-Euclidean distance matrix using the betadisper function in vegan.
#' @param factorname The name of a treatment factor file containing the treatment factors and other sources of variation and a grouping variable for calculation of centroids in the columns and observations in rows
#' @param speciesname The name of species file which has species in columns and observations in rows in the same order as in the factorname file and of the same length
#' @param groupvarname The name of the grouping variable in the factorname file for which centroids are calculated
#' @param distancetype The type of distance or dissimilarity matrix to be calculated from the species file using the vegdist function in vegan Default is "bray"
#' @export
#' @examples
#' centroidmatrix()

centroidmatrix <- function(factorname, speciesname, groupvarname, distancetype){
groupvar <- factor(groupvarname)
braydist <- vegdist(speciesname, method = distancetype)
betadisperout <- betadisper(braydist, groupvar, type = 'centroid')
braycent <- betadispout$centroids


return(braycent)


}

Stephen Brewer
jbrewer using olemiss.edu<mailto:jbrewer using olemiss.edu>
Professor
Department of Biology
PO Box 1848
 University of Mississippi
University, Mississippi 38677-1848
 Brewer web page - https://jstephenbrewer.wordpress.com
FAX - 662-915-5144 Phone - 662-202-5877





On Jan 8, 2019, at 7:49 AM, Pedro Neves <pedro.neves using oom.arditi.pt<mailto:pedro.neves using oom.arditi.pt>> wrote:

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

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology using r-project.org<mailto:R-sig-ecology using r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology


	[[alternative HTML version deleted]]