[R-sig-eco] PERMANOVA contrasts by combination of levels

[ASANTOS]

Dear Members,

I started to creat a script for a PERMANOVA contrasts by combination of 
levels using adonis function, but doesn't seem to be working a 
combination of levels matrix with adonis object created, my code was:
#Packages

require(vegan)
require(doBy)
require(wzRfun)
require(multcomp)

#Data set

data(mite)
A = c(rep(c(0), 30), rep(c(1), 30))
B = rep(c(rep(c(0), 15), rep(c(1), 15)), 2)

#Create data frame

A <- as.factor(A)
B <- as.factor(B)
species <- mite[1:60,]

#PERMANOVA with Jaccard index

man.com<-adonis(species ~ A * B, method = "jaccard",permutations=999)
man.com

#Two-Way PERMANOVA Contrasts
#Interaction

A_B<- interaction(A, B)
levels(A_B)
do.call(rbind, strsplit(levels(A_B), "\\."))


g0 <- adonis(species ~ A * B, method = "jaccard",permutations=999)
g1 <- adonis(species ~ A_B, method = "jaccard",permutations=999)

M <- LSmatrix(g0, effect=c("A","B"))

#Mean estimation

data.frame(g0=M%*%coef(g0), g1=coef(g1))

#Combination of levels

str(M)
grid <- attr(M, "grid")

#Matrix of contrasts between levels of treatement

B <- "b"
A <- "a"
spl <- interaction(grid[,2])
i <- 1:nrow(grid)
l <- split(i, f=spl)
contr <- lapply(l,
                 function(row){
                     ## Contrast matrix parwise
                     a <- apc(M[row,], lev=levels(d[,2]))
                     rownames(a) <- paste(spl[row[1]],
                                          rownames(a), sep="/")
                     return(a)
                 })
contr <- do.call(rbind, contr)
contr

#Constrasts

summary(glht(g0, linfct=contr),
         test=adjusted(type="fdr"))

#

Someone could you please help me,

Thanks,

-- 
======================================================================
Alexandre dos Santos
Proteção Florestal
IFMT - Instituto Federal de Educação, Ciência e Tecnologia de Mato Grosso
Campus Cáceres
Caixa Postal 244
Avenida dos Ramires, s/n
Bairro: Distrito Industrial
Cáceres - MT                      CEP: 78.200-000
Fone: (+55) 65 8132-8112 (TIM)   (+55) 65 9686-6970 (VIVO)

         alexandre.santos at cas.ifmt.edu.br
Lattes: http://lattes.cnpq.br/1360403201088680
OrcID: orcid.org/0000-0001-8232-6722
Researchgate: https://www.researchgate.net/profile/Alexandre_Santos10
LinkedIn: https://br.linkedin.com/in/alexandre-dos-santos-87961635