Question

我试图在PERMANOVA创造超过三个独立对比，有4个因素没有成功。我需要在我的contr2df对象中使用因子级别的所有可能的成对组合。有什么方法可以让这成为可能吗？在我的代码中：

#1st factor
treat <- gl(4, 15, labels = paste("t", 1:4, sep="")); treat 

#Variables
set.seed(124)
sp  <- cbind(c(rnorm(10,  5, 0.25), rnorm(50, 2.5, 0.25)), rnorm(60, 2.5, 0.25),
             c(rnorm(10, 12, 0.25), rnorm(50, 2.5, 0.25)), rnorm(60, 2.5, 0.25))
colnames(sp) <- c("sp1", "sp2", "sp3", "sp4")
head(sp))


#create a design matrix of the contrasts for "treat" 
Treat_Imp<-model.matrix(~treat-1)

require(vegan)

fullModel <- adonis(sp ~ treat, method = "euclidean", permutations = 9999)

fullModel

#Comparisons
TI    <- model.matrix(~ treat-1)
head(TI)

f <- nlevels(treat)
comb <- t(combn(1:f, 2))
n    <- nrow(comb)

contr2 <- NULL
for (x in 1:n) {
      i <- comb[x, 1]
      j <- comb[x, 2]
      tmp <- list(TI[,i] - TI[,j]); names(tmp) <- paste0("TI",i, "_", j)
       contr2 <- c(contr2, tmp) }
contr2


contr2df <- as.data.frame(contr2)

adonis(
     sp ~ ., data = contr2df,
     method = "euclidean",
     permutations = 9999)
#

谢谢，

亚历山大

PERMANOVA有三个以上的独立对比

0 个答案: