R/PerMANOVA.Simple.R

In laura20vg/permanova: MANOVA and PERMANOVA

PerMANOVA.Simple<- function(D, grupo, nperm = 999, seed=NULL, C=NULL ){
  cl <- match.call()
  if (!is.factor(grupo)) stop("The grouping variable must be a factor")
  if (!is.null(seed)) set.seed(seed)
  Result=list()
  Result$call=cl
  Result$nperm=nperm
  Result$Inicial=PerMANOVAF(D, grupo)
  n = length(grupo)
  Result$Fvals=rep(0, nperm)
  set.seed(1)
  for (i in 1:nperm){
    print(i)
    muestra=sample.int(n)
    Result$Fvals[i]=PerMANOVAF(D[muestra, muestra], grupo)$Fexp
  }
  Result$pval= (sum(Result$Fvals >= Result$Inicial$Fexp) +1 )/ (nperm+1)
  class(Result)="permanova"
  return(Result)
}