R/randtest.between.R

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

"randtest.between" <- function(xtest, nrepet = 999, ...) {
  if (!inherits(xtest,"dudi"))
        stop("Object of class dudi expected")
    if (!inherits(xtest,"between"))
        stop ("Type 'between' expected")
    appel <- as.list(xtest$call)
    dudi1 <- eval.parent(appel[[2]]) ## could work with bca (appel$x) or between (appel$dudi)
    fac <- eval.parent(appel$fac)
    X <- as.matrix(dudi1$tab)
    X.lw <- dudi1$lw
    if ((!(identical(all.equal(X.lw,rep(1/nrow(X), nrow(X))),TRUE)))) {
      if(as.list(dudi1$call)[[1]] == "dudi.acm" )
    	stop ("Not implemented for non-uniform weights in the case of dudi.acm")
      else if(as.list(dudi1$call)[[1]] == "dudi.hillsmith" )
        stop ("Not implemented for non-uniform weights in the case of dudi.hillsmith")
      else if(as.list(dudi1$call)[[1]] == "dudi.mix" )
        stop ("Not implemented for non-uniform weights in the case of dudi.mix")
    }
    
    inertot <- sum(dudi1$eig)
    isim <- testinterCpp(nrepet, dudi1$lw, dudi1$cw, fac, X)
    isim <- isim/inertot
    obs <- isim[1]
    return(as.randtest(sim = isim[-1], obs = obs, call = match.call(), ...))
}