[R] testing significance of axis loadings from multivariate dudi.mix

[Francisco Mora Ardila]

Hi all

I´m trying to tests the significance of loadings from a ordination of 46 variables 
(caategorical, ordinal and nominal). I used dudi.mix from ade4 for the ordination. A 
years ago Jari Oksanen wrote this script implementing Peres-Neto et al. 2003 (Ecology) 
bootstraping method:



netoboot <- function (x, permutations=1000, ...) 
{

   pcnull <- princomp(x, cor = TRUE, ...) 
   res <- pcnull$loadings 
   out <- matrix(0, nrow=nrow(res), ncol=ncol(res))
   N <- nrow(x) 
   for (i in 1:permutations) {

       pc <- princomp(x[sample(N, replace=TRUE), ], cor = TRUE ...)
       pred <- predict(pc, newdata = x)
       r <-  cor(pcnull$scores, pred)
       k <- apply(abs(r), 2, which.max)
       reve <- sign(diag(r[k,]))
       sol <- pc$loadings[ ,k]
       sol <- sweep(sol, 2, reve, "*")
       out <- out + ifelse(res > 0, sol <=  0, sol >= 0)
   } 
   out/permutations 
}



I tried to aply it to the case of dudi.mix instead of princomp this way:




netoboot1<-function (x, permutations=1000,...) {

   dudinull <- dudi.mix(x, scannf = FALSE, nf = 3) 
   res <- dudinull$c1 
   out <- matrix(0, nrow=nrow(res), ncol=ncol(res))
   N <- nrow(x) 
   for (i in 1:permutations) {

       dudi <- dudi.mix(x[sample(N, replace=TRUE), ], scannf = FALSE, nf = 3)
       pred <- predict(dudi, newdata = x)
       r <-  cor(dudinull$li, pred) 
       k <- apply(abs(r), 2, which.max)
       reve <- sign(diag(r[k,]))
       sol <- dudi$c1[ ,k]
       sol <- sweep(sol, 2, reve, "*")
       out <- out + ifelse(res > 0, sol <=  0, sol >= 0)
   } 
   out/permutations 
}

But a problem arised with the predict function: it doesn´t seem to work with an object 
from dudi.mix and I dont understand why. Can somebody tell me why? Any suggestions to 
modify the script or to use other method?

Thanks in advance.

Francisco

Francisco Mora Ardila
Laboratorio de Biodiversidad y Funcionamiento del Ecosistema
Centro de Investigaciones en Ecosistemas
UNAM-Campus Morelia
Tel 3222777 ext. 42621
Morelia , MIchoacán, México.

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