R/chisq.test2.R

In compareGroups: Descriptive Analysis by Groups

chisq.test2 <-
function(obj, chisq.test.perm, chisq.test.B, chisq.test.seed){

  if (any(dim(obj)<2) || is.null(dim(obj)) || sum(rowSums(obj)>0)<2 || sum(colSums(obj)>0)<2)
    return(NaN)
  obj<-obj[,colSums(obj)>0] # erase columns full of zeros.
  expect<-outer(rowSums(obj),colSums(obj))/sum(obj)    
  if (any(expect<5)){
    if (chisq.test.perm){
      if (!is.null(chisq.test.seed)) set.seed(chisq.test.seed)
      test<-try(chisq.test(obj, simulate.p.value=chisq.test.perm, B = chisq.test.B),silent=TRUE) 
    } else 
      test <- try(fisher.test(obj),silent=TRUE)
  } else {
    test <- try(chisq.test(obj),silent=TRUE)
  }
  if (inherits(test,"try-error"))
    return(NaN)
  ans <- test$p.value
  
  ans
}