Nothing
test.Null <-
function( trtsel, alpha){
# 6/6/12 changed from test based on the bootstrap to the likelihood ratio test.
# below is the old code
#n.boot <- ncol(boot.data)
#potential.pvals <- (1:n.boot)/n.boot
#a3.b <- boot.data[4,]
#if(!bounded){
# first check to see if the max and min cover 0,
# if this is true the pvalue is less than our lowest possible detectable value
# if(!cover(min(a3.b), max(a3.b), 0) ){
# p.val<- paste("<", 1/n.boot)
# reject <- TRUE
# }else{
# reject.all <- unname( mapply( cover,
# quantile(a3.b, potential.pvals/2, , study.design = 1, na.rm = TRUE),
# quantile(a3.b, 1 - potential.pvals/2, study.design = 1, na.rm = TRUE),
# rep(0, n.boot)) )
# tmp <- which(reject.all==FALSE)[1]
# p.val <- potential.pvals[ifelse(tmp==1, 1, tmp - 1)]
# reject <- p.val <= alpha
# }
# }
#we only do this test if we have a single marker:
if(length(trtsel$model.fit$marker.names)==1){
if(trtsel$model.fit$outcome != "time-to-event"){
if(is.null(trtsel$model.fit$coefficients)) p.val <- NA
else p.val <- trtsel$model.fit$coefficients[4,4]
reject <- p.val <= alpha
z.value <- trtsel$model.fit$coefficients[4,3]
}else{
if(is.null(trtsel$model.fit$coefficients)) p.val <- NA
else p.val <- trtsel$model.fit$coefficients[3,5]
reject <- p.val <= alpha
z.value <- trtsel$model.fit$coefficients[3,4]
}
}else{
p.val <- NA
reject <- NA
z.value <- NA
}
list( reject = reject, p.value = p.val, z.statistic = z.value, alpha = alpha)
}
test.Null.warning <-
function(x, a1a3.pval){
if(!x & is.null(a1a3.pval)){
cat("\n")
cat(" ##############################################\n")
cat(" ### WARNING! ###\n")
cat(" ##############################################\n\n")
cat(" ### Not enough evidence to reject the ###\n")
cat(" ### hypothesis test of: ###\n")
cat(" ### ###\n")
cat(" ### H_0 : No marker-by-treatment ###\n")
cat(" ### interaction ###\n")
cat(" ### ###\n")
cat(" ### Inference for Theta may be unreliable! ###\n\n")
cat(" ##############################################\n\n")
}else if(!x & !is.null(a1a3.pval)){
cat("\n")
cat(" ##############################################\n")
cat(" ### WARNING! ###\n")
cat(" ##############################################\n\n")
cat(" ### Not enough evidence to reject both ###\n")
cat(" ### hypothesis tests of: ###\n")
cat(" ### H_0 : ###\n")
cat(" ### 1. No marker-by-treatment interaction ###\n")
cat(" ### ###\n")
cat(" ### 2. The marker positivity threshold ###\n")
cat(" ### is outside marker bounds ###\n")
cat(" ### ###\n")
cat(" ### Inference for Theta may be unreliable! ###\n\n")
cat(" ##############################################\n\n")
}
}
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