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#'
#' Makes a qqplot and Wilcoxon test between the two columns of \code{val}
#'
#' @param val a matrix with two columns containing the two samples to be compared
#' @param xlab,ylab,main see \code{\link{plot.default}}
#' @param xlim,ylim see \code{\link{plot.default}}
#' @param diff logical variable, if \code{TRUE} the function is applied to \code{diff(val)} instead of \code{val}. See \code{\link{diff}}
#' @param quantile quantile value on which data samples in \code{val} are considered. Default is 0.
#'
#' @author Emanuele Cordano, Emanuele Eccel
#'
#' @export
#'
#'
#' @return Wilcoxon test between the two columns of 'val'
qqplotWGEN <-
function (val,xlab="simulated",ylab="measured",main="title",ylim=c(min(val),max(val)),xlim=c(min(val),max(val)),diff=FALSE,quantile=0) {
# =cbind(Tn_gen[,1]-SplineAdvTn[,1],Tn_mes[,1]-SplineAdvTn[,1])
if(diff) val <- diff(val)
v1 <- val[,1]
v2 <- val[,2]
if (quantile>0) {
v1 <- v1[v1>quantile(v1,probs=quantile,na.rm=TRUE)]
v2 <- v2[v2>quantile(v2,probs=quantile,na.rm=TRUE)]
}
qqplot(v1,v2,xlab=xlab,ylab=ylab,xlim=xlim,ylim=ylim,main=main)
abline(0,1)
out <- wilcox.test(v1,v2)
return(out)
}
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