"confident"<-function(x,y= NULL,z,type = c("means","medians","proportions"),paired=FALSE,k=1,na.rm = FALSE)
{
	if (!is.numeric(x) || is.complex(x))
		stop("x is not numeric or x is complex.",call. = FALSE)
	if (!is.null(y) && (!is.numeric(y) || is.complex(y) ))
		stop("y is not numeric or y is complex.",call. = FALSE)
	if (z!="conf.curve" && !is.numeric(z))
		stop("z has to be numeric or conf.curve.",call. = FALSE)
	if (!type=="means" && !type=="medians" && !type=="proportions")
		stop("Type has to be one of means, medians or proportions.",call. = FALSE)
	if (is.null(y) && na.rm){
		if (length(x[is.na(x)]) > 0) warning("NAs have been removed.",call. = FALSE)		
		x=x[!is.na(x)]
	}
	if (is.null(y) && (!na.rm) && length(x[is.na(x)])>=1)
		stop("Vector contains NAs. Set na.rm=TRUE and repeat.",call. = FALSE)
	if (!is.logical(na.rm))
		stop("na.rm is logical.",call. = FALSE)
	if (is.numeric(z) & (z<0 || z>1))
		stop("Level of confidence (z) needs to be in the boundaries of 0 and 1.",call. = FALSE)
	if (!is.null(y) && na.rm && !paired && (length(which(is.na(x)))>=1 | length(which(is.na(y)))>=1)){
		x=x[!is.na(x)]
		y=y[!is.na(y)]
		warning("NAs have been removed.",call. = FALSE)		
	}
	if (!is.null(y) && na.rm && paired && (length(which(is.na(x)))>=1 | length(which(is.na(x)))>=1)){
		if(length(which(is.na(x)))>=1 && length(which(is.na(y)))==0){
			B=which(is.na(x))
			A=0
		} else if(length(which(is.na(x)))==0 && length(which(is.na(y)))>=1){
			B=0
			A=which(is.na(y))
		} else if(length(which(is.na(x)))>=0 && length(which(is.na(y)))>=1){
			B=which(is.na(x))
			A=which(is.na(y))
		}
		x=x[c(-A,-B)]
		y=y[c(-A,-B)]
		warning("NAs have been removed.",call. = FALSE)		
	}
	if (!is.null(y) && paired && length(x)!=length(y))
		stop("For paired=TRUE, x and y have to be of same length.",call. = FALSE)
	if (!is.null(y) && !na.rm && (length(x[is.na(x)])>=1 || length(y[is.na(y)])>=1))
		stop("x or y contains NAs. Set na.rm=TRUE and repeat.",call. = FALSE)
	if (!is.null(y) && !is.logical(paired))
		stop("paired is logical.",call. = FALSE)
	if (z=="conf.curve") c(seq(0,0.8,0.01),seq(0.801,1,0.001))->z
	if ((k%%2!=0 && k%%2!=1) || k<1)
		stop("k needs to be natural number with minimum 1.",call. = FALSE)
	if (length(k)>1)
		stop("k has to be of length one.")
	if (k>1)
		warning(c("Note: confidence intervals were adjusted for ",paste(k)," comparisons."),call. = FALSE)

	if (type=="means" && is.null(y)){
		if(length(x)<2)
			stop("Length of x too small. Mean with CIs requires at least length  of 2.")
		final=data.frame()
		for (i in 1:length(z)){
		conf=1-(1-z[i])/(2*k)
		mean=round(mean(x),3)
		Upper=round(mean+qt(conf,length(x)-1)*sd(x)/sqrt(length(x)),3)
		Lower=round(mean-qt(conf,length(x)-1)*sd(x)/sqrt(length(x)),3)
		temp=c(z[i],Lower,round(mean,3),Upper)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Mean with CI(s)"
		Effectsize="Effect size (ES): Mean"
	}
	else

	if (type=="medians" && is.null(y)){
		final=data.frame()
		for (i in 1:length(z)){
		conf=1-(1-z[i])/(2*k)
		median=median(x)
		r=round(length(x)/2-(qnorm(conf)*sqrt(length(x))/2))
		s=round(1+length(x)/2+(qnorm(conf)*sqrt(length(x))/2))
		sort=sort(x)
		Lower=sort[r]
		Upper=sort[s]
		if (r<1 | s>length(x)){
			temp=c(z[i],NA,round(median,3),NA)
			warning("One or more desired levels of confidence were too high for length(x).",call. = FALSE)
			}else temp=c(z[i],Lower,round(median,3),Upper)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Median with CI(s)"
		Effectsize="Effect size (ES): Median"
	}
	else

	if (type=="proportions" && is.null(y)){
		if(x[2]<x[1] | length(x)!=2)
			stop("To obtain a proportion, x must have length 2 and x[2] has to be larger than or equal to x[1].",call. = FALSE)
		final=data.frame()
		for (i in 1:length(z)){
		conf=1-(1-z[i])/(2*k)
		r=x[1]
		n=x[2]
		p=r/n
		q=1-p
		A=2*r+qnorm(conf)^2
		B=qnorm(conf)*sqrt(qnorm(conf)^2+4*r*q)
		C=2*(n+qnorm(conf)^2)
		Lower=round((A-B)/C,3)
		Upper=round((A+B)/C,3)
		temp=c(z[i],Lower,round(p,3),Upper)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Proportion with CI(s)"
		Effectsize="Effect size (ES): Proportion"
	}
	else

	if (type=="means" && !paired && !is.null(y)){
	if(length(x)<2 & length(y)<2)
		stop("Length of x and y needs to be >=2.",call. = FALSE)
		final=data.frame()
		for (i in 1:length(z)){
		conf=1-(1-z[i])/(2*k)
		d=mean(x)-mean(y)
		sxy=sqrt(((length(x)-1)*sd(x)^2+(length(y)-1)*sd(y)^2)/(length(x)+length(y)-2))
		sexy=sxy*sqrt(1/length(x)+1/length(y))
		Lower=round((d-qt(conf,(length(x)+length(y)-2))*sexy),3)
		Upper=round((d+qt(conf,(length(x)+length(y)-2))*sexy),3)
		temp=c(z[i],Lower,round(d,3),Upper)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Mean difference with CI(s); unpaired"
		Effectsize="Effect size (ES): mean(x) - mean(y)"
	}
	else

	if(type=="means" && paired && !is.null(y)){
	if(length(x)<2 & length(y)<2)
		stop("Length of x and y needs to be >=2.",call. = FALSE)
		final=data.frame()
		for (i in 1:length(z)){
		conf=1-(1-z[i])/(2*k)
		Diff=y-x
		meanDiff=mean(Diff)
		sdDiff=sd(Diff)
		Upper=round((meanDiff+qt(conf,(length(Diff)-1))*sdDiff/sqrt(length(Diff))),3)
		Lower=round((meanDiff-qt(conf,(length(Diff)-1))*sdDiff/sqrt(length(Diff))),3)
		temp=c(z[i],Lower,round(meanDiff,3),Upper)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Mean difference with CI(s); paired"
		Effectsize="Effect size (ES): mean(y - x)"
	}
	else

	if(type=="medians" && !paired && !is.null(y)){
	if(length(x)<5 & length(y)<5)
		stop("Length of x and y needs to be >=5.",call. = FALSE)
		final=data.frame()
		for (i in 1:length(z)){
		conf=(1-z[i])/(2*k)
		W=qwilcox(conf,length(x),length(y))
		Out=sort(as.vector(unlist(outer(x,y,"-"))))
		Lower=Out[W]
		Upper=Out[length(Out)-W+1]
		median=median(Out)
		if(W<1){
		temp=c(z[i],NA,round(median,3),NA)
		warning("One or more desired levels of confidence were too high for length x or y.",call. = FALSE)
		} else temp=c(z[i],Lower,round(median,3),Upper)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Median difference with CI(s); unpaired"
		Effectsize="Effect size (ES): Median of all possible differences x - y"
	}
	else

	if(type=="medians" && paired && !is.null(y)){
		Out=sort(y-x)
		M=outer(Out,Out,"+")/2
		Final=numeric()
		for(i in 1:length(Out))
		{
			temp <-M[c(1:i),i]
			append(Final, temp) -> Final
		}
		Final=sort(Final)
		final=data.frame()
		for (i in 1:length(z)){
		conf=(1-z[i])/(2*k)
		W=qsignrank(conf,length(x))
		Lower=Final[W]
		Upper=Final[length(Final)-W+1]
		median=median(Final)
		if(W<1){
		Temp=c(z[i],NA,round(median,3),NA)
		warning("One or more desired levels of confidence were too high for length of x and y.",call. = FALSE)
		} else Temp=c(z[i],Lower,round(median,3),Upper)
		final=rbind(final, Temp,row.names=NULL)
		}
		Name="    Median difference with CI(s); paired"
		Effectsize="Effect size (ES): Median of all possible averages of the paired differences y - x"
	}
	else

	if(type=="proportions" && !paired && !is.null(y)){
		
	if(x[2]<x[1] | y[2]<y[1] | length(x)!=2 | length(y)!=2)
		stop("x and y need to be integer vectors of length 2 with second object larger than first one.",call. = FALSE)
		final=data.frame()
		for (i in 1:length(z)){
		conf=1-(1-z[i])/(2*k)
		r=x[1]
		r2=y[1]
		n=x[2]
		n2=y[2]
		p=r/n
		q=1-p
		p2=r2/n2
		q2=1-p2
		A=2*r+qnorm(conf)^2
		B=qnorm(conf)*sqrt(qnorm(conf)^2+4*r*q)
		C=2*(n+qnorm(conf)^2)
		A2=2*r2+qnorm(conf)^2
		B2=qnorm(conf)*sqrt(qnorm(conf)^2+4*r2*q2)
		C2=2*(n2+qnorm(conf)^2)
		Lower=round((A-B)/C,3)
		Upper=round((A+B)/C,3)
		Lower2=round((A2-B2)/C2,3)
		Upper2=round((A2+B2)/C2,3)
		D=-(round(q-q2,3))
		Lower3=round(D-sqrt((p-Lower)^2+(Upper2-p2)^2),3)
		Upper3=round(D+sqrt((p2-Lower2)^2+(Upper-p)^2),3)
		temp=c(z[i],Lower3,D,Upper3)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Difference of proportions with CI(s); unpaired"
		Effectsize="Effect size (ES): Difference in proportions x - y."
	}
	else

	if(type=="proportions" && paired && !is.null(y)){
		
	if(length(x)!=length(y))
		stop("x and y need to be of same length.",call. = FALSE)
	if((length(x[x==1])+length(x[x==0]))!=length(x) || (length(y[y==1])+length(y[y==0]))!=length(y))
		stop("Only binary data is valid.",call. = FALSE)
		final=data.frame()
		for (i in 1:length(z)){
		conf=1-(1-z[i])/(2*k)
		r=sum(x)
		r2=sum(y)
		n=length(x)
		p=r/n
		q=1-p
		p2=r2/n
		q2=1-p2
		A=2*r+qnorm(conf)^2
		B=qnorm(conf)*sqrt(qnorm(conf)^2+4*r*q)
		C=2*(n+qnorm(conf)^2)
		A2=2*r2+qnorm(conf)^2
		B2=qnorm(conf)*sqrt(qnorm(conf)^2+4*r2*q2)
		C2=2*(n+qnorm(conf)^2)
		Lower=(A-B)/C
		Upper=(A+B)/C
		Lower2=(A2-B2)/C2
		Upper2=(A2+B2)/C2
		D=p-p2
		r3=length(which(x+y>1))
		t3=length(which(x>y))
		s3=length(which(y>x))
		u3=length(which((x+y)<1))
		A=(r3+s3)*(t3+u3)*(r3+t3)*(s3+u3)
		B=r3*u3-s3*t3
		if(r3+s3==0 | t3+u3==0 | r3+t3==0 | s3+u3==0){0->Psi}else if(B>n/2){(B-n/2)/sqrt(A)->Psi} else if(0<=B & B<=n/2){0->Psi} else if(B<0){B/sqrt(A)->Psi}
		Lower3=round(D-sqrt((p-Lower)^2-2*Psi*(p-Lower)*(Upper2-p2)+(Upper2-p2)^2),3)
		Upper3=round(D+sqrt((p2-Lower2)^2-2*Psi*(p2-Lower2)*(Upper-p)+(Upper-p)^2),3)
		Prop=D
		temp=c(z[i],Lower3,round(Prop,3),Upper3)
		final=rbind(final, temp,row.names=NULL)
		}
		Name="    Difference of proportions with CI(s); paired"
		Effectsize="Effect size (ES): Proportion of pairewise differences x - y."
	}
	names(final)=c("CI","LCL","ES","UCL")
	setClass("confidence", contains="data.frame")
	final<-as(final,"confidence")
	cat("","\n")
	cat(Name,"\n")
	cat("","\n")
	cat(Effectsize,"\n")
	cat("","\n")
	final
}