# published on: 
# http://www.r-statistics.com/2010/02/barnards-exact-test-a-powerful-alternative-for-fishers-exact-test-implemented-in-r/
 
Barnardextest<-function(Ta,Tb =NULL,Tc =NULL,Td =NULL, to.print = F, to.plot = T)
{
# The first argument (Ta) can be either a table or a matrix of 2X2.
# Or instead, the values of the table can be entered one by one to the function
 
#Barnard's test calculates the probabilities for contingency tables.  It has been shown that for 2x2 tables, Barnard's test
#has a higher power than Fisher's Exact test.  Barnard's test is a non-parametric test that relies upon a computer to generate
#the distribution of the Wald statistic.  Using a computer program, one could find the nuisance parameter that maximizes the 
#probability of the observations displayed from a table.
#Despite giving lower p-values for 2x2 tables, Barnard's test hasn't been used as often as Fisher's test because of its
#computational difficulty.  This code gives the Wald statistic, the nuisance parameter, and the p-value for any 2x2 table.
#The table can be written as:
#			Var.1
#		 ---------------
#		   a		b	 r1=a+b
#	Var.2
#		   c		d	 r2=c+d
#		 ---------------
#		 c1=a+c   c2=b+d	 n=c1+c2
 
#One example would be 
#				Physics
#			 Pass	     Fail
#			 ---------------
#		Crane	   8		14
#  Collage	
#		Egret	   1		3
#			 ---------------
#
#After implementing the function, simply call it by the command:
#Barnardextest(8,14,1,3)
#This will display the results:
 
#"The contingency table is:"
#      [,1] [,2]
#[1,]    8   14
#[2,]    1    3
#"Wald Statistic:"
#0.43944
#"Nuisance parameter:"
#0.9001
#"The 1-tailed p-value:"
#0.4159073
 
#On a side note, I believe there are more efficient codes than this one.  For example, I've seen codes in Matlab that run
#faster and display nicer-looking graphs.  However, this code will still provide accurate results and a plot that gives the
#p-value based on the nuisance parameter.  I did not come up with the idea of this code, I simply translated Matlab code 
#into R, occasionally using different methods to get the same result.  The code was translated from:
#
#Trujillo-Ortiz, A., R. Hernandez-Walls, A. Castro-Perez, L. Rodriguez-Cardozo. Probability Test.  A MATLAB file. URL
#http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=6198
#
#My goal was to make this test accessible to everyone.  Although there are many ways to run this test through Matlab, I hadn't
#seen any code to implement this test in R.  I hope it is useful for you, and if you have any questions or ways to improve
#this code, please contact me at calhoun.peter@gmail.com.
 
 
	# Tal edit: choosing if to work with a 2X2 table or with 4 numbers:
	if(is.null(Tb) | is.null(Tc) | is.null(Td) )
	{
		# If one of them is null, then Ta should have an entire table, and we can take it's values
		if(is.table(Ta) | is.matrix(Ta))
		{
			if(sum(dim(Ta) == c(2,2))==2)
			{
				Tb <- Ta[1,2]
				Tc <- Ta[2,1]
				Td <- Ta[2,2]
				Ta <- Ta[1,1]		
			} else {stop("The table is not 2X2, please check it again...") }		
		} else {stop("We are missing value in the table") }		
	}
 
 
	c1<-Ta+Tc
	c2<-Tb+Td
	n<-c1+c2
	pao<-Ta/c1
	pbo<-Tb/c2
	pxo<-(Ta+Tb)/n
	TXO<-abs(pao-pbo)/sqrt(pxo*(1-pxo)*(1/c1+1/c2))
	n1<-prod(1:c1)
	n2<-prod(1:c2)
 
	P<-{}
	for( p in (0:99+.01)/100)
	{
		TX<-{}
		S<-{}
		for( i in c(0:c1))
		{
			for( j in c(0:c2))
			{
				if(prod(1:i)==0){fac1<-1} else {fac1<-prod(1:i)}
				if(prod(1:j)==0){fac2<-1} else {fac2<-prod(1:j)}
				if(prod(1:(c1-i))==0){fac3<-1} else {fac3<-prod(1:(c1-i))}
				if(prod(1:(c2-j))==0){fac4<-1} else {fac4<-prod(1:(c2-j))}
 
				small.s<-(n1*n2*(p^(i+j))*(1-p)^(n-(i+j))/(fac1*fac2*fac3*fac4))
				S<-cbind(S,small.s)
				pa<- i/c1
				pb<-j/c2
				px <- (i+j)/n
				if(is.nan((pa-pb)/sqrt(px*(1-px)*((1/c1)+(1/c2)))))
					{
						tx<-0
					} else {
						tx <- (pa-pb)/sqrt(px*(1-px)*((1/c1)+(1/c2)))
					}
				TX<-cbind(TX,tx)
			}
		}
 
		P<-cbind(P,sum(S[which(TX>=TXO)]))
	}
 
	np<-which(P==max(P))
	p <- (0:99+.01)/100
	nuisance<-p[np]
	pv<-P[np]
 
 
	if(to.print)
	{ 
		print("The contingency table is:")
		print(matrix(c(Ta,Tc,Tb,Td),2,2))
		print("Wald Statistic:")
		print(TXO)
		print("Nuisance parameter:")
		print(nuisance)
		print("The 1-tailed p-value:")
		print(pv)
	}
	if(to.plot)
	{
		plot(p,P,type="l",main="Barnard's exact P-value", xlab="Nuisance parameter", ylab="P-value")
		points(nuisance,pv,col=2)
	}
 
	return(	
			list(
					contingency.table = as.table(matrix(c(Ta,Tc,Tb,Td),2,2)),
					Wald.Statistic = TXO,
					Nuisance.parameter = nuisance,
					p.value.one.tailed = pv					
				)
			)
}
 
 
Barnardextest(matrix(c(8,1,14,3),2,2))
fisher.test(matrix(c(8,1,14,3),2,2))
 
 
Convictions <-
matrix(c(2, 10, 15, 3),
		   nrow = 2,
		   dimnames =
		   list(c("Dizygotic", "Monozygotic"),
				c("Convicted", "Not convicted")))
Convictions
fisher.test(Convictions, alternative = "less")
Barnardextest(Convictions)