numsplits<-1000

f=file.choose()
text<-readLines(f,encoding="UTF-8")
nrows<-length(text)
writeLines(text[length(text)], con = "D:\\projects\\basicToR\\junk.txt", sep = "\n", useBytes = FALSE)
k<-read.table("D:\\projects\\basicToR\\junk.txt",sep=",")
ncolumns<-length(k)
print("nrows="); print(nrows)
print("ncolumns="); print(ncolumns)

t<-read.table(f,sep=",")
nentries=0;for (i in t){for (k in i){nentries=nentries+1}}
print("nentries=");print(nentries)

if(nentries==nrows*ncolumns)	{
	 print("Columns, rows, and entries check; we're good to go.")
	}
else{
     print("Columns, rows, and entries don't check; please look at your data file to make sure each line has equal no. of entries.")
	}



#t<-read.table(f,sep=",")
#for (i in seq(1, nrows, 1)) {
#	for (j in seq(1, ncolumns, 1)) {
#		if(j!=ncolumns){
#			print(t[i,j]);print(",");
#		}
#		else{
#			print(t[i,j]);#chr$(10) 
#		}
#	}
#}



nfirsthalf<-ncolumns/2
nsechalf<-ncolumns-nfirsthalf
sumr<-0
sumsteppedr<-0

for (split in seq(1, numsplits, 1)){
	firstsofar=0
	sum1=0
	count1=0
	sum2=0
	count2=0
	sumsteppedrspear=0
	sumsteppedrrulon=0
	randnum<-list()
  score1<-list()
  randnum2<-list()

	for (i in seq(1, nfirsthalf, 1)) {
		randnum[i]=round(ncolumns*runif(1, min=0, max=1)+1)
		taken<-"no"
		for (q in seq(1,firstsofar,1)) {
			if( randnum[i]==randnum[q]) {taken="yes"}
		}
		if (taken=="yes"){randnum[i]=round(ncolumns*runif(1, min=0, max=1)+1)}
	    print("Keeper is");print(randnum(i))
   		firstsofar=firstsofar+1
	}

	for (i in seq(1, nfirsthalf, 1)) {
		print(randnum[i])
	}

	j<-0
	for (i in seq(1, ncolumns, 1)) {
		taken<-"no"
		for (q in seq(1, nfirsthalf, 1)) {
			if (randnum[q]==i){taken="yes"}
		}
		if (taken=="no"){
			j=j+1
			randnum2[j]=i
		}
	}

	for (i in seq(1, nsechalf, 1)) {
		print("randnum2="); print(randnum2[i])
	}


	sum1=0
	count1=0
	for (z in seq(1, nrows, 1)) {
		sum1=0
		count1=0	
		for (i in seq(1, nfirsthalf, 1)) {
			y=randnum[i]
			if (t[z,y]!="n"){sum1=sum1+as.numeric(t[z,y]);count1=count1+1}
		}
		if(count1==0){print("a split where all were missing! line number=");print(z);count1=1}
		av1[z]=sum1/count1
		score1[z]=av1[z]*nfirsthalf
	}


	sum2=0
	count2=0
	for (z in seq(1, nrows, 1)) {
		sum2=0
		count2=0
		for (i in seq(1, nfirsthalf, 1)) {
			y=randnum2[i]
			if(t[z,y]!="n"){sum2=sum2+as.numeric(t[z,y]);count2=count2+1}
		}
		av2[z]=sum2/count2
		score2[z]=av2[z]*nsechalf
	}

	for (z in seq(1, nrows, 1)) {
		scoretot[z]=score1[z]+score2[z]
	}

	sumxy=0
	sumx=0
	sumy=0
	sumx2=0
	sumy2=0
	sumscoretot2=0
	sumscoretot=0

	for (i in seq(1, nrows, 1)) {
		sumxy=sumxy+score1[i]*score2[i]
		sumx=sumx+score1[i]
		sumy=sumy+score2[i]
		sumx2=sumx2+(score1[i])^2
		sumy2=sumy2+(score2[i])^2
		sumscoretot2=sumscoretot2+scoretot[i]^2
		sumscoretot=sumscoretot+scoretot[i]
	}

	r=(sumxy-sumx*sumy/nrows)/((sumx2-sumx^2/nrows)*(sumy2-sumy^2/nrows))^0.5
	sdforx=((1/nrows)*(sumx2-sumx^2/nrows))^0.5
	sdfory=((1/nrows)*(sumy2-sumy^2/nrows))^0.5
	varfortot=((1/nrows)*(sumscoretot2-sumscoretot^2/nrows))

	steppedrspear=(2*r)/(1+r)
	steppedrrulon=4*r*sdforx*sdfory/varfortot
	sumsteppedrspear=sumsteppedrspear+steppedrspear
	sumsteppedrrulon=sumsteppedrrulon+steppedrrulon
}

avsteppedrspear=sumsteppedrspear/numsplits
print("average of stepped up r's, using Spearman method=");print(avsteppedrspear)
avsteppedrrulon=sumsteppedrrulon/numsplits
print("average of stepped up r's, using Rulon method="); print(avsteppedrrulon)

sumvariances=0
for (i in seq(1, ncolumns, 1)) {
	sumfirsts=0
	sumsq=0
	variance=0
	for (j in seq(1, nrows, 1)) {
		sumfirsts=sumfirsts+as.numeric(t[j,i])
		sumsq=sumsq+(as.numeric(t[j,i]))^2
	}
	sfs=sumfirsts^2
	variance=(1/nrows)*(sumsq-sfs/nrows)
	sumvariances=sumvariances+variance
}

for (i in seq(1, ncolumns, 1)) {
	mean=0
	sumdevs2=0
	sumfirsts=0
	for (j in seq(1, nrows, 1)) {
		sumfirsts=sumfirsts+as.numeric(t[j,i])
	}
	mean=sumfirsts/nrows
	for (j in seq(1, nrows, 1)) {
		sumdevs2=sumdevs2+(as.numeric(t[j,i])-mean)^2
	}
	sumvariances=sumvariances+sumdevs2/nrows
}	

alphatrad=(ncolumns/(ncolumns-1))*(1-sumvariances/varfortot)

print("alphatrad=");print(alphatrad)