#########################################
# function "casecontrol" calls "ftns.R" #
#########################################

casecontrol = function(r0,r1,r2,s0,s1,s2,N_bootstrap){

	source("casecontrol_ftns.R")

	xx = matrix(c(r0,r1,r2,s0,s1,s2),nrow=2,byrow=T)

	x = 0
	trendt = ftn_catt(xx,c(0,x,1))
	z0 = trendt$estimate
	pz0 = trendt$p.value

	x = 0.5
	trendt = ftn_catt(xx,c(0,x,1))
	z0.5 = trendt$estimate
	pz0.5 = trendt$p.value

	x = 1
	trendt = ftn_catt(xx,c(0,x,1))
	z1 = trendt$estimate
	pz1 = trendt$p.value

	chit = chisq.test(xx)
	chi2 = chit$statistic
	pchi2 = chit$p.value

	min2 = min(pz0.5,pchi2)
	pmin2 = ftn_pmin2(min2)

	CLRT = ftn_CLRT(r0,r1,r2,s0,s1,s2)
	MAX = max(abs(z0),abs(z0.5),abs(z1))

	output = ftn_p_MAX_CLRT(N_bootstrap,r0,r1,r2,s0,s1,s2,MAX,CLRT)
	pMAX = output$pMAX
	pCLRT = output$pCLRT


	output = list(REC = c(z0,pz0), ADD = c(z0.5,pz0.5), DOM = c(z1,pz1), CHI2=c(chi2,pchi2),MAX3 = c(MAX,pMAX), CLRT=c(CLRT,pCLRT),MIN2=c(min2,pmin2))
	return(output)
} # end function casecontrol 

#r0 = 25
#r1 = 274
#r2 = 387
#s0 = 65
#s1 = 251
#s2 = 353
#casecontrol(r0,r1,r2,s0,s1,s2,1000000)