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R/tcov.R
In SMARTAR: Sequential Multiple Assignment Randomized Trial and Adaptive Randomization
Defines functions
tcov
#tcov() to get var-cov component for effect size
#input two strategies and sequence information
#matrix, also the method to estimate
tcov<-function(ats1,ats2,sim,family="gaussian",method="Gest"){
ATS1<-ats1
ATS2<-ats2
Smat<-sim
FA<-family
MA<-method
if (is.null(Smat$O1)) {Base<-0} else {Base<-1}
Nstage<-nstage(data=Smat)
I<-overlap(ats1=ATS1,ats2=ATS2,nstage=Nstage,baseline=Base)
if (Nstage==1 && Base==0) {
pi1<-Smat$PI1[which(Smat$A1==ATS1[1])] #P(A1==1)
uJ<-Smat$MEAN[which(Smat$A1==ATS1[1])]
if (FA=="gaussian") {vJ<-Smat$SD[which(Smat$A1==ATS1[1])]^2} else
if (FA=="binomial") {vJ<-uJ*(1-uJ)} else
stop("invalid enter for argument 'family'")
tvc<-I[1]*vJ/pi1
} else
if (Nstage==1 && Base==1) {
pr<-mean(Smat$P1[which(Smat$O1==1)]) #P(O1==1)
pi0<-Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[1])] #P(A1==1|O1==0)
pi1<-Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[1])] #P(A1==1|O1==1)
u0J<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS1[1])]
if (is.na(u0J)) {u0J<-0}
# within-sequence true mean (EY)
u1J<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS1[2])]
if (is.na(u1J)) {u1J<-0}
u0K<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS2[1])]
if (is.na(u0K)) {u0K<-0}
u1K<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS2[2])]
if (is.na(u1K)) {u1K<-0}
if (FA=="gaussian"){v0J<-Smat$SD[which(Smat$O1==0 &
Smat$A1==ATS1[1])]^2
#within-sequence variance for cont outcome
v1J<-Smat$SD[which(Smat$O1==1 &
Smat$A1==ATS1[2])]^2
v0K<-Smat$SD[which(Smat$O1==0 &
Smat$A1==ATS2[1])]^2
v1K<-Smat$SD[which(Smat$O1==1 &
Smat$A1==ATS2[2])]^2} else
if (FA=="binomial"){v0J<-u0J*(1-u0J)
v1J<-u1J*(1-u1J)
v0K<-u0K*(1-u0K)
v1K<-u1K*(1-u1K)} else
stop("invalid enter for argument 'family'")
if (is.na(v0J)) {v0J<-0}
if (is.na(v1J)) {v1J<-0}
if (is.na(v0K)) {v0K<-0}
if (is.na(v1K)) {v1K<-0}
B1<-1*pr*(1-pr)*(u1J-u0J)*(u1K-u0K)
#MLE for cont outcome without com assumption
B2<-I[1]*(1-pr)*v0J/pi0
B3<-I[2]*pr*v1J/pi1
tvc<-B1+B2+B3
} else
if (Nstage==2 && Base==0) {
pi1<-mean(Smat$PI1[which(Smat$A1==ATS1[1])])
pr <-mean(Smat$P2[which(Smat$A1==ATS1[1] &
Smat$O2==1)])
pi20J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2])])
pi21J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3])])
u0J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2])]
u1J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3])]
u0K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2])]
u1K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[3])]
if (FA=="gaussian"){v0J<-Smat$SD[which(Smat$A1==ATS1[1]
& Smat$O2==0 &
Smat$A2==ATS1[2])]^2
v1J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==1 &
Smat$A2==ATS1[3])]^2
v0K<-Smat$SD[which(Smat$A1==ATS2[1] &
Smat$O2==0 &
Smat$A2==ATS2[2])]^2
v1K<-Smat$SD[which(Smat$A1==ATS2[1] &
Smat$O2==1 &
Smat$A2==ATS2[3])]^2}
else
if (FA=="binomial"){v0J<-u0J*(1-u0J)
v1J<-u1J*(1-u1J)
v0K<-u0K*(1-u0K)
v1K<-u1K*(1-u1K)} else
stop("invalid enter for argument 'family'")
if (is.na(u0J)) {u0J<-0}
if (is.na(u1J)) {u1J<-0}
if (is.na(u0K)) {u0K<-0}
if (is.na(u1K)) {u1K<-0}
if (length(v0J)==0) {v0J<-0}
if (length(v1J)==0) {v1J<-0}
if (length(v0K)==0) {v0K<-0}
if (length(v1K)==0) {v1K<-0}
if (is.nan(pr)) {pr<-0}
if (is.nan(pi1)) {pi1<-1}
if (is.nan(pi20J)) {pi20J<-1}
if (is.nan(pi21J)) {pi21J<-1}
B1<-I[1]*(u1J-u0J)*(u1K-u0K)*pr*(1-pr)/pi1
B2<-I[2]*v0J*(1-pr)/(pi1*pi20J)
B3<-I[3]*v1J*pr /(pi1*pi21J)
tvc<-B1+B2+B3
} else
if (Nstage==2 && Base==1) {
P0<-mean(Smat$P1[which(Smat$O1==0)]); if (is.nan(P0)) {P0<-0}
P1<-mean(Smat$P1[which(Smat$O1==1)]); if (is.nan(P1)) {P1<-0}
pi0J<-mean(Smat$PI1[which(Smat$O1==0 & Smat$A1==ATS1[1])])
if (is.nan(pi0J)) {pi0J<-1}
pi1J<-mean(Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[2])])
if (is.nan(pi1J)) {pi1J<-1}
P00J<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS1[1] & Smat$O2==0)])
if (is.nan(P00J)) {P00J<-0}
P01J<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS1[1] & Smat$O2==1)])
if (is.nan(P01J)) {P01J<-0}
P10J<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS1[2] & Smat$O2==0)])
if (is.nan(P10J)) {P10J<-0}
P11J<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS1[2] & Smat$O2==1)])
if (is.nan(P11J)) {P11J<-0}
P00K<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS2[1] & Smat$O2==0)])
if (is.nan(P00K)) {P00K<-0}
P01K<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS2[1] & Smat$O2==1)])
if (is.nan(P01K)) {P01K<-0}
P10K<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS2[2] & Smat$O2==0)])
if (is.nan(P10K)) {P10K<-0}
P11K<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS2[2] & Smat$O2==1)])
if (is.nan(P11K)) {P11K<-0}
pi00J<-mean(Smat$PI2[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3])])
if (is.nan(pi00J)) {pi00J<-1}
pi01J<-mean(Smat$PI2[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[4])])
if (is.nan(pi01J)) {pi01J<-1}
pi10J<-mean(Smat$PI2[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==0 & Smat$A2==ATS1[5])])
if (is.nan(pi10J)) {pi10J<-1}
pi11J<-mean(Smat$PI2[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==1 & Smat$A2==ATS1[6])])
if (is.nan(pi11J)) {pi11J<-1}
u00J<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3])]
if (is.na(u00J)) {u00J<-0}
u01J<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[4])]
if (is.na(u01J)) {u01J<-0}
u10J<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==0 & Smat$A2==ATS1[5])]
if (is.na(u10J)) {u10J<-0}
u11J<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==1 & Smat$A2==ATS1[6])]
if (is.na(u11J)) {u11J<-0}
u00K<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[3])]
if (is.na(u00K)) {u00K<-0}
u01K<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[4])]
if (is.na(u01K)) {u01K<-0}
u10K<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS2[2] &
Smat$O2==0 & Smat$A2==ATS2[5])]
if (is.na(u10K)) {u10K<-0}
u11K<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS2[2] &
Smat$O2==1 & Smat$A2==ATS2[6])]
if (is.na(u11K)) {u11K<-0}
if (FA=="gaussian"){
v00J<-Smat$SD[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3])]^2
v01J<-Smat$SD[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[4])]^2
v10J<-Smat$SD[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==0 & Smat$A2==ATS1[5])]^2
v11J<-Smat$SD[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==1 & Smat$A2==ATS1[6])]^2} else
if (FA=="binomial"){v00J<-u00J*(1-u00J)
v01J<-u01J*(1-u01J)
v10J<-u10J*(1-u10J)
v11J<-u11J*(1-u11J)}else
stop("invalid enter for argument 'family'")
if (length(v00J)==0) {v00J<-0}
if (length(v01J)==0) {v01J<-0}
if (length(v10J)==0) {v10J<-0}
if (length(v11J)==0) {v11J<-0}
A0000<- (P0*(1-P0)*P00J*P00K+I[1]*P0*P0*P00J*
(1-P00J)/(P0*pi0J))*u00J*u00K
A0001<- (P0*(1-P0)*P00J*P01K-I[1]*P0*P0*P00J*
(1-P00J)/(P0*pi0J))*u00J*u01K
A0010<--(P0*(1-P0)*P00J*P10K)*u00J*u10K
A0011<--(P0*(1-P0)*P00J*P11K)*u00J*u11K
A0100<- (P0*(1-P0)*P01J*P00K-I[1]*P0*P0*P01J*
(1-P01J)/(P0*pi0J))*u01J*u00K
A0101<- (P0*(1-P0)*P01J*P01K+I[1]*P0*P0*P01J*
(1-P01J)/(P0*pi0J))*u01J*u01K
A0110<--(P0*(1-P0)*P01J*P10K)*u01J*u10K
A0111<--(P0*(1-P0)*P01J*P11K)*u01J*u11K
A1000<--(P1*(1-P1)*P10J*P00K)*u10J*u10K
A1001<--(P1*(1-P1)*P10J*P01K)*u10J*u11K
A1010<- (P1*(1-P1)*P10J*P10K+I[1]*P1*P1*P10J*
(1-P10J)/(P1*pi1J))*u10J*u10K
A1011<- (P1*(1-P1)*P10J*P11K-I[1]*P1*P1*P10J*
(1-P10J)/(P1*pi1J))*u10J*u11K
A1100<--(P1*(1-P1)*P10J*P00K)*u10J*u10K
A1101<--(P1*(1-P1)*P10J*P01K)*u10J*u11K
A1110<- (P1*(1-P1)*P11J*P10K+I[1]*P1*P1*P11J*
(1-P11J)/(P1*pi1J))*u11J*u10K
A1111<- (P1*(1-P1)*P10J*P11K-I[1]*P1*P1*P11J*
(1-P11J)/(P1*pi1J))*u11J*u11K
A<-sum(A0000,A0001,A0010,A0011,
A0100,A0101,A0110,A0111,
A1000,A1001,A1010,A1011,
A1100,A1101,A1110,A1111)
if (I[1]==1 && I[3]==1) {B0000<-P0*P0*P00J*P00J*
v00J/(P0*pi0J*P00J*pi00J)} else {B0000<-0}
if (I[1]==1 && I[4]==1) {B0101<-P0*P0*P01J*P01J*
v01J/(P0*pi0J*P01J*pi01J)} else {B0101<-0}
if (I[2]==1 && I[5]==1) {B1010<-P1*P1*P10J*P10J*
v10J/(P1*pi1J*P10J*pi10J)} else {B1010<-0}
if (I[2]==1 && I[6]==1) {B1111<-P1*P1*P11J*P11J*
v11J/(P1*pi1J*P11J*pi11J)} else {B1111<-0}
B<-sum(B0000,B0101,B1010,B1111)
tvc<-A+B
} else
if (Nstage==3 && Base==0) {
piJ<-mean(Smat$PI1[which(Smat$A1==ATS1[1])])
if (is.nan(piJ)) {piJ<-0} # A1<-dJ[1]
P0J<-mean(Smat$P2[which(Smat$A1==ATS1[1] & Smat$O2==0)])
if (is.nan(P0J)) {P0J<-0}
P1J<-mean(Smat$P2[which(Smat$A1==ATS1[1] & Smat$O2==1)])
if (is.nan(P1J)) {P1J<-0}
P0K<-mean(Smat$P2[which(Smat$A1==ATS2[1] & Smat$O2==0)])
if (is.nan(P0K)) {P0K<-0}
P1K<-mean(Smat$P2[which(Smat$A1==ATS2[1] & Smat$O2==1)])
if (is.nan(P1K)) {P1K<-0}
pi0J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2])])
if (is.nan(pi0J)) {pi0J<-0}
pi1J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3])])
if (is.nan(pi1J)) {pi1J<-0}
P00J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] & Smat$O3==0)])
if (is.nan(P00J)) {P00J<-0}
P01J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] & Smat$O3==1)])
if (is.nan(P01J)) {P01J<-0}
P10J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3] & Smat$O3==0)])
if (is.nan(P10J)) {P10J<-0}
P11J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3] & Smat$O3==1)])
if (is.nan(P11J)) {P11J<-0}
P00K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] & Smat$O3==0)])
if (is.nan(P00K)) {P00K<-0}
P01K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] & Smat$O3==1)])
if (is.nan(P01K)) {P01K<-0}
P10K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[3] & Smat$O3==0)])
if (is.nan(P10K)) {P10K<-0}
P11K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[3] & Smat$O3==1)])
if (is.nan(P11K)) {P11K<-0}
pi00J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==0 &
Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[4])])
if (is.nan(pi00J)) {pi00J<-0}
pi01J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==0 &
Smat$A2==ATS1[2] &
Smat$O3==1 & Smat$A3==ATS1[5])])
if (is.nan(pi01J)) {pi01J<-0}
pi10J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==1 &
Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[6])])
if (is.nan(pi10J)) {pi10J<-0}
pi11J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==1 &
Smat$A2==ATS1[3] &
Smat$O3==1 & Smat$A3==ATS1[7])])
if (is.nan(pi11J)) {pi11J<-0}
u00J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[4])]
if (is.nan(u00J)) {u00J<-0} # within-sequence true mean (EY)
u01J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[5])]
if (is.nan(u01J)) {u01J<-0}
u10J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[6])]
if (is.nan(u10J)) {u10J<-0}
u11J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[7])]
if (is.nan(u11J)) {u11J<-0}
u00K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] &
Smat$O3==0 & Smat$A3==ATS2[4])]
if (is.nan(u00K)) {u00K<-0} # within-sequence true mean (EY)
u01K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] &
Smat$O3==0 & Smat$A3==ATS2[5])]
if (is.nan(u01K)) {u01K<-0}
u10K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[3] &
Smat$O3==0 & Smat$A3==ATS2[6])]
if (is.nan(u10K)) {u10K<-0}
u11K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[3] &
Smat$O3==0 & Smat$A3==ATS2[7])]
if (is.nan(u11K)) {u11K<-0}
if (FA=="gaussian"){
v00J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[4])]^2
# within-sequence true mean (EY)
v01J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[5])]^2
v10J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[6])]^2
v11J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 &
Smat$A3==ATS1[7])]^2}else
if (FA=="binomial") {bv00J<-u00J*(1-u00J)
if (is.na(bv00J)) {bv00J<-0}
#within-sequence var est for bin outcome
bv01J<-u01J*(1-u01J)
if (is.na(bv01J)) {bv01J<-0}
bv10J<-u10J*(1-u10J)
if (is.na(bv10J)) {bv10J<-0}
bv11J<-u11J*(1-u11J)
if (is.na(bv11J)) {bv11J<-0}}else
stop("invalid enter for argument 'family'")
if (length(v00J)==0) {v00J<-0}
if (length(v01J)==0) {v01J<-0}
if (length(v10J)==0) {v10J<-0}
if (length(v11J)==0) {v11J<-0}
A0000<- (I[1]*P0J*(1-P0J)*P00J*P00K/piJ+I[2]*
P0J*P0J*P00J*(1-P00J)/
(piJ*P0J*pi00J))*u00J*u00K
A0001<- (I[1]*P0J*(1-P0J)*P00J*P01K/piJ-I[2]*
P0J*P0J*P00J*(1-P00J)/
(piJ*P0J*pi00J))*u00J*u01K
A0010<--(I[1]*P0J*(1-P0J)*P00J*P10K/piJ)*
u00J*u10K
A0011<--(I[1]*P0J*(1-P0J)*P00J*P11K/piJ)*
u00J*u11K
A0100<- (I[1]*P0J*(1-P0J)*P01J*P00K/piJ-I[2]*
P0J*P0J*P01J*(1-P01J)/(piJ*P0J*pi01J))*u01J*u00K
A0101<- (I[1]*P0J*(1-P0J)*P01J*P01K/piJ+I[2]*
P0J*P0J*P01J*(1-P01J)/(piJ*P0J*pi01J))*u01J*u01K
A0110<--(I[1]*P0J*(1-P0J)*P01J*P10K/piJ)*u01J*u10K
A0111<--(I[1]*P0J*(1-P0J)*P01J*P11K/piJ)*u01J*u11K
A1000<--(I[1]*P1J*(1-P1J)*P10J*P00K/piJ)*u10J*u10K
A1001<--(I[1]*P1J*(1-P1J)*P10J*P01K/piJ)*u10J*u11K
A1010<- (I[1]*P1J*(1-P1J)*P10J*P10K/piJ+I[3]*
P1J*P1J*P10J*(1-P10J)/(piJ*P1J*pi10J))*u10J*u10K
A1011<- (I[1]*P1J*(1-P1J)*P10J*P11K/piJ-I[3]*
P1J*P1J*P10J*(1-P10J)/(piJ*P1J*pi10J))*u10J*u11K
A1100<--(I[1]*P1J*(1-P1J)*P10J*P00K/piJ)*u10J*u10K
A1101<--(I[1]*P1J*(1-P1J)*P10J*P01K/piJ)*u10J*u11K
A1110<- (I[1]*P1J*(1-P1J)*P11J*P10K/piJ+I[3]*
P1J*P1J*P11J*(1-P11J)/(piJ*P1J*pi11J))*u11J*u10K
A1111<- (I[1]*P1J*(1-P1J)*P10J*P11K/piJ-I[3]*
P1J*P1J*P11J*(1-P11J)/(piJ*P1J*pi11J))*u11J*u11K
A<-sum(A0000,A0001,A0010,A0011,
A0100,A0101,A0110,A0111,
A1000,A1001,A1010,A1011,
A1100,A1101,A1110,A1111)
if (FA=="binomial"){
if (I[1]==1 && I[2]==1 && I[4]==1) {B0000<-P0J*P0J*P00J*
P00K*bv00J/(piJ*P0J*pi00J*P00J*pi00J)} else {B0000<-0}
if (I[1]==1 && I[2]==1 && I[5]==1) {B0101<-P0J*P0J*P01J*
P01K*bv01J/(piJ*P0J*pi00J*P01J*pi01J)} else {B0101<-0}
if (I[1]==1 && I[3]==1 && I[6]==1) {B1010<-P1J*P1J*P10J*
P10K*bv10J/(piJ*P1J*pi10J*P10J*pi10J)} else {B1010<-0}
if (I[1]==1 && I[3]==1 && I[7]==1) {B1111<-P1J*P1J*P11J*
P11K*bv11J/(piJ*P1J*pi11J*P11J*pi11J)} else {B1111<-0}
} else
if (FA=="gaussian") {
if (I[1]==1 && I[2]==1 && I[4]==1) {B0000<-P0J*P0J*P00J*
P00K*v00J/(piJ*P0J*pi00J*P00J*pi00J)} else {B0000<-0}
if (I[1]==1 && I[2]==1 && I[5]==1) {B0101<-P0J*P0J*P01J*
P01K*v01J/(piJ*P0J*pi00J*P01J*pi01J)} else {B0101<-0}
if (I[1]==1 && I[3]==1 && I[6]==1) {B1010<-P1J*P1J*P10J*
P10K*v10J/(piJ*P1J*pi10J*P10J*pi10J)} else {B1010<-0}
if (I[1]==1 && I[3]==1 && I[7]==1) {B1111<-P1J*P1J*P11J*
P11K*v11J/(piJ*P1J*pi11J*P11J*pi11J)} else {B1111<-0}
}else
stop("invalid enter for argument 'family'")
B<-sum(B0000,B0101,B1010,B1111)
tvc<-A+B
}
##else
## if (Nstage==3 && Base==1) {
## P0<-mean(Smat$P1[which(Smat$O1==0)])
## if (is.nan(P0)) {P0<-0}
## P1<-mean(Smat$P1[which(Smat$O1==1)])
## if (is.nan(P1)) {P1<-0}
##
## pi0J<-mean(Smat$PI1[which(Smat$O1==0 & Smat$A1==ATS1[1])])
## if (is.nan(pi0J)) {pi0J<-1}
## pi1J<-mean(Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[2])])
## if (is.nan(pi1J)) {pi1J<-1}
##
##P00J<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0)])
##if (is.nan(P00J)) {P00J<-0}
##P01J<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1)])
##if (is.nan(P01J)) {P01J<-0}
##P10J<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0)])
##if (is.nan(P10J)) {P10J<-0}
##P11J<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1)])
##if (is.nan(P11J)) {P11J<-0}
##P00K<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0)])
##if (is.nan(P00K)) {P00K<-0}
##P01K<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1)])
##if (is.nan(P01K)) {P01K<-0}
##P10K<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0)])
##if (is.nan(P10K)) {P10K<-0}
##P11K<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1)])
##if (is.nan(P11K)) {P11K<-0}
##pi00J<-mean(Smat$PI2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==0 &
## Smat$A2==ATS1[3])])
##if (is.nan(pi00J)) {pi00J<-1}
##pi01J<-mean(Smat$PI2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==1 &
## Smat$A2==ATS1[4])])
##if (is.nan(pi01J)) {pi01J<-1}
##pi10J<-mean(Smat$PI2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] &
## Smat$O2==0 &
## Smat$A2==ATS1[5])])
##if (is.nan(pi10J)) {pi10J<-1}
##pi11J<-mean(Smat$PI2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] &
## Smat$O2==1 &
## Smat$A2==ATS1[6])])
##if (is.nan(pi11J)) {pi11J<-1}
##P000J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==0 &
## Smat$A2==ATS1[3] &
## Smat$O3==0)])
##if (is.nan(P000J)) {P000J<-0}
##P001J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==0 &
## Smat$A2==ATS1[3] &
## Smat$O3==1)])
##if (is.nan(P001J)) {P001J<-0}
##P010J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==1 &
## Smat$A2==ATS1[4] &
## Smat$O3==0)])
##if (is.nan(P010J)) {P010J<-0}
##P011J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==1 &
## Smat$A2==ATS1[4] &
## Smat$O3==1)])
##if (is.nan(P011J)) {P011J<-0}
##P100J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0)])
##if (is.nan(P100J)) {P100J<-0}
##P101J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1)])
##if (is.nan(P101J)) {P101J<-0}
##P110J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0)])
##if (is.nan(P110J)) {P110J<-0}
##P111J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1)])
##if (is.nan(P111J)) {P111J<-0}
##P000K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==0)])
##if (is.nan(P000K)) {P000K<-0}
##P001K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==1)])
##if (is.nan(P001K)) {P001K<-0}
##P010K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==0)])
##if (is.nan(P010K)) {P010K<-0}
##P011K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==1)])
##if (is.nan(P011K)) {P011K<-0}
##P100K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==0)])
##if (is.nan(P100K)) {P100K<-0}
##P101K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==1)])
##if (is.nan(P101K)) {P101K<-0}
##P110K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==0)])
##if (is.nan(P110K)) {P110K<-0}
##P111K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==1)])
##if (is.nan(P111K)) {P111K<-0}
##pi000J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==0 &
## Smat$A3==ATS1[7])])
##if (is.nan(P000J)) {P000J<-0}
##pi001J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==1 &
## Smat$A3==ATS1[8])])
##if (is.nan(P001J)) {P001J<-0}
##pi010J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==0 &
## Smat$A3==ATS1[9])])
##if (is.nan(P010J)) {P010J<-0}
##pi011J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==1 &
## Smat$A3==ATS1[10])])
##if (is.nan(P011J)) {P011J<-0}
##pi100J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0 &
## Smat$A3==ATS1[11])])
##if (is.nan(P100J)) {P100J<-0}
##pi101J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1 &
## Smat$A3==ATS1[12])])
##if (is.nan(P101J)) {P101J<-0}
##pi110J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0 &
## Smat$A3==ATS1[13])])
##if (is.nan(P110J)) {P110J<-0}
##pi111J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1 &
## Smat$A3==ATS1[14])])
##if (is.nan(P111J)) {P111J<-0}
##u000J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==0 &
## Smat$A3==ATS1[7])]
##if (is.na(u000J)) {u000J<-0}
##u001J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==1 &
## Smat$A3==ATS1[8])]
##if (is.na(u001J)) {u001J<-0}
##u010J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==0 &
## Smat$A3==ATS1[9])]
##if (is.na(u010J)) {u010J<-0}
##u011J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==1 &
## Smat$A3==ATS1[10])]
##if (is.na(u011J)) {u011J<-0}
##u100J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0 &
## Smat$A3==ATS1[11])]
##if (is.na(u100J)) {u100J<-0}
##u101J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1 &
## Smat$A3==ATS1[12])]
##if (is.na(u101J)) {u101J<-0}
##u110J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0 &
## Smat$A3==ATS1[13])]
##if (is.na(u110J)) {u110J<-0}
##u111J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1 &
## Smat$A3==ATS1[14])]
##if (is.na(u111J)) {u111J<-0}
##u000K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==0 &
## Smat$A3==ATS2[7])]
##if (is.na(u000K)) {u000K<-0}
##u001K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==1 &
## Smat$A3==ATS2[8])]
##if (is.na(u001K)) {u001K<-0}
##u010K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==0 &
## Smat$A3==ATS2[9])]
##if (is.na(u010K)) {u010K<-0}
##u011K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==1 &
## Smat$A3==ATS2[10])]
##if (is.na(u011K)) {u011K<-0}
##u100K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==0 &
## Smat$A3==ATS2[11])]
##if (is.na(u100K)) {u100K<-0}
##u101K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==1 &
## Smat$A3==ATS2[12])]
##if (is.na(u101K)) {u101K<-0}
##u110K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==0 &
## Smat$A3==ATS2[13])]
##if (is.na(u110K)) {u110K<-0}
##u111K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==1 &
## Smat$A3==ATS2[14])]
##if (is.na(u111K)) {u111K<-0}
##if (FA=="gaussian"){
## v000J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==0 &
## Smat$A3==ATS1[7])]^2
## v001J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==1 &
## Smat$A3==ATS1[8])]^2
## v010J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==0 &
## Smat$A3==ATS1[9])]^2
## v011J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==1 &
## Smat$A3==ATS1[10])]^2
## v100J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0 &
## Smat$A3==ATS1[11])]^2
## v101J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1 &
## Smat$A3==ATS1[12])]^2
## v110J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0 &
## Smat$A3==ATS1[13])]^2
## v111J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1 &
## Smat$A3==ATS1[14])]^2} else
## if (FA=="binomial") {bv000J<-u000J*(1-u000J)
## bv001J<-u001J*(1-u001J)
## bv010J<-u010J*(1-u010J)
## bv011J<-u011J*(1-u011J)
## bv100J<-u100J*(1-u100J)
## bv101J<-u101J*(1-u101J)
## bv110J<-u110J*(1-u110J)
## bv111J<-u111J*(1-u111J)}else
## stop("invalid enter for argument 'family'")
## if (length(v000J)==0) {v000J<-0}
## if (length(v001J)==0) {v001J<-0}
## if (length(v010J)==0) {v010J<-0}
## if (length(v011J)==0) {v011J<-0}
## if (length(v100J)==0) {v100J<-0}
## if (length(v101J)==0) {v101J<-0}
## if (length(v110J)==0) {v110J<-0}
## if (length(v111J)==0) {v111J<-0}
##
## A000.000<-( P0*(1-P0)*P00J*P00K*P000J*P000K+
## I[1]*P0*P0*P00J*(1-P00J)*P000J*P000K/(P0*pi0J)+
## I[1]*I[3]*P0*P0*P00J*P00K*P000J*
## (1-P000J)/(P0*pi0J*P00J*pi00J))*u000J*u000K
## A000.001<-( P0*(1-P0)*P00J*P00K*P000J*P001K+
## I[1]*P0*P0*P00J*(1-P00J)*P000J*
## P001K/(P0*pi0J)-
## I[1]*I[3]*P0*P0*P00J*P00K*P000J*
## (1-P000J)/(P0*pi0J*P00J*pi00J))*u000J*u001K
## A000.010<-( P0*(1-P0)*P00J*P10K*P000J*P010K-
## I[1]*P0*P0*P00J*(1-P00J)*P000J*
## P010K/(P0*pi0J))*u000J*u010K
## A000.011<-( P0*(1-P0)*P00J*P01K*P000J*P011K-
## I[1]*P0*P0*P00J*(1-P00J)*P000J*
## P011K/(P0*pi0J))*u000J*u011K
## A000.100<-(-P0*(1-P0)*P00J*P10K*P000J*P100K)*u000J*u100K
## A000.101<-(-P0*(1-P0)*P00J*P10K*P000J*P101K)*u000J*u101K
## A000.110<-(-P0*(1-P0)*P00J*P11K*P000J*P110K)*u000J*u110K
## A000.111<-(-P0*(1-P0)*P00J*P11K*P000J*P111K)*u000J*u111K
## A001.000<-( P0*(1-P0)*P00J*P00K*P001J*P000K+
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P000K/(P0*pi0J)-I[1]*I[3]*P0*P0*P00J*
## P00K*P001J*(1-P001J)/(P0*pi0J*P00J*pi00J))*u001J*u000K
## A001.001<-( P0*(1-P0)*P00J*P00K*P001J*P001K+
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P001K/(P0*pi0J)+I[1]*I[3]*P0*P0*P00J*P00K*P001J*
## (1-P001J)/(P0*pi0J*P00J*pi00J))*u001J*u001K
## A001.010<-( P0*(1-P0)*P00J*P10K*P001J*P010K-
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P010K/(P0*pi0J))*u001J*u010K
## A001.011<-( P0*(1-P0)*P00J*P10K*P001J*P011K-
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P011K/(P0*pi0J))*u001J*u011K
## A001.100<-(-P0*(1-P0)*P00J*P10K*P001J*P100K)*u001J*u100K
## A001.101<-(-P0*(1-P0)*P00J*P10K*P001J*P101K)*u001J*u101K
## A001.110<-(-P0*(1-P0)*P00J*P11K*P001J*P110K)*u001J*u110K
## A001.111<-(-P0*(1-P0)*P00J*P11K*P001J*P111K)*u001J*u111K
## A010.000<-( P0*(1-P0)*P01J*P00K*P010J*P000K-
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P000K/(P0*pi0J))*u010J*u000K
## A010.001<-( P0*(1-P0)*P01J*P00K*P010J*P001K-
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P001K/(P0*pi0J))*u010J*u001K
## A010.010<-( P0*(1-P0)*P01J*P01K*P010J*P010K+
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P010K/(P0*pi0J)+I[1]*I[3]*P0*P0*P01J*
## P01K*P010J*(1-P010J)/(P0*pi0J*P01J*pi01J))*u010J*u010K
## A010.011<-( P0*(1-P0)*P01J*P01K*P010J*P011K+
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P011K/(P0*pi0J)-I[1]*I[3]*P0*P0*P01J*
## P01K*P010J*(1-P010J)/(P0*pi0J*P01J*pi01J))*u010J*u011K
## A010.100<-(-P0*(1-P0)*P01J*P10K*P010J*P100K)*u010J*u100K
## A010.101<-(-P0*(1-P0)*P01J*P10K*P010J*P101K)*u010J*u101K
## A010.110<-(-P0*(1-P0)*P01J*P11K*P010J*P110K)*u010J*u110K
## A010.111<-(-P0*(1-P0)*P01J*P11K*P010J*P111K)*u010J*u111K
## A011.000<-( P0*(1-P0)*P01J*P00K*P011J*P000K-
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P000K/(P0*pi0J))*u011J*u000K
## A011.001<-( P0*(1-P0)*P01J*P00K*P011J*P001K-
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P001K/(P0*pi0J))*u011J*u001K
## A011.010<-( P0*(1-P0)*P01J*P01K*P011J*P010K+
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P010K/(P0*pi0J)-I[1]*I[3]*P0*P0*P01J*P01K*
## P011J*(1-P011J)/(P0*pi0J*P01J*pi01J))*u011J*u010K
## A011.011<-( P0*(1-P0)*P01J*P01K*P011J*P011K+
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P011K/(P0*pi0J)+I[1]*I[3]*P0*P0*P01J*
## P01K*P011J*(1-P011J)/(P0*pi0J*P01J*pi01J))*u011J*u011K
## A011.100<-(-P0*(1-P0)*P01J*P10K*P011J*P100K)*u011J*u100K
## A011.101<-(-P0*(1-P0)*P01J*P10K*P011J*P101K)*u011J*u101K
## A011.110<-(-P0*(1-P0)*P01J*P11K*P011J*P110K)*u011J*u110K
## A011.111<-(-P0*(1-P0)*P01J*P11K*P011J*P111K)*u011J*u111K
## A100.000<-(-P1*(1-P1)*P10J*P00K*P100J*P000K)*u100J*u000K
## A100.001<-(-P1*(1-P1)*P10J*P00K*P100J*P001K)*u100J*u001K
## A100.010<-(-P1*(1-P1)*P10J*P01K*P100J*P010K)*u100J*u010K
## A100.011<-(-P1*(1-P1)*P10J*P01K*P100J*P011K)*u100J*u011K
## A100.100<-( P1*(1-P1)*P10J*P10K*P100J*P100K+
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P100K/(P1*pi1J)+I[1]*I[3]*P1*P1*
## P10J*P10K*P100J*(1-P100J)/(P1*pi1J*P10J*pi10J))*
## u100J*u100K
## A100.101<-( P1*(1-P1)*P10J*P10K*P100J*P101K+
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P101K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P10J*P10K*P100J*(1-P100J)/(P1*pi1J*P10J*pi10J))*
## u100J*u101K
## A100.110<-( P1*(1-P1)*P10J*P11K*P100J*P110K-
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P110K/(P1*pi1J))*u100J*u110K
## A100.111<-( P1*(1-P1)*P10J*P11K*P100J*P111K-
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P111K/(P1*pi1J))*u100J*u111K
## A101.000<-(-P1*(1-P1)*P10J*P00K*P101J*P000K)*u101J*u000K
## A101.001<-(-P1*(1-P1)*P10J*P00K*P101J*P001K)*u101J*u001K
## A101.010<-(-P1*(1-P1)*P10J*P01K*P101J*P010K)*u101J*u010K
## A101.011<-(-P1*(1-P1)*P10J*P01K*P101J*P011K)*u101J*u011K
## A101.100<-( P1*(1-P1)*P10J*P10K*P101J*P100K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P100K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P10J*P10K*P101J*(1-P101J)/(P1*pi1J*
## P10J*pi10J))*u101J*u100K
## A101.101<-( P1*(1-P1)*P10J*P10K*P101J*P101K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P101K/(P1*pi1J)+I[1]*I[3]*P1*P1*P10J*
## P10K*P101J*(1-P101J)/(P1*pi1J*
## P10J*pi10J))*u101J*u101K
## A101.110<-( P1*(1-P1)*P10J*P11K*P101J*P110K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P110K/(P1*pi1J))*u101J*u110K
## A101.111<-( P1*(1-P1)*P10J*P11K*P101J*P111K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P111K/(P1*pi1J))*u101J*u111K
##
## A110.000<-(-P1*(1-P1)*P11J*P00K*P110J*P000K)*u110J*u000K
## A110.001<-(-P1*(1-P1)*P11J*P00K*P110J*P001K)*u110J*u001K
## A110.010<-(-P1*(1-P1)*P11J*P01K*P110J*P010K)*u110J*u010K
## A110.011<-(-P1*(1-P1)*P11J*P01K*P110J*P011K)*u110J*u011K
## A110.100<-( P1*(1-P1)*P11J*P10K*P110J*P100K-
## I[1]*P1*P1*P11J*(1-P11J)*P110J*
## P100K/(P1*pi1J))*u110J*u100K
## A110.101<-( P1*(1-P1)*P11J*P10K*P110J*P101K-
## I[1]*P1*P1*P11J*(1-P11J)*P110J*
## P101K/(P1*pi1J))*u110J*u101K
## A110.110<-( P1*(1-P1)*P11J*P11K*P110J*P110K+
## I[1]*P1*P1*P11J*(1-P11J)*P110J*
## P110K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P11J*P11K*P110J*(1-P110J)/(P1*pi1J*P11J*pi11J))*
## u110J*u110K
## A110.111<-( P1*(1-P1)*P11J*P11K*P110J*P111K+
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P111K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P11J*P11K*P110J*(1-P110J)/(P1*pi1J*P11J*pi11J))*u110J*u111K
## A111.000<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u000K
## A111.001<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u001K
## A111.010<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u010K
## A111.011<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u011K
## A111.100<-( P1*(1-P1)*P11J*P10K*P111J*P100K-
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P100K/(P1*pi1J))*u111J*u100K
## A111.101<-( P1*(1-P1)*P11J*P10K*P111J*P101K-
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P101K/(P1*pi1J))*u111J*u101K
## A111.110<-( P1*(1-P1)*P11J*P11K*P111J*P110K+
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P110K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P11J*P11K*P111J*(1-P111J)/(P1*pi1J*P11J*pi11J))*
## u111J*u110K
## A111.111<-( P1*(1-P1)*P11J*P11K*P111J*P111K+
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P111K/(P1*pi1J)+I[1]*I[3]*P1*P1*P11J*
## P11K*P111J*(1-P111J)/(P1*pi1J*P11J*pi11J))*u111J*u111K
## A<-sum(A000.000,A000.001,A000.010,A000.011,A000.100,
## A000.101,A000.110,A000.111,
## A001.000,A001.001,A001.010,A001.011,A001.100,
## A001.101,A001.110,A001.111,
## A010.000,A010.001,A010.010,A010.011,A010.100,
## A010.101,A010.110,A010.111,
## A011.000,A011.001,A011.010,A011.011,A011.100,
## A011.101,A011.110,A011.111,
## A100.000,A100.001,A100.010,A100.011,A100.100,
## A100.101,A100.110,A100.111,
## A101.000,A101.001,A101.010,A101.011,A101.100,
## A101.101,A101.110,A101.111,
## A110.000,A110.001,A110.010,A110.011,A110.100,
## A110.101,A110.110,A110.111,
## A111.000,A111.001,A111.010,A111.011,A111.100,
## A111.101,A111.110,A111.111)
##
## if (FA=="binomial"){
## if (I[1]==1 && I[3]==1 && I[ 7]==1) {
## B000.000<-P0*P0*P00J*P00K*P000J*
## P000K*bv000J/(P0*pi0J*P00J*pi00J*P000J*pi000J)}
## else {B000.000<-0}
## if (I[1]==1 && I[3]==1 && I[ 8]==1) {
## B001.001<-P0*P0*P01J*P01K*P001J*
## P001K*bv001J/(P0*pi0J*P00J*pi00J*P001J*pi001J)}
## else {B001.001<-0}
## if (I[1]==1 && I[4]==1 && I[ 9]==1) {
## B010.010<-P0*P0*P01J*P01K*P010J*
## P010K*bv010J/(P0*pi0J*P01J*pi01J*P010J*pi010J)}
## else {B010.010<-0}
## if (I[1]==1 && I[4]==1 && I[10]==1) {
## B011.011<-P0*P0*P01J*P01K*P011J*
## P011K*bv011J/(P0*pi0J*P01J*pi01J*P011J*pi011J)}
## else {B011.011<-0}
## if (I[1]==1 && I[5]==1 && I[11]==1) {
## B100.100<-P1*P1*P10J*P10K*P100J*
## P100K*bv100J/(P1*pi1J*P10J*pi10J*P100J*pi100J)}
## else {B100.100<-0}
## if (I[1]==1 && I[5]==1 && I[12]==1) {
## B101.101<-P1*P1*P10J*P10K*P101J*
## P101K*bv101J/(P1*pi1J*P10J*pi10J*P101J*pi101J)}
## else {B101.101<-0}
## if (I[1]==1 && I[6]==1 && I[13]==1) {
## B110.110<-P1*P1*P11J*P11K*P110J*
## P110K*bv110J/(P1*pi1J*P11J*pi11J*P110J*pi110J)}
## else {B110.110<-0}
## if (I[1]==1 && I[6]==1 && I[14]==1) {
## B111.111<-P1*P1*P11J*P11K*P111J*
## P111K*bv111J/(P1*pi1J*P11J*pi11J*P111J*pi111J)}
## else {B111.111<-0}
## } else
## if(FA=="gaussian"){
## if (I[1]==1 && I[3]==1 && I[ 7]==1) {
## B000.000<-P0*P0*P00J*P00K*P000J*P000K*
## v000J/(P0*pi0J*P00J*pi00J*P000J*pi000J)}
## else {B000.000<-0}
## if (I[1]==1 && I[3]==1 && I[ 8]==1) {
## B001.001<-P0*P0*P01J*P01K*P001J*
## P001K*v001J/(P0*pi0J*P00J*pi00J*P001J*pi001J)}
## else {B001.001<-0}
## if (I[1]==1 && I[4]==1 && I[ 9]==1) {
## B010.010<-P0*P0*P01J*P01K*P010J*
## P010K*v010J/(P0*pi0J*P01J*pi01J*P010J*pi010J)}
## else {B010.010<-0}
## if (I[1]==1 && I[4]==1 && I[10]==1) {
## B011.011<-P0*P0*P01J*P01K*P011J*P011K*
## v011J/(P0*pi0J*P01J*pi01J*P011J*pi011J)}
## else {B011.011<-0}
## if (I[1]==1 && I[5]==1 && I[11]==1) {
## B100.100<-P1*P1*P10J*P10K*P100J*P100K*
## v100J/(P1*pi1J*P10J*pi10J*P100J*pi100J)}
## else {B100.100<-0}
## if (I[1]==1 && I[5]==1 && I[12]==1) {
## B101.101<-P1*P1*P10J*P10K*P101J*P101K*
## v101J/(P1*pi1J*P10J*pi10J*P101J*pi101J)}
## else {B101.101<-0}
## if (I[1]==1 && I[6]==1 && I[13]==1) {
## B110.110<-P1*P1*P11J*P11K*P110J*P110K*
## v110J/(P1*pi1J*P11J*pi11J*P110J*pi110J)}
## else {B110.110<-0}
## if (I[1]==1 && I[6]==1 && I[14]==1) {
## B111.111<-P1*P1*P11J*P11K*P111J*P111K*
## v111J/(P1*pi1J*P11J*pi11J*P111J*pi111J)}
## else {B111.111<-0}
## }else
## stop("invalid enter for argument 'family'")
## B<-sum(B000.000,B001.001,B010.010,B011.011,
## B100.100,B101.101,B110.110,B111.111)
## tvc<-A+B
## }
return(tvc)
}
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Defines functions tcov
#tcov() to get var-cov component for effect size
#input two strategies and sequence information
#matrix, also the method to estimate
tcov<-function(ats1,ats2,sim,family="gaussian",method="Gest"){
ATS1<-ats1
ATS2<-ats2
Smat<-sim
FA<-family
MA<-method
if (is.null(Smat$O1)) {Base<-0} else {Base<-1}
Nstage<-nstage(data=Smat)
I<-overlap(ats1=ATS1,ats2=ATS2,nstage=Nstage,baseline=Base)
if (Nstage==1 && Base==0) {
pi1<-Smat$PI1[which(Smat$A1==ATS1[1])] #P(A1==1)
uJ<-Smat$MEAN[which(Smat$A1==ATS1[1])]
if (FA=="gaussian") {vJ<-Smat$SD[which(Smat$A1==ATS1[1])]^2} else
if (FA=="binomial") {vJ<-uJ*(1-uJ)} else
stop("invalid enter for argument 'family'")
tvc<-I[1]*vJ/pi1
} else
if (Nstage==1 && Base==1) {
pr<-mean(Smat$P1[which(Smat$O1==1)]) #P(O1==1)
pi0<-Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[1])] #P(A1==1|O1==0)
pi1<-Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[1])] #P(A1==1|O1==1)
u0J<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS1[1])]
if (is.na(u0J)) {u0J<-0}
# within-sequence true mean (EY)
u1J<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS1[2])]
if (is.na(u1J)) {u1J<-0}
u0K<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS2[1])]
if (is.na(u0K)) {u0K<-0}
u1K<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS2[2])]
if (is.na(u1K)) {u1K<-0}
if (FA=="gaussian"){v0J<-Smat$SD[which(Smat$O1==0 &
Smat$A1==ATS1[1])]^2
#within-sequence variance for cont outcome
v1J<-Smat$SD[which(Smat$O1==1 &
Smat$A1==ATS1[2])]^2
v0K<-Smat$SD[which(Smat$O1==0 &
Smat$A1==ATS2[1])]^2
v1K<-Smat$SD[which(Smat$O1==1 &
Smat$A1==ATS2[2])]^2} else
if (FA=="binomial"){v0J<-u0J*(1-u0J)
v1J<-u1J*(1-u1J)
v0K<-u0K*(1-u0K)
v1K<-u1K*(1-u1K)} else
stop("invalid enter for argument 'family'")
if (is.na(v0J)) {v0J<-0}
if (is.na(v1J)) {v1J<-0}
if (is.na(v0K)) {v0K<-0}
if (is.na(v1K)) {v1K<-0}
B1<-1*pr*(1-pr)*(u1J-u0J)*(u1K-u0K)
#MLE for cont outcome without com assumption
B2<-I[1]*(1-pr)*v0J/pi0
B3<-I[2]*pr*v1J/pi1
tvc<-B1+B2+B3
} else
if (Nstage==2 && Base==0) {
pi1<-mean(Smat$PI1[which(Smat$A1==ATS1[1])])
pr <-mean(Smat$P2[which(Smat$A1==ATS1[1] &
Smat$O2==1)])
pi20J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2])])
pi21J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3])])
u0J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2])]
u1J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3])]
u0K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2])]
u1K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[3])]
if (FA=="gaussian"){v0J<-Smat$SD[which(Smat$A1==ATS1[1]
& Smat$O2==0 &
Smat$A2==ATS1[2])]^2
v1J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==1 &
Smat$A2==ATS1[3])]^2
v0K<-Smat$SD[which(Smat$A1==ATS2[1] &
Smat$O2==0 &
Smat$A2==ATS2[2])]^2
v1K<-Smat$SD[which(Smat$A1==ATS2[1] &
Smat$O2==1 &
Smat$A2==ATS2[3])]^2}
else
if (FA=="binomial"){v0J<-u0J*(1-u0J)
v1J<-u1J*(1-u1J)
v0K<-u0K*(1-u0K)
v1K<-u1K*(1-u1K)} else
stop("invalid enter for argument 'family'")
if (is.na(u0J)) {u0J<-0}
if (is.na(u1J)) {u1J<-0}
if (is.na(u0K)) {u0K<-0}
if (is.na(u1K)) {u1K<-0}
if (length(v0J)==0) {v0J<-0}
if (length(v1J)==0) {v1J<-0}
if (length(v0K)==0) {v0K<-0}
if (length(v1K)==0) {v1K<-0}
if (is.nan(pr)) {pr<-0}
if (is.nan(pi1)) {pi1<-1}
if (is.nan(pi20J)) {pi20J<-1}
if (is.nan(pi21J)) {pi21J<-1}
B1<-I[1]*(u1J-u0J)*(u1K-u0K)*pr*(1-pr)/pi1
B2<-I[2]*v0J*(1-pr)/(pi1*pi20J)
B3<-I[3]*v1J*pr /(pi1*pi21J)
tvc<-B1+B2+B3
} else
if (Nstage==2 && Base==1) {
P0<-mean(Smat$P1[which(Smat$O1==0)]); if (is.nan(P0)) {P0<-0}
P1<-mean(Smat$P1[which(Smat$O1==1)]); if (is.nan(P1)) {P1<-0}
pi0J<-mean(Smat$PI1[which(Smat$O1==0 & Smat$A1==ATS1[1])])
if (is.nan(pi0J)) {pi0J<-1}
pi1J<-mean(Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[2])])
if (is.nan(pi1J)) {pi1J<-1}
P00J<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS1[1] & Smat$O2==0)])
if (is.nan(P00J)) {P00J<-0}
P01J<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS1[1] & Smat$O2==1)])
if (is.nan(P01J)) {P01J<-0}
P10J<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS1[2] & Smat$O2==0)])
if (is.nan(P10J)) {P10J<-0}
P11J<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS1[2] & Smat$O2==1)])
if (is.nan(P11J)) {P11J<-0}
P00K<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS2[1] & Smat$O2==0)])
if (is.nan(P00K)) {P00K<-0}
P01K<-mean(Smat$P2[which(Smat$O1==0 & Smat$A1==ATS2[1] & Smat$O2==1)])
if (is.nan(P01K)) {P01K<-0}
P10K<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS2[2] & Smat$O2==0)])
if (is.nan(P10K)) {P10K<-0}
P11K<-mean(Smat$P2[which(Smat$O1==1 & Smat$A1==ATS2[2] & Smat$O2==1)])
if (is.nan(P11K)) {P11K<-0}
pi00J<-mean(Smat$PI2[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3])])
if (is.nan(pi00J)) {pi00J<-1}
pi01J<-mean(Smat$PI2[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[4])])
if (is.nan(pi01J)) {pi01J<-1}
pi10J<-mean(Smat$PI2[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==0 & Smat$A2==ATS1[5])])
if (is.nan(pi10J)) {pi10J<-1}
pi11J<-mean(Smat$PI2[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==1 & Smat$A2==ATS1[6])])
if (is.nan(pi11J)) {pi11J<-1}
u00J<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3])]
if (is.na(u00J)) {u00J<-0}
u01J<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[4])]
if (is.na(u01J)) {u01J<-0}
u10J<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==0 & Smat$A2==ATS1[5])]
if (is.na(u10J)) {u10J<-0}
u11J<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==1 & Smat$A2==ATS1[6])]
if (is.na(u11J)) {u11J<-0}
u00K<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[3])]
if (is.na(u00K)) {u00K<-0}
u01K<-Smat$MEAN[which(Smat$O1==0 & Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[4])]
if (is.na(u01K)) {u01K<-0}
u10K<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS2[2] &
Smat$O2==0 & Smat$A2==ATS2[5])]
if (is.na(u10K)) {u10K<-0}
u11K<-Smat$MEAN[which(Smat$O1==1 & Smat$A1==ATS2[2] &
Smat$O2==1 & Smat$A2==ATS2[6])]
if (is.na(u11K)) {u11K<-0}
if (FA=="gaussian"){
v00J<-Smat$SD[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3])]^2
v01J<-Smat$SD[which(Smat$O1==0 & Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[4])]^2
v10J<-Smat$SD[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==0 & Smat$A2==ATS1[5])]^2
v11J<-Smat$SD[which(Smat$O1==1 & Smat$A1==ATS1[2] &
Smat$O2==1 & Smat$A2==ATS1[6])]^2} else
if (FA=="binomial"){v00J<-u00J*(1-u00J)
v01J<-u01J*(1-u01J)
v10J<-u10J*(1-u10J)
v11J<-u11J*(1-u11J)}else
stop("invalid enter for argument 'family'")
if (length(v00J)==0) {v00J<-0}
if (length(v01J)==0) {v01J<-0}
if (length(v10J)==0) {v10J<-0}
if (length(v11J)==0) {v11J<-0}
A0000<- (P0*(1-P0)*P00J*P00K+I[1]*P0*P0*P00J*
(1-P00J)/(P0*pi0J))*u00J*u00K
A0001<- (P0*(1-P0)*P00J*P01K-I[1]*P0*P0*P00J*
(1-P00J)/(P0*pi0J))*u00J*u01K
A0010<--(P0*(1-P0)*P00J*P10K)*u00J*u10K
A0011<--(P0*(1-P0)*P00J*P11K)*u00J*u11K
A0100<- (P0*(1-P0)*P01J*P00K-I[1]*P0*P0*P01J*
(1-P01J)/(P0*pi0J))*u01J*u00K
A0101<- (P0*(1-P0)*P01J*P01K+I[1]*P0*P0*P01J*
(1-P01J)/(P0*pi0J))*u01J*u01K
A0110<--(P0*(1-P0)*P01J*P10K)*u01J*u10K
A0111<--(P0*(1-P0)*P01J*P11K)*u01J*u11K
A1000<--(P1*(1-P1)*P10J*P00K)*u10J*u10K
A1001<--(P1*(1-P1)*P10J*P01K)*u10J*u11K
A1010<- (P1*(1-P1)*P10J*P10K+I[1]*P1*P1*P10J*
(1-P10J)/(P1*pi1J))*u10J*u10K
A1011<- (P1*(1-P1)*P10J*P11K-I[1]*P1*P1*P10J*
(1-P10J)/(P1*pi1J))*u10J*u11K
A1100<--(P1*(1-P1)*P10J*P00K)*u10J*u10K
A1101<--(P1*(1-P1)*P10J*P01K)*u10J*u11K
A1110<- (P1*(1-P1)*P11J*P10K+I[1]*P1*P1*P11J*
(1-P11J)/(P1*pi1J))*u11J*u10K
A1111<- (P1*(1-P1)*P10J*P11K-I[1]*P1*P1*P11J*
(1-P11J)/(P1*pi1J))*u11J*u11K
A<-sum(A0000,A0001,A0010,A0011,
A0100,A0101,A0110,A0111,
A1000,A1001,A1010,A1011,
A1100,A1101,A1110,A1111)
if (I[1]==1 && I[3]==1) {B0000<-P0*P0*P00J*P00J*
v00J/(P0*pi0J*P00J*pi00J)} else {B0000<-0}
if (I[1]==1 && I[4]==1) {B0101<-P0*P0*P01J*P01J*
v01J/(P0*pi0J*P01J*pi01J)} else {B0101<-0}
if (I[2]==1 && I[5]==1) {B1010<-P1*P1*P10J*P10J*
v10J/(P1*pi1J*P10J*pi10J)} else {B1010<-0}
if (I[2]==1 && I[6]==1) {B1111<-P1*P1*P11J*P11J*
v11J/(P1*pi1J*P11J*pi11J)} else {B1111<-0}
B<-sum(B0000,B0101,B1010,B1111)
tvc<-A+B
} else
if (Nstage==3 && Base==0) {
piJ<-mean(Smat$PI1[which(Smat$A1==ATS1[1])])
if (is.nan(piJ)) {piJ<-0} # A1<-dJ[1]
P0J<-mean(Smat$P2[which(Smat$A1==ATS1[1] & Smat$O2==0)])
if (is.nan(P0J)) {P0J<-0}
P1J<-mean(Smat$P2[which(Smat$A1==ATS1[1] & Smat$O2==1)])
if (is.nan(P1J)) {P1J<-0}
P0K<-mean(Smat$P2[which(Smat$A1==ATS2[1] & Smat$O2==0)])
if (is.nan(P0K)) {P0K<-0}
P1K<-mean(Smat$P2[which(Smat$A1==ATS2[1] & Smat$O2==1)])
if (is.nan(P1K)) {P1K<-0}
pi0J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2])])
if (is.nan(pi0J)) {pi0J<-0}
pi1J<-mean(Smat$PI2[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3])])
if (is.nan(pi1J)) {pi1J<-0}
P00J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] & Smat$O3==0)])
if (is.nan(P00J)) {P00J<-0}
P01J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] & Smat$O3==1)])
if (is.nan(P01J)) {P01J<-0}
P10J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3] & Smat$O3==0)])
if (is.nan(P10J)) {P10J<-0}
P11J<-mean(Smat$P3[which(Smat$A1==ATS1[1] &
Smat$O2==1 & Smat$A2==ATS1[3] & Smat$O3==1)])
if (is.nan(P11J)) {P11J<-0}
P00K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] & Smat$O3==0)])
if (is.nan(P00K)) {P00K<-0}
P01K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] & Smat$O3==1)])
if (is.nan(P01K)) {P01K<-0}
P10K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[3] & Smat$O3==0)])
if (is.nan(P10K)) {P10K<-0}
P11K<-mean(Smat$P3[which(Smat$A1==ATS2[1] &
Smat$O2==1 & Smat$A2==ATS2[3] & Smat$O3==1)])
if (is.nan(P11K)) {P11K<-0}
pi00J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==0 &
Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[4])])
if (is.nan(pi00J)) {pi00J<-0}
pi01J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==0 &
Smat$A2==ATS1[2] &
Smat$O3==1 & Smat$A3==ATS1[5])])
if (is.nan(pi01J)) {pi01J<-0}
pi10J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==1 &
Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[6])])
if (is.nan(pi10J)) {pi10J<-0}
pi11J<-mean(Smat$PI3[which(Smat$A1==ATS1[1] & Smat$O2==1 &
Smat$A2==ATS1[3] &
Smat$O3==1 & Smat$A3==ATS1[7])])
if (is.nan(pi11J)) {pi11J<-0}
u00J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[4])]
if (is.nan(u00J)) {u00J<-0} # within-sequence true mean (EY)
u01J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[5])]
if (is.nan(u01J)) {u01J<-0}
u10J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[6])]
if (is.nan(u10J)) {u10J<-0}
u11J<-Smat$MEAN[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[7])]
if (is.nan(u11J)) {u11J<-0}
u00K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] &
Smat$O3==0 & Smat$A3==ATS2[4])]
if (is.nan(u00K)) {u00K<-0} # within-sequence true mean (EY)
u01K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[2] &
Smat$O3==0 & Smat$A3==ATS2[5])]
if (is.nan(u01K)) {u01K<-0}
u10K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[3] &
Smat$O3==0 & Smat$A3==ATS2[6])]
if (is.nan(u10K)) {u10K<-0}
u11K<-Smat$MEAN[which(Smat$A1==ATS2[1] &
Smat$O2==0 & Smat$A2==ATS2[3] &
Smat$O3==0 & Smat$A3==ATS2[7])]
if (is.nan(u11K)) {u11K<-0}
if (FA=="gaussian"){
v00J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[4])]^2
# within-sequence true mean (EY)
v01J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[2] &
Smat$O3==0 & Smat$A3==ATS1[5])]^2
v10J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 & Smat$A3==ATS1[6])]^2
v11J<-Smat$SD[which(Smat$A1==ATS1[1] &
Smat$O2==0 & Smat$A2==ATS1[3] &
Smat$O3==0 &
Smat$A3==ATS1[7])]^2}else
if (FA=="binomial") {bv00J<-u00J*(1-u00J)
if (is.na(bv00J)) {bv00J<-0}
#within-sequence var est for bin outcome
bv01J<-u01J*(1-u01J)
if (is.na(bv01J)) {bv01J<-0}
bv10J<-u10J*(1-u10J)
if (is.na(bv10J)) {bv10J<-0}
bv11J<-u11J*(1-u11J)
if (is.na(bv11J)) {bv11J<-0}}else
stop("invalid enter for argument 'family'")
if (length(v00J)==0) {v00J<-0}
if (length(v01J)==0) {v01J<-0}
if (length(v10J)==0) {v10J<-0}
if (length(v11J)==0) {v11J<-0}
A0000<- (I[1]*P0J*(1-P0J)*P00J*P00K/piJ+I[2]*
P0J*P0J*P00J*(1-P00J)/
(piJ*P0J*pi00J))*u00J*u00K
A0001<- (I[1]*P0J*(1-P0J)*P00J*P01K/piJ-I[2]*
P0J*P0J*P00J*(1-P00J)/
(piJ*P0J*pi00J))*u00J*u01K
A0010<--(I[1]*P0J*(1-P0J)*P00J*P10K/piJ)*
u00J*u10K
A0011<--(I[1]*P0J*(1-P0J)*P00J*P11K/piJ)*
u00J*u11K
A0100<- (I[1]*P0J*(1-P0J)*P01J*P00K/piJ-I[2]*
P0J*P0J*P01J*(1-P01J)/(piJ*P0J*pi01J))*u01J*u00K
A0101<- (I[1]*P0J*(1-P0J)*P01J*P01K/piJ+I[2]*
P0J*P0J*P01J*(1-P01J)/(piJ*P0J*pi01J))*u01J*u01K
A0110<--(I[1]*P0J*(1-P0J)*P01J*P10K/piJ)*u01J*u10K
A0111<--(I[1]*P0J*(1-P0J)*P01J*P11K/piJ)*u01J*u11K
A1000<--(I[1]*P1J*(1-P1J)*P10J*P00K/piJ)*u10J*u10K
A1001<--(I[1]*P1J*(1-P1J)*P10J*P01K/piJ)*u10J*u11K
A1010<- (I[1]*P1J*(1-P1J)*P10J*P10K/piJ+I[3]*
P1J*P1J*P10J*(1-P10J)/(piJ*P1J*pi10J))*u10J*u10K
A1011<- (I[1]*P1J*(1-P1J)*P10J*P11K/piJ-I[3]*
P1J*P1J*P10J*(1-P10J)/(piJ*P1J*pi10J))*u10J*u11K
A1100<--(I[1]*P1J*(1-P1J)*P10J*P00K/piJ)*u10J*u10K
A1101<--(I[1]*P1J*(1-P1J)*P10J*P01K/piJ)*u10J*u11K
A1110<- (I[1]*P1J*(1-P1J)*P11J*P10K/piJ+I[3]*
P1J*P1J*P11J*(1-P11J)/(piJ*P1J*pi11J))*u11J*u10K
A1111<- (I[1]*P1J*(1-P1J)*P10J*P11K/piJ-I[3]*
P1J*P1J*P11J*(1-P11J)/(piJ*P1J*pi11J))*u11J*u11K
A<-sum(A0000,A0001,A0010,A0011,
A0100,A0101,A0110,A0111,
A1000,A1001,A1010,A1011,
A1100,A1101,A1110,A1111)
if (FA=="binomial"){
if (I[1]==1 && I[2]==1 && I[4]==1) {B0000<-P0J*P0J*P00J*
P00K*bv00J/(piJ*P0J*pi00J*P00J*pi00J)} else {B0000<-0}
if (I[1]==1 && I[2]==1 && I[5]==1) {B0101<-P0J*P0J*P01J*
P01K*bv01J/(piJ*P0J*pi00J*P01J*pi01J)} else {B0101<-0}
if (I[1]==1 && I[3]==1 && I[6]==1) {B1010<-P1J*P1J*P10J*
P10K*bv10J/(piJ*P1J*pi10J*P10J*pi10J)} else {B1010<-0}
if (I[1]==1 && I[3]==1 && I[7]==1) {B1111<-P1J*P1J*P11J*
P11K*bv11J/(piJ*P1J*pi11J*P11J*pi11J)} else {B1111<-0}
} else
if (FA=="gaussian") {
if (I[1]==1 && I[2]==1 && I[4]==1) {B0000<-P0J*P0J*P00J*
P00K*v00J/(piJ*P0J*pi00J*P00J*pi00J)} else {B0000<-0}
if (I[1]==1 && I[2]==1 && I[5]==1) {B0101<-P0J*P0J*P01J*
P01K*v01J/(piJ*P0J*pi00J*P01J*pi01J)} else {B0101<-0}
if (I[1]==1 && I[3]==1 && I[6]==1) {B1010<-P1J*P1J*P10J*
P10K*v10J/(piJ*P1J*pi10J*P10J*pi10J)} else {B1010<-0}
if (I[1]==1 && I[3]==1 && I[7]==1) {B1111<-P1J*P1J*P11J*
P11K*v11J/(piJ*P1J*pi11J*P11J*pi11J)} else {B1111<-0}
}else
stop("invalid enter for argument 'family'")
B<-sum(B0000,B0101,B1010,B1111)
tvc<-A+B
}
##else
## if (Nstage==3 && Base==1) {
## P0<-mean(Smat$P1[which(Smat$O1==0)])
## if (is.nan(P0)) {P0<-0}
## P1<-mean(Smat$P1[which(Smat$O1==1)])
## if (is.nan(P1)) {P1<-0}
##
## pi0J<-mean(Smat$PI1[which(Smat$O1==0 & Smat$A1==ATS1[1])])
## if (is.nan(pi0J)) {pi0J<-1}
## pi1J<-mean(Smat$PI1[which(Smat$O1==1 & Smat$A1==ATS1[2])])
## if (is.nan(pi1J)) {pi1J<-1}
##
##P00J<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0)])
##if (is.nan(P00J)) {P00J<-0}
##P01J<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1)])
##if (is.nan(P01J)) {P01J<-0}
##P10J<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0)])
##if (is.nan(P10J)) {P10J<-0}
##P11J<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1)])
##if (is.nan(P11J)) {P11J<-0}
##P00K<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0)])
##if (is.nan(P00K)) {P00K<-0}
##P01K<-mean(Smat$P2[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1)])
##if (is.nan(P01K)) {P01K<-0}
##P10K<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0)])
##if (is.nan(P10K)) {P10K<-0}
##P11K<-mean(Smat$P2[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1)])
##if (is.nan(P11K)) {P11K<-0}
##pi00J<-mean(Smat$PI2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==0 &
## Smat$A2==ATS1[3])])
##if (is.nan(pi00J)) {pi00J<-1}
##pi01J<-mean(Smat$PI2[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==1 &
## Smat$A2==ATS1[4])])
##if (is.nan(pi01J)) {pi01J<-1}
##pi10J<-mean(Smat$PI2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] &
## Smat$O2==0 &
## Smat$A2==ATS1[5])])
##if (is.nan(pi10J)) {pi10J<-1}
##pi11J<-mean(Smat$PI2[which(Smat$O1==1 &
## Smat$A1==ATS1[2] &
## Smat$O2==1 &
## Smat$A2==ATS1[6])])
##if (is.nan(pi11J)) {pi11J<-1}
##P000J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==0 &
## Smat$A2==ATS1[3] &
## Smat$O3==0)])
##if (is.nan(P000J)) {P000J<-0}
##P001J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==0 &
## Smat$A2==ATS1[3] &
## Smat$O3==1)])
##if (is.nan(P001J)) {P001J<-0}
##P010J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==1 &
## Smat$A2==ATS1[4] &
## Smat$O3==0)])
##if (is.nan(P010J)) {P010J<-0}
##P011J<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] &
## Smat$O2==1 &
## Smat$A2==ATS1[4] &
## Smat$O3==1)])
##if (is.nan(P011J)) {P011J<-0}
##P100J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0)])
##if (is.nan(P100J)) {P100J<-0}
##P101J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1)])
##if (is.nan(P101J)) {P101J<-0}
##P110J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0)])
##if (is.nan(P110J)) {P110J<-0}
##P111J<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1)])
##if (is.nan(P111J)) {P111J<-0}
##P000K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==0)])
##if (is.nan(P000K)) {P000K<-0}
##P001K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==1)])
##if (is.nan(P001K)) {P001K<-0}
##P010K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==0)])
##if (is.nan(P010K)) {P010K<-0}
##P011K<-mean(Smat$P3[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==1)])
##if (is.nan(P011K)) {P011K<-0}
##P100K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==0)])
##if (is.nan(P100K)) {P100K<-0}
##P101K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==1)])
##if (is.nan(P101K)) {P101K<-0}
##P110K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==0)])
##if (is.nan(P110K)) {P110K<-0}
##P111K<-mean(Smat$P3[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==1)])
##if (is.nan(P111K)) {P111K<-0}
##pi000J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==0 &
## Smat$A3==ATS1[7])])
##if (is.nan(P000J)) {P000J<-0}
##pi001J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==1 &
## Smat$A3==ATS1[8])])
##if (is.nan(P001J)) {P001J<-0}
##pi010J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==0 &
## Smat$A3==ATS1[9])])
##if (is.nan(P010J)) {P010J<-0}
##pi011J<-mean(Smat$PI3[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==1 &
## Smat$A3==ATS1[10])])
##if (is.nan(P011J)) {P011J<-0}
##pi100J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0 &
## Smat$A3==ATS1[11])])
##if (is.nan(P100J)) {P100J<-0}
##pi101J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1 &
## Smat$A3==ATS1[12])])
##if (is.nan(P101J)) {P101J<-0}
##pi110J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0 &
## Smat$A3==ATS1[13])])
##if (is.nan(P110J)) {P110J<-0}
##pi111J<-mean(Smat$PI3[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1 &
## Smat$A3==ATS1[14])])
##if (is.nan(P111J)) {P111J<-0}
##u000J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==0 &
## Smat$A3==ATS1[7])]
##if (is.na(u000J)) {u000J<-0}
##u001J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==1 &
## Smat$A3==ATS1[8])]
##if (is.na(u001J)) {u001J<-0}
##u010J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==0 &
## Smat$A3==ATS1[9])]
##if (is.na(u010J)) {u010J<-0}
##u011J<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==1 &
## Smat$A3==ATS1[10])]
##if (is.na(u011J)) {u011J<-0}
##u100J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0 &
## Smat$A3==ATS1[11])]
##if (is.na(u100J)) {u100J<-0}
##u101J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1 &
## Smat$A3==ATS1[12])]
##if (is.na(u101J)) {u101J<-0}
##u110J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0 &
## Smat$A3==ATS1[13])]
##if (is.na(u110J)) {u110J<-0}
##u111J<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1 &
## Smat$A3==ATS1[14])]
##if (is.na(u111J)) {u111J<-0}
##u000K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==0 &
## Smat$A3==ATS2[7])]
##if (is.na(u000K)) {u000K<-0}
##u001K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==0 &
## Smat$A2==ATS2[3] & Smat$O3==1 &
## Smat$A3==ATS2[8])]
##if (is.na(u001K)) {u001K<-0}
##u010K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==0 &
## Smat$A3==ATS2[9])]
##if (is.na(u010K)) {u010K<-0}
##u011K<-Smat$MEAN[which(Smat$O1==0 &
## Smat$A1==ATS2[1] & Smat$O2==1 &
## Smat$A2==ATS2[4] & Smat$O3==1 &
## Smat$A3==ATS2[10])]
##if (is.na(u011K)) {u011K<-0}
##u100K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==0 &
## Smat$A3==ATS2[11])]
##if (is.na(u100K)) {u100K<-0}
##u101K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==0 &
## Smat$A2==ATS2[5] & Smat$O3==1 &
## Smat$A3==ATS2[12])]
##if (is.na(u101K)) {u101K<-0}
##u110K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==0 &
## Smat$A3==ATS2[13])]
##if (is.na(u110K)) {u110K<-0}
##u111K<-Smat$MEAN[which(Smat$O1==1 &
## Smat$A1==ATS2[2] & Smat$O2==1 &
## Smat$A2==ATS2[6] & Smat$O3==1 &
## Smat$A3==ATS2[14])]
##if (is.na(u111K)) {u111K<-0}
##if (FA=="gaussian"){
## v000J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==0 &
## Smat$A3==ATS1[7])]^2
## v001J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==0 &
## Smat$A2==ATS1[3] & Smat$O3==1 &
## Smat$A3==ATS1[8])]^2
## v010J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==0 &
## Smat$A3==ATS1[9])]^2
## v011J<-Smat$SD[which(Smat$O1==0 &
## Smat$A1==ATS1[1] & Smat$O2==1 &
## Smat$A2==ATS1[4] & Smat$O3==1 &
## Smat$A3==ATS1[10])]^2
## v100J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==0 &
## Smat$A3==ATS1[11])]^2
## v101J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==0 &
## Smat$A2==ATS1[5] & Smat$O3==1 &
## Smat$A3==ATS1[12])]^2
## v110J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==0 &
## Smat$A3==ATS1[13])]^2
## v111J<-Smat$SD[which(Smat$O1==1 &
## Smat$A1==ATS1[2] & Smat$O2==1 &
## Smat$A2==ATS1[6] & Smat$O3==1 &
## Smat$A3==ATS1[14])]^2} else
## if (FA=="binomial") {bv000J<-u000J*(1-u000J)
## bv001J<-u001J*(1-u001J)
## bv010J<-u010J*(1-u010J)
## bv011J<-u011J*(1-u011J)
## bv100J<-u100J*(1-u100J)
## bv101J<-u101J*(1-u101J)
## bv110J<-u110J*(1-u110J)
## bv111J<-u111J*(1-u111J)}else
## stop("invalid enter for argument 'family'")
## if (length(v000J)==0) {v000J<-0}
## if (length(v001J)==0) {v001J<-0}
## if (length(v010J)==0) {v010J<-0}
## if (length(v011J)==0) {v011J<-0}
## if (length(v100J)==0) {v100J<-0}
## if (length(v101J)==0) {v101J<-0}
## if (length(v110J)==0) {v110J<-0}
## if (length(v111J)==0) {v111J<-0}
##
## A000.000<-( P0*(1-P0)*P00J*P00K*P000J*P000K+
## I[1]*P0*P0*P00J*(1-P00J)*P000J*P000K/(P0*pi0J)+
## I[1]*I[3]*P0*P0*P00J*P00K*P000J*
## (1-P000J)/(P0*pi0J*P00J*pi00J))*u000J*u000K
## A000.001<-( P0*(1-P0)*P00J*P00K*P000J*P001K+
## I[1]*P0*P0*P00J*(1-P00J)*P000J*
## P001K/(P0*pi0J)-
## I[1]*I[3]*P0*P0*P00J*P00K*P000J*
## (1-P000J)/(P0*pi0J*P00J*pi00J))*u000J*u001K
## A000.010<-( P0*(1-P0)*P00J*P10K*P000J*P010K-
## I[1]*P0*P0*P00J*(1-P00J)*P000J*
## P010K/(P0*pi0J))*u000J*u010K
## A000.011<-( P0*(1-P0)*P00J*P01K*P000J*P011K-
## I[1]*P0*P0*P00J*(1-P00J)*P000J*
## P011K/(P0*pi0J))*u000J*u011K
## A000.100<-(-P0*(1-P0)*P00J*P10K*P000J*P100K)*u000J*u100K
## A000.101<-(-P0*(1-P0)*P00J*P10K*P000J*P101K)*u000J*u101K
## A000.110<-(-P0*(1-P0)*P00J*P11K*P000J*P110K)*u000J*u110K
## A000.111<-(-P0*(1-P0)*P00J*P11K*P000J*P111K)*u000J*u111K
## A001.000<-( P0*(1-P0)*P00J*P00K*P001J*P000K+
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P000K/(P0*pi0J)-I[1]*I[3]*P0*P0*P00J*
## P00K*P001J*(1-P001J)/(P0*pi0J*P00J*pi00J))*u001J*u000K
## A001.001<-( P0*(1-P0)*P00J*P00K*P001J*P001K+
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P001K/(P0*pi0J)+I[1]*I[3]*P0*P0*P00J*P00K*P001J*
## (1-P001J)/(P0*pi0J*P00J*pi00J))*u001J*u001K
## A001.010<-( P0*(1-P0)*P00J*P10K*P001J*P010K-
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P010K/(P0*pi0J))*u001J*u010K
## A001.011<-( P0*(1-P0)*P00J*P10K*P001J*P011K-
## I[1]*P0*P0*P00J*(1-P00J)*P001J*
## P011K/(P0*pi0J))*u001J*u011K
## A001.100<-(-P0*(1-P0)*P00J*P10K*P001J*P100K)*u001J*u100K
## A001.101<-(-P0*(1-P0)*P00J*P10K*P001J*P101K)*u001J*u101K
## A001.110<-(-P0*(1-P0)*P00J*P11K*P001J*P110K)*u001J*u110K
## A001.111<-(-P0*(1-P0)*P00J*P11K*P001J*P111K)*u001J*u111K
## A010.000<-( P0*(1-P0)*P01J*P00K*P010J*P000K-
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P000K/(P0*pi0J))*u010J*u000K
## A010.001<-( P0*(1-P0)*P01J*P00K*P010J*P001K-
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P001K/(P0*pi0J))*u010J*u001K
## A010.010<-( P0*(1-P0)*P01J*P01K*P010J*P010K+
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P010K/(P0*pi0J)+I[1]*I[3]*P0*P0*P01J*
## P01K*P010J*(1-P010J)/(P0*pi0J*P01J*pi01J))*u010J*u010K
## A010.011<-( P0*(1-P0)*P01J*P01K*P010J*P011K+
## I[1]*P0*P0*P01J*(1-P01J)*P010J*
## P011K/(P0*pi0J)-I[1]*I[3]*P0*P0*P01J*
## P01K*P010J*(1-P010J)/(P0*pi0J*P01J*pi01J))*u010J*u011K
## A010.100<-(-P0*(1-P0)*P01J*P10K*P010J*P100K)*u010J*u100K
## A010.101<-(-P0*(1-P0)*P01J*P10K*P010J*P101K)*u010J*u101K
## A010.110<-(-P0*(1-P0)*P01J*P11K*P010J*P110K)*u010J*u110K
## A010.111<-(-P0*(1-P0)*P01J*P11K*P010J*P111K)*u010J*u111K
## A011.000<-( P0*(1-P0)*P01J*P00K*P011J*P000K-
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P000K/(P0*pi0J))*u011J*u000K
## A011.001<-( P0*(1-P0)*P01J*P00K*P011J*P001K-
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P001K/(P0*pi0J))*u011J*u001K
## A011.010<-( P0*(1-P0)*P01J*P01K*P011J*P010K+
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P010K/(P0*pi0J)-I[1]*I[3]*P0*P0*P01J*P01K*
## P011J*(1-P011J)/(P0*pi0J*P01J*pi01J))*u011J*u010K
## A011.011<-( P0*(1-P0)*P01J*P01K*P011J*P011K+
## I[1]*P0*P0*P01J*(1-P01J)*P011J*
## P011K/(P0*pi0J)+I[1]*I[3]*P0*P0*P01J*
## P01K*P011J*(1-P011J)/(P0*pi0J*P01J*pi01J))*u011J*u011K
## A011.100<-(-P0*(1-P0)*P01J*P10K*P011J*P100K)*u011J*u100K
## A011.101<-(-P0*(1-P0)*P01J*P10K*P011J*P101K)*u011J*u101K
## A011.110<-(-P0*(1-P0)*P01J*P11K*P011J*P110K)*u011J*u110K
## A011.111<-(-P0*(1-P0)*P01J*P11K*P011J*P111K)*u011J*u111K
## A100.000<-(-P1*(1-P1)*P10J*P00K*P100J*P000K)*u100J*u000K
## A100.001<-(-P1*(1-P1)*P10J*P00K*P100J*P001K)*u100J*u001K
## A100.010<-(-P1*(1-P1)*P10J*P01K*P100J*P010K)*u100J*u010K
## A100.011<-(-P1*(1-P1)*P10J*P01K*P100J*P011K)*u100J*u011K
## A100.100<-( P1*(1-P1)*P10J*P10K*P100J*P100K+
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P100K/(P1*pi1J)+I[1]*I[3]*P1*P1*
## P10J*P10K*P100J*(1-P100J)/(P1*pi1J*P10J*pi10J))*
## u100J*u100K
## A100.101<-( P1*(1-P1)*P10J*P10K*P100J*P101K+
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P101K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P10J*P10K*P100J*(1-P100J)/(P1*pi1J*P10J*pi10J))*
## u100J*u101K
## A100.110<-( P1*(1-P1)*P10J*P11K*P100J*P110K-
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P110K/(P1*pi1J))*u100J*u110K
## A100.111<-( P1*(1-P1)*P10J*P11K*P100J*P111K-
## I[1]*P1*P1*P10J*(1-P10J)*P100J*
## P111K/(P1*pi1J))*u100J*u111K
## A101.000<-(-P1*(1-P1)*P10J*P00K*P101J*P000K)*u101J*u000K
## A101.001<-(-P1*(1-P1)*P10J*P00K*P101J*P001K)*u101J*u001K
## A101.010<-(-P1*(1-P1)*P10J*P01K*P101J*P010K)*u101J*u010K
## A101.011<-(-P1*(1-P1)*P10J*P01K*P101J*P011K)*u101J*u011K
## A101.100<-( P1*(1-P1)*P10J*P10K*P101J*P100K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P100K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P10J*P10K*P101J*(1-P101J)/(P1*pi1J*
## P10J*pi10J))*u101J*u100K
## A101.101<-( P1*(1-P1)*P10J*P10K*P101J*P101K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P101K/(P1*pi1J)+I[1]*I[3]*P1*P1*P10J*
## P10K*P101J*(1-P101J)/(P1*pi1J*
## P10J*pi10J))*u101J*u101K
## A101.110<-( P1*(1-P1)*P10J*P11K*P101J*P110K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P110K/(P1*pi1J))*u101J*u110K
## A101.111<-( P1*(1-P1)*P10J*P11K*P101J*P111K+
## I[1]*P1*P1*P10J*(1-P10J)*P101J*
## P111K/(P1*pi1J))*u101J*u111K
##
## A110.000<-(-P1*(1-P1)*P11J*P00K*P110J*P000K)*u110J*u000K
## A110.001<-(-P1*(1-P1)*P11J*P00K*P110J*P001K)*u110J*u001K
## A110.010<-(-P1*(1-P1)*P11J*P01K*P110J*P010K)*u110J*u010K
## A110.011<-(-P1*(1-P1)*P11J*P01K*P110J*P011K)*u110J*u011K
## A110.100<-( P1*(1-P1)*P11J*P10K*P110J*P100K-
## I[1]*P1*P1*P11J*(1-P11J)*P110J*
## P100K/(P1*pi1J))*u110J*u100K
## A110.101<-( P1*(1-P1)*P11J*P10K*P110J*P101K-
## I[1]*P1*P1*P11J*(1-P11J)*P110J*
## P101K/(P1*pi1J))*u110J*u101K
## A110.110<-( P1*(1-P1)*P11J*P11K*P110J*P110K+
## I[1]*P1*P1*P11J*(1-P11J)*P110J*
## P110K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P11J*P11K*P110J*(1-P110J)/(P1*pi1J*P11J*pi11J))*
## u110J*u110K
## A110.111<-( P1*(1-P1)*P11J*P11K*P110J*P111K+
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P111K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P11J*P11K*P110J*(1-P110J)/(P1*pi1J*P11J*pi11J))*u110J*u111K
## A111.000<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u000K
## A111.001<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u001K
## A111.010<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u010K
## A111.011<-(-P1*(1-P1)*P11J*P00K*P111J*P000K)*u111J*u011K
## A111.100<-( P1*(1-P1)*P11J*P10K*P111J*P100K-
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P100K/(P1*pi1J))*u111J*u100K
## A111.101<-( P1*(1-P1)*P11J*P10K*P111J*P101K-
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P101K/(P1*pi1J))*u111J*u101K
## A111.110<-( P1*(1-P1)*P11J*P11K*P111J*P110K+
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P110K/(P1*pi1J)-I[1]*I[3]*P1*P1*
## P11J*P11K*P111J*(1-P111J)/(P1*pi1J*P11J*pi11J))*
## u111J*u110K
## A111.111<-( P1*(1-P1)*P11J*P11K*P111J*P111K+
## I[1]*P1*P1*P11J*(1-P11J)*P111J*
## P111K/(P1*pi1J)+I[1]*I[3]*P1*P1*P11J*
## P11K*P111J*(1-P111J)/(P1*pi1J*P11J*pi11J))*u111J*u111K
## A<-sum(A000.000,A000.001,A000.010,A000.011,A000.100,
## A000.101,A000.110,A000.111,
## A001.000,A001.001,A001.010,A001.011,A001.100,
## A001.101,A001.110,A001.111,
## A010.000,A010.001,A010.010,A010.011,A010.100,
## A010.101,A010.110,A010.111,
## A011.000,A011.001,A011.010,A011.011,A011.100,
## A011.101,A011.110,A011.111,
## A100.000,A100.001,A100.010,A100.011,A100.100,
## A100.101,A100.110,A100.111,
## A101.000,A101.001,A101.010,A101.011,A101.100,
## A101.101,A101.110,A101.111,
## A110.000,A110.001,A110.010,A110.011,A110.100,
## A110.101,A110.110,A110.111,
## A111.000,A111.001,A111.010,A111.011,A111.100,
## A111.101,A111.110,A111.111)
##
## if (FA=="binomial"){
## if (I[1]==1 && I[3]==1 && I[ 7]==1) {
## B000.000<-P0*P0*P00J*P00K*P000J*
## P000K*bv000J/(P0*pi0J*P00J*pi00J*P000J*pi000J)}
## else {B000.000<-0}
## if (I[1]==1 && I[3]==1 && I[ 8]==1) {
## B001.001<-P0*P0*P01J*P01K*P001J*
## P001K*bv001J/(P0*pi0J*P00J*pi00J*P001J*pi001J)}
## else {B001.001<-0}
## if (I[1]==1 && I[4]==1 && I[ 9]==1) {
## B010.010<-P0*P0*P01J*P01K*P010J*
## P010K*bv010J/(P0*pi0J*P01J*pi01J*P010J*pi010J)}
## else {B010.010<-0}
## if (I[1]==1 && I[4]==1 && I[10]==1) {
## B011.011<-P0*P0*P01J*P01K*P011J*
## P011K*bv011J/(P0*pi0J*P01J*pi01J*P011J*pi011J)}
## else {B011.011<-0}
## if (I[1]==1 && I[5]==1 && I[11]==1) {
## B100.100<-P1*P1*P10J*P10K*P100J*
## P100K*bv100J/(P1*pi1J*P10J*pi10J*P100J*pi100J)}
## else {B100.100<-0}
## if (I[1]==1 && I[5]==1 && I[12]==1) {
## B101.101<-P1*P1*P10J*P10K*P101J*
## P101K*bv101J/(P1*pi1J*P10J*pi10J*P101J*pi101J)}
## else {B101.101<-0}
## if (I[1]==1 && I[6]==1 && I[13]==1) {
## B110.110<-P1*P1*P11J*P11K*P110J*
## P110K*bv110J/(P1*pi1J*P11J*pi11J*P110J*pi110J)}
## else {B110.110<-0}
## if (I[1]==1 && I[6]==1 && I[14]==1) {
## B111.111<-P1*P1*P11J*P11K*P111J*
## P111K*bv111J/(P1*pi1J*P11J*pi11J*P111J*pi111J)}
## else {B111.111<-0}
## } else
## if(FA=="gaussian"){
## if (I[1]==1 && I[3]==1 && I[ 7]==1) {
## B000.000<-P0*P0*P00J*P00K*P000J*P000K*
## v000J/(P0*pi0J*P00J*pi00J*P000J*pi000J)}
## else {B000.000<-0}
## if (I[1]==1 && I[3]==1 && I[ 8]==1) {
## B001.001<-P0*P0*P01J*P01K*P001J*
## P001K*v001J/(P0*pi0J*P00J*pi00J*P001J*pi001J)}
## else {B001.001<-0}
## if (I[1]==1 && I[4]==1 && I[ 9]==1) {
## B010.010<-P0*P0*P01J*P01K*P010J*
## P010K*v010J/(P0*pi0J*P01J*pi01J*P010J*pi010J)}
## else {B010.010<-0}
## if (I[1]==1 && I[4]==1 && I[10]==1) {
## B011.011<-P0*P0*P01J*P01K*P011J*P011K*
## v011J/(P0*pi0J*P01J*pi01J*P011J*pi011J)}
## else {B011.011<-0}
## if (I[1]==1 && I[5]==1 && I[11]==1) {
## B100.100<-P1*P1*P10J*P10K*P100J*P100K*
## v100J/(P1*pi1J*P10J*pi10J*P100J*pi100J)}
## else {B100.100<-0}
## if (I[1]==1 && I[5]==1 && I[12]==1) {
## B101.101<-P1*P1*P10J*P10K*P101J*P101K*
## v101J/(P1*pi1J*P10J*pi10J*P101J*pi101J)}
## else {B101.101<-0}
## if (I[1]==1 && I[6]==1 && I[13]==1) {
## B110.110<-P1*P1*P11J*P11K*P110J*P110K*
## v110J/(P1*pi1J*P11J*pi11J*P110J*pi110J)}
## else {B110.110<-0}
## if (I[1]==1 && I[6]==1 && I[14]==1) {
## B111.111<-P1*P1*P11J*P11K*P111J*P111K*
## v111J/(P1*pi1J*P11J*pi11J*P111J*pi111J)}
## else {B111.111<-0}
## }else
## stop("invalid enter for argument 'family'")
## B<-sum(B000.000,B001.001,B010.010,B011.011,
## B100.100,B101.101,B110.110,B111.111)
## tvc<-A+B
## }
return(tvc)
}
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