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543.5	540	519	557.5
963	1026.5	966	996.5
729	710.5	648.5	690
1543.5 1672 1643.5 1731
474 459.5 461.5 481.5
599.5 590 583.5 548
691 799 795.5 763
577 525 566.5 582
450.5	 466.5 433	484
633 662 726.5 715
606 554.5 568.5 575.5
932 623.5 817.5 1282.5
1004.5 1061 1033 1071.5
876.5	 950.5 891.5 973
461 467.5 480 459
784 755.5 769 783
511 561.5 523.5	533.5
826.5	 961.5 833 1015
507.5	 520 560.5	492
508 514 455.5 504
465 505.5 438.5 483.5
609 531.5 641 729.5
454.5	 468	462 435
388 383 386 342.5

rm2mcp<-function(J,K,x,est=tmean,alpha=.05,grp=NA,dif=T,nboot=NA,
plotit=FALSE,BA=F,hoch=F,...){
JK <- J * K
if(is.matrix(x))
x <- listm(x)
if(!is.na(grp[1])) {
yy <- x
for(j in 1:length(grp))
x[[j]] <- yy[[grp[j]]]
}
if(!is.list(x))
stop('Data must be stored in list mode or a matrix.')
for(j in 1:JK) {
xx <- x[[j]]
x[[j]] <- xx[!is.na(xx)]
}
temp<-con2way(J,K)
conA<-temp$conA
conB<-temp$conB
conAB<-temp$conAB
ncon <- max(nrow(conA), nrow(conB), nrow(conAB))
FacA<-rmmcppb(x,con=conA,est=est,plotit=plotit,dif=dif,grp=grp,
nboot=nboot,BA=T,hoch=F,...)
FacB<-rmmcppb(x,con=conB,est=est,plotit=plotit,dif=dif,grp=grp,
nboot=nboot,BA=T,hoch=F,...)
FacAB<-rmmcppb(x,con=conAB,est=est,plotit=plotit,dif=dif,grp=grp,
nboot=nboot,BA=T,hoch=F,...)
list(Factor.A=FacA,Factor.B=FacB,Factor.AB=FacAB)
}
listm<-function(x){
if(is.null(dim(x)))stop('The argument x must be a matrix or data frame')
y<-list()
for(j in 1:ncol(x))y[[j]]<-x[,j]
y
}
con2way<-function(J,K){
JK <- J * K
Ja<-(J^2-J)/2
Ka<-(K^2-K)/2
JK<-J*K
conA<-matrix(0,nrow=JK,ncol=Ja)
ic<-0
for(j in 1:J){
for(jj in 1:J){
if(j < jj){
ic<-ic+1
mat<-matrix(0,nrow=J,ncol=K)
mat[j,]<-1
mat[jj,]<-0-1
conA[,ic]<-t(mat)
}}}
conB<-matrix(0,nrow=JK,ncol=Ka)
ic<-0
for(k in 1:K){
for(kk in 1:K){
if(kic<-ic+1
mat<-matrix(0,nrow=J,ncol=K)
mat[,k]<-1
mat[,kk]<-0-1
conB[,ic]<-t(mat)
}}}
conAB<-matrix(0,nrow=JK,ncol=Ka*Ja)
ic<-0
for(j in 1:J){
for(jj in 1:J){
if(j < jj){
for(k in 1:K){
for(kk in 1:K){
if(kic<-ic+1
mat<-matrix(0,nrow=J,ncol=K)
mat[j,k]<-1
mat[j,kk]<-0-1
mat[jj,k]<-0-1
mat[jj,kk]<-1
}
conAB[,ic]<-t(mat)
}}}}}
list(conA=conA,conB=conB,conAB=conAB)
}
rmmcppbd<-function(x,y=NULL,alpha=.05,con=0,est=onestep,plotit=TRUE,grp=NA,nboot=NA,
hoch=T,SEED=TRUE,...){
if(!is.null(y[1]))x<-cbind(x,y)
if(!is.list(x) && !is.matrix(x))stop('Data must be stored in a matrix or in list mode.')
if(is.list(x)){
if(is.matrix(con)){
if(length(x)!=nrow(con))stop('The number of rows in con is not equal to the number of groups.')
}}
if(is.list(x)){
mat<-matl(x)
}
if(is.matrix(x) && is.matrix(con)){
if(ncol(x)!=nrow(con))stop('The number of rows in con is not equal to the number of groups.')
mat<-x
}
if(is.matrix(x))mat<-x
if(!is.na(sum(grp)))mat<-mat[,grp]
x<-mat
mat<-elimna(mat) # Remove rows with missing values.
x<-mat
J<-ncol(mat)
n=nrow(mat)
if(n>=80)hoch=T
Jm<-J-1
if(sum(con^2)==0){
d<-(J^2-J)/2
con<-matrix(0,J,d)
id<-0
for (j in 1:Jm){
jp<-j+1
for (k in jp:J){
id<-id+1
con[j,id]<-1
con[k,id]<-0-1
}}}
d<-ncol(con)
if(is.na(nboot)){
nboot<-5000
if(d<=10)nboot<-3000
if(d<=6)nboot<-2000
if(d<=4)nboot<-1000
}
n<-nrow(mat)
crit.vec<-alpha/c(1:d)
connum<-ncol(con)
xx<-x%*%con
xx<-as.matrix(xx)
if(SEED)set.seed(2) # set seed of random number generator so that
psihat<-matrix(0,connum,nboot)
bvec<-matrix(NA,ncol=connum,nrow=nboot)
data<-matrix(sample(n,size=n*nboot,replace=T),nrow=nboot)
if(ncol(xx)==1){
for(ib in 1:nboot)psihat[1,ib]<-est(xx[data[ib,]],...)
}
if(ncol(xx)>1){
for(ib in 1:nboot)psihat[,ib]<-apply(xx[data[ib,],],2,est,...)
}
test<-1
for (ic in 1:connum){
test[ic]<-(sum(psihat[ic,]>0)+.5*sum(psihat[ic,]==0))/nboot
test[ic]<-min(test[ic],1-test[ic])
}
test<-2*test
ncon<-ncol(con)
if(alpha==.05){
dvec<-c(.025,.025,.0169,.0127,.0102,.00851,.0073,.00639,.00568,.00511)
if(ncon > 10){
avec<-.05/c(11:ncon)
dvec<-c(dvec,avec)
}}
if(alpha==.01){
dvec<-c(.005,.005,.00334,.00251,.00201,.00167,.00143,.00126,.00112,.00101)
if(ncon > 10){
avec<-.01/c(11:ncon)
dvec<-c(dvec,avec)
}}
if(alpha != .05 && alpha != .01){
dvec<-alpha/c(1:ncon)
dvec[2]<-alpha/2
}
if(hoch)dvec<-alpha/(2*c(1:ncon))
dvec<-2*dvec
if(plotit && connum==1){
plot(c(psihat[1,],0),xlab='',ylab='Est. Difference')
points(psihat[1,])
abline(0,0)
}
temp2<-order(0-test)
ncon<-ncol(con)
zvec<-dvec[1:ncon]
sigvec<-(test[temp2]>=zvec)
output<-matrix(0,connum,6)
dimnames(output)<-list(NULL,c('con.num','psihat','p.value','p.crit','ci.lower','ci.upper'))
tmeans<-apply(xx,2,est,...)
psi<-1
icl<-round(dvec[ncon]*nboot/2)+1
icu<-nboot-icl-1
for (ic in 1:ncol(con)){
output[ic,2]<-tmeans[ic]
output[ic,1]<-ic
output[ic,3]<-test[ic]
output[temp2,4]<-zvec
temp<-sort(psihat[ic,])
output[ic,5]<-temp[icl]
output[ic,6]<-temp[icu]
}
num.sig<-sum(output[,3]<=output[,4])
list(output=output,con=con,num.sig=num.sig)
}
rmmcppb<-function(x,y=NULL,alpha=.05,con=0,est=onestep,plotit=TRUE,dif=T,grp=NA,nboot=NA,BA=F,hoch=F,xlab='Group 1',ylab='Group 2',pr=TRUE,SEED=TRUE,...){
if(dif){
if(pr)print('dif=T, so analysis is done on difference scores')
temp<-rmmcppbd(x,y=y,alpha=.05,con=con,est,plotit=plotit,grp=grp,nboot=nboot,
hoch=T,...)
output<-temp$output
con<-temp$con
}
if(!dif){
if(pr){
print('dif=F, so analysis is done on marginal distributions')
if(!BA)print('With M-estimator or MOM, suggest using BA=T and hoch=T')
}
if(!is.null(y[1]))x<-cbind(x,y)
if(!is.list(x) && !is.matrix(x))stop('Data must be stored in a matrix or in list mode.')
if(is.list(x)){
if(is.matrix(con)){
if(length(x)!=nrow(con))stop('The number of rows in con is not equal to the number of groups.')
}}
if(is.list(x)){
mat<-matl(x)
}
if(is.matrix(x) && is.matrix(con)){
if(ncol(x)!=nrow(con))stop('The number of rows in con is not equal to the number of groups.')
mat<-x
}
if(is.matrix(x))mat<-x
if(!is.na(sum(grp)))mat<-mat[,grp]
mat<-elimna(mat) # Remove rows with missing values.
x<-mat
J<-ncol(mat)
xcen<-x
for(j in 1:J)xcen[,j]<-x[,j]-est(x[,j])
Jm<-J-1
if(sum(con^2)==0){
d<-(J^2-J)/2
con<-matrix(0,J,d)
id<-0
for (j in 1:Jm){
jp<-j+1
for (k in jp:J){
id<-id+1
con[j,id]<-1
con[k,id]<-0-1
}}}
d<-ncol(con)
if(is.na(nboot)){
if(d<=4)nboot<-1000
if(d>4)nboot<-5000
}
n<-nrow(mat)
crit.vec<-alpha/c(1:d)
connum<-ncol(con)
if(SEED)set.seed(2) # set seed of random number generator so that
xbars<-apply(mat,2,est)
psidat<-NA
for (ic in 1:connum)psidat[ic]<-sum(con[,ic]*xbars)
psihat<-matrix(0,connum,nboot)
psihatcen<-matrix(0,connum,nboot)
bvec<-matrix(NA,ncol=J,nrow=nboot)
bveccen<-matrix(NA,ncol=J,nrow=nboot)
if(pr)print('Taking bootstrap samples. Please wait.')
data<-matrix(sample(n,size=n*nboot,replace=T),nrow=nboot)
for(ib in 1:nboot){
bvec[ib,]<-apply(x[data[ib,],],2,est,...)
bveccen[ib,]<-apply(xcen[data[ib,],],2,est,...)
}
test<-1
bias<-NA
for (ic in 1:connum){
psihat[ic,]<-apply(bvec,1,bptdpsi,con[,ic])
psihatcen[ic,]<-apply(bveccen,1,bptdpsi,con[,ic])
bias[ic]<-sum((psihatcen[ic,]>0))/nboot-.5
ptemp<-(sum(psihat[ic,]>0)+.5*sum(psihat[ic,]==0))/nboot
if(BA)test[ic]<-ptemp-.1*bias[ic]
if(!BA)test[ic]<-ptemp
test[ic]<-min(test[ic],1-test[ic])
test[ic]<-max(test[ic],0)
}
test<-2*test
ncon<-ncol(con)
if(alpha==.05){
dvec<-c(.025,.025,.0169,.0127,.0102,.00851,.0073,.00639,.00568,.00511)
dvecba<-c(.05,.025,.0169,.0127,.0102,.00851,.0073,.00639,.00568,.00511)
if(ncon > 10){
avec<-.05/c(11:ncon)
dvec<-c(dvec,avec)
}}
if(alpha==.01){
dvec<-c(.005,.005,.00334,.00251,.00201,.00167,.00143,.00126,.00112,.00101)
dvecba<-c(.01,.005,.00334,.00251,.00201,.00167,.00143,.00126,.00112,.00101)
if(ncon > 10){
avec<-.01/c(11:ncon)
dvec<-c(dvec,avec)
}}
if(alpha != .05 && alpha != .01){
dvec<-alpha/c(1:ncon)
dvecba<-dvec
dvec[2]<-alpha
}
if(hoch)dvec<-alpha/c(1:ncon)
dvec<-2*dvec
dvecba<-dvec
if(plotit && ncol(bvec)==2){
z<-c(0,0)
one<-c(1,1)
plot(rbind(bvec,z,one),xlab=xlab,ylab=ylab,type='n')
points(bvec)
totv<-apply(x,2,est,...)
cmat<-var(bvec)
dis<-mahalanobis(bvec,totv,cmat)
temp.dis<-order(dis)
ic<-round((1-alpha)*nboot)
xx<-bvec[temp.dis[1:ic],]
xord<-order(xx[,1])
xx<-xx[xord,]
temp<-chull(xx)
lines(xx[temp,])
lines(xx[c(temp[1],temp[length(temp)]),])
abline(0,1)
}
temp2<-order(0-test)
ncon<-ncol(con)
zvec<-dvec[1:ncon]
if(BA)zvec<-dvecba[1:ncon]
sigvec<-(test[temp2]>=zvec)
output<-matrix(0,connum,6)
dimnames(output)<-list(NULL,c('con.num','psihat','p.value','p.sig','ci.lower','ci.upper'))
tmeans<-apply(mat,2,est,...)
psi<-1
output[temp2,4]<-zvec
for (ic in 1:ncol(con)){
output[ic,2]<-sum(con[,ic]*tmeans)
output[ic,1]<-ic
output[ic,3]<-test[ic]
temp<-sort(psihat[ic,])
icl<-round(output[ic,4]*nboot/2)+1
icu<-nboot-(icl-1)
output[ic,5]<-temp[icl]
output[ic,6]<-temp[icu]
}
}
num.sig<-sum(output[,3]<=output[,4])
list(output=output,con=con,num.sig=num.sig)
}
matl<-function(x){
J=length(x)
nval=NA
for(j in 1:J)nval[j]=length(x[[j]])
temp<-matrix(NA,ncol=J,nrow=max(nval))
for(j in 1:J)temp[1:nval[j],j]<-x[[j]]
temp
}
Aband<-function(x,alpha=.05,plotit=TRUE,sm=T,SEED=TRUE,nboot=500,grp=c(1:4),
xlab='X (First Factor)',ylab='Delta',crit=NA,print.all=F,plot.op=F){
if(!is.list(x) && !is.matrix(x))stop('store data in list mode or a matrix')
if(SEED)set.seed(2)
if(is.matrix(x))x<-listm(x)
for(j in 1:length(x))x[[j]]=elimna(x[[j]])/2
if(length(grp)<4)stop('There must be at least 4 groups')
if(length(x)!=4)stop('The argument grp must have 4 values')
x<-x[grp]
n<-c(length(x[[1]]),length(x[[2]]),length(x[[3]]),length(x[[4]]))
vals<-NA
y<-list()
if(is.na(crit)){
print('Approximating critical value. Please wait.')
for(i in 1:nboot){
for(j in 1:4)
y[[j]]<-rnorm(n[j])
temp<-ks.test(outer(y[[1]],y[[2]],FUN='+'),outer(y[[3]],y[[4]],FUN='+'))
vals[i]<-temp[1]$statistic
}
vals<-sort(vals)
ic<-(1-alpha)*nboot
crit<-vals[ic]
}
if(plot.op){
plotit<-F
g2plot(v1,v2)
}
output<-sband(outer(x[[1]],x[[2]],FUN='+'),outer(x[[3]],x[[4]],FUN='+'),
plotit=plotit,crit=crit,flag=F,sm=sm,xlab=xlab,ylab=ylab)
if(!print.all){
numsig<-output$numsig
ks.test.stat<-ks.test(outer(x[[1]],x[[2]],FUN='+'),
outer(x[[3]],x[[4]],FUN='+'))$statistic
output<-matrix(c(numsig,crit,ks.test.stat),ncol=1)
dimnames(output)<-list(c('number sig','critical value','KS test statistics'),
NULL)
}
output
}
elimna<-function(m){
if(is.null(dim(m)))m<-as.matrix(m)
ikeep<-c(1:nrow(m))
for(i in 1:nrow(m))if(sum(is.na(m[i,])>=1))ikeep[i]<-0
elimna<-m[ikeep[ikeep>=1],]
elimna
}
tmean<-function(x,tr=.2,na.rm=FALSE){
if(na.rm)x<-x[!is.na(x)]
val<-mean(x,tr)
val
}
bptdpsi<-function(x,con){
bptdpsi<-sum(con*x)
bptdpsi
}
bptdsub<-function(isub,x,tr,con){
h1 <- nrow(x) - 2 * floor(tr * nrow(x))
se<-0
for(j in 1:ncol(x)){
for(k in 1:ncol(x)){
djk<-(nrow(x) - 1) * wincor(x[isub,j],x[isub,k], tr)$cov
se<-se+con[j]*con[k]*djk
}
}
se/(h1*(h1-1))
}
y<-t(y)
head(y)
dimnames(y)
bitmap(file='test1.png')
boxplot(y)
dev.off()
bitmap(file='test2.png')
layout(matrix(c(1,2,3,4), 2, 2))
(rmout<-rm2mcp(2,2,y, plotit=TRUE) )
dev.off()
load(file='createtable')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,'Information on data table  format.',3,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'For this repeated measures design you must')
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'have only one participant /subject on each row.')
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'The order of factors is also constrained so that')
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'for factors A B each with two levels the column order is.')
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'A1B1 A1B2 A2B1 A2B2 as given in the default example.')
a<-table.row.end(a)
a<-table.end(a)
table.save(a,file='myinfo1.tab')
load(file='createtable')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,names(rmout)[1],3,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.A$output)[[2]][1],header=TRUE)
a<-table.element(a,rmout$Factor.A$output[1])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.A$output)[[2]][2],header=TRUE)
a<-table.element(a,rmout$Factor.A$output[2])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.A$output)[[2]][3],header=TRUE)
a<-table.element(a,rmout$Factor.A$output[3])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.A$output)[[2]][4],header=TRUE)
a<-table.element(a,rmout$Factor.A$output[4])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.A$output)[[2]][5],header=TRUE)
a<-table.element(a,rmout$Factor.A$output[5])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.A$output)[[2]][6],header=TRUE)
a<-table.element(a,rmout$Factor.A$output[6])
a<-table.row.end(a)
a<-table.end(a)
table.save(a,file='mytable1.tab')
load(file='createtable')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,names(rmout)[2],3,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.B$output)[[2]][1],header=TRUE)
a<-table.element(a,rmout$Factor.B$output[1])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.B$output)[[2]][2],header=TRUE)
a<-table.element(a,rmout$Factor.B$output[2])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.B$output)[[2]][3],header=TRUE)
a<-table.element(a,rmout$Factor.B$output[3])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.B$output)[[2]][4],header=TRUE)
a<-table.element(a,rmout$Factor.B$output[4])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.B$output)[[2]][5],header=TRUE)
a<-table.element(a,rmout$Factor.B$output[5])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.B$output)[[2]][6],header=TRUE)
a<-table.element(a,rmout$Factor.B$output[6])
a<-table.row.end(a)
a<-table.end(a)
table.save(a,file='mytable2.tab')
load(file='createtable')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,names(rmout)[3],3,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.AB$output)[[2]][1],header=TRUE)
a<-table.element(a,rmout$Factor.AB$output[1])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.AB$output)[[2]][2],header=TRUE)
a<-table.element(a,rmout$Factor.AB$output[2])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.AB$output)[[2]][3],header=TRUE)
a<-table.element(a,rmout$Factor.AB$output[3])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.AB$output)[[2]][4],header=TRUE)
a<-table.element(a,rmout$Factor.AB$output[4])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.AB$output)[[2]][5],header=TRUE)
a<-table.element(a,rmout$Factor.AB$output[5])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,dimnames(rmout$Factor.AB$output)[[2]][6],header=TRUE)
a<-table.element(a,rmout$Factor.AB$output[6])
a<-table.row.end(a)
a<-table.end(a)
table.save(a,file='mytable3.tab')