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onerunfam <- function(i,n,alr=0,manual=1,time=0,simplealr=1,theta=1) { ## {{{
### n=200; beta=0.2; theta=1; time=0; i=1
print(i)
dd <- simBinFam(n,beta=0,theta)
ddl <- fast.reshape(dd,varying="y",keep="y")
out2t <- system.time(
marg <- glm(y~+1,data=ddl,family=binomial())
)
ps <- predict(marg,type="response")
if (time==1) print(out2t)
if (manual==1) {
if (time==1) print(date())
ddl$ps <- ps
fam <- familycluster.index(ddl$id)
prtfam <- ddl[fam$familypairindex,]
prtfam$subfam <- fam$subfamilyindex
### lave afhængighedsdesign pba af wide format zyg1*zyg2 feks
prtfamclust <- data.frame(fast.reshape(prtfam,id="subfam"))
### des <- model.matrix(~-1+factor(num1):factor(num2),data=prtfamclust)
mf <- with(prtfamclust,(num1=="m")*(num2=="f")*1)
mb <- with(prtfamclust,(num1=="m" | num1=="f")*(num2=="b1" | num2=="b2")*1)
bb <- with(prtfamclust,(num1=="b1" )*(num2=="b1" | num2=="b2")*1)
des <- cbind(mf,mb,bb)*1
mulig <- (apply(des,2,sum)>0)
names <- colnames(des)
prtfamclust <- cbind(prtfamclust,des)
prtfam <- fast.reshape(prtfamclust,varying=c("y","ps","num"),keep=c("y","ps","num","subfam","id",names))
prtfam$famclust <- prtfam$id1
destheta <- prtfam[,names]
if (time==1) print(date())
udt <- system.time(
udf <- binomial.twostage(prtfam$y,data=prtfam,
clusters=prtfam$subfam, detail=0,
### score.method="nlminb",
score.method="fisher.scoring",
theta.des=prtfam[,names],
max.clust=1000,iid=1,
Nit=60,marginal.p=prtfam$ps,se.clusters=prtfam$famclust)
)
if (time==1) print(udt)
zfam <- rbind(c(1,0,0), ## m-f
c(0,1,0), ## m-b1
c(0,1,0), ## m-b2
c(1,0,0), ## f-m
c(0,1,0), ## f-b1
c(0,1,0), ## f-b2
c(0,1,0), ## b1-m
c(0,1,0), ## b1-f
c(0,0,1), ## b1-b2
c(0,1,0), ## b2-m
c(0,1,0), ## b2-f
c(0,0,1)) ## b2-b1
if (alr==1) {
if (simplealr==0) {
### cvec <- (ddl$num=="m"| ddl$num=="f")*1 +(ddl$num=="b1"| ddl$num=="b2")*2
### k <- 2
### dmat <- rbind(c(1,0,0),c(0,1,0),c(0,0,1))
### udz <- class2z(cvec,ddl$id,k,dmat)
###
### ZMAST <- rep(1,12)
### ZMAST <- cbind(ZMAST,c(0,0,0,0,1,1,0,1,1,0,1,1))
###
### outl <- alr(ddl$y~+1,id=ddl$id,depmodel="general",ainit=rep(0.01,3),z=udz$z,zmast=0)
if (!require(alr)) stop("'alr' package required")
out4t <- system.time(
outl <- alr(ddl$y~+1,id=ddl$id,depmodel="general",zlocs=rep(1:4,n),ainit=rep(0.01,3),z=zfam,zmast=1)
)
if (time==1) print(out4t)
outl <- c(summary(outl)$alpha[,1],summary(outl)$alpha[,2])
names(outl) <- c(rep("alr",3),rep("se-alr",3))
} else {
outl <- alr(ddl$y~+1,id=ddl$id,depmodel="exchangeable",ainit=rep(0.01,1))
outl <- c(summary(outl)$alpha[,1],summary(outl)$alpha[,2])
names(outl) <- c(rep("alr",1),rep("se-alr",1))
}
}
} else { ### med design formula
form <- ~factor(num1)*factor(num2)
udbin <- easy.binomial.twostage(marg,data=ddl,
response="y",id="id",theta.formula=form,
marginal.p=ps,
score.method="fisher.scoring")
}
### if (alr==1) { ### alr til simpelt design
### outl <- alr(ddl$y~ddl$x,id=ddl$id,depm="exchangeable", ainit=0.01)
### outl <- summary(outl)$alpha
### ud <- c(udbin$theta,udbin$var.theta^.5,udbin$hessi^.5,c(outl)[1:2])
### names(ud) <- c("TWO","se-two","se-twoR","alr","se-alr")
### }
ud <- c(udf$theta,diag(udf$var.theta)^.5)
if (alr==1) ud <- c(ud,outl)
return(ud)
} ## }}}
onerunfam2 <- function(i,n,alr=0,manual=1,time=0,theta=1) { ## {{{
### n=1000; beta=0.2; theta=1; time=0; i=1
print(i)
dd <- simBinFam(n,beta=0,theta)
ddl <- fast.reshape(dd,varying="y",keep="y")
desfs <- function(x,num1="num1",num2="num2")
{ ## {{{
mf <- (x[num1]=="m")*(x[num2]=="f")*1
mb <- (x[num1]=="m" | x[num1]=="f")*(x[num2]=="b1" | x[num2]=="b2")*1
bb <- (x[num1]=="b1")*(x[num2]=="b1" | x[num2]=="b2")*1
c(mf,mb,bb)
} ## }}}
ud <- easy.binomial.twostage(y~+1,data=ddl,
response="y",id="id",
score.method="fisher.scoring",deshelp=0,
theta.formula=desfs,desnames=c("pp","pc","cc"))
ud <- c(ud$theta[,1],diag(ud$var.theta)^.5)
zfam <- rbind(c(1,0,0), ## m-f
c(0,1,0), ## m-b1
c(0,1,0), ## m-b2
c(1,0,0), ## f-m
c(0,1,0), ## f-b1
c(0,1,0), ## f-b2
c(0,1,0), ## b1-m
c(0,1,0), ## b1-f
c(0,0,1), ## b1-b2
c(0,1,0), ## b2-m
c(0,1,0), ## b2-f
c(0,0,1)) ## b2-b1
if (alr==1) {
if (!require(alr)) stop("'alr' package required")
outl <- alr(ddl$y~+1,id=ddl$id,
depmodel="general",zlocs=rep(1:4,n),ainit=rep(0.01,3),z=zfam,zmast=1)
outl <- c(summary(outl)$alpha[,1],summary(outl)$alpha[,2])
names(outl) <- c(rep("alr",3),rep("se-alr",3))
}
if (alr==1) ud <- c(ud,outl)
return(ud)
} ## }}}
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