Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(mets)
## -----------------------------------------------------------------------------
library(mets)
data(twinstut)
twinstut$binstut <- 1*(twinstut$stutter=="yes")
twinsall <- twinstut
twinstut <- subset(twinstut,zyg%in%c("mz","dz"))
head(twinstut)
twinstut <- subset(twinstut,tvparnr < 3000)
## -----------------------------------------------------------------------------
margbin <- glm(binstut~factor(sex)+age,data=twinstut,family=binomial())
summary(margbin)
## ----twostage1----------------------------------------------------------------
bina <- binomial.twostage(margbin,data=twinstut,var.link=1,
clusters=twinstut$tvparnr,detail=0)
summary(bina)
## ----twostage2----------------------------------------------------------------
# design for OR dependence
theta.des <- model.matrix( ~-1+factor(zyg),data=twinstut)
bin <- binomial.twostage(margbin,data=twinstut,var.link=1,
clusters=twinstut$tvparnr,theta.des=theta.des)
summary(bin)
## ----twostage3----------------------------------------------------------------
twinstut$cage <- scale(twinstut$age)
theta.des <- model.matrix( ~-1+factor(zyg)+factor(sex),data=twinstut)
bina <- binomial.twostage(margbin,data=twinstut,var.link=1,
clusters=twinstut$tvparnr,theta.des=theta.des)
summary(bina)
## ----altsyntax1---------------------------------------------------------------
# refers to zygosity of first subject in eash pair : zyg1
# could also use zyg2 (since zyg2=zyg1 within twinpair's)
out <- easy.binomial.twostage(stutter~factor(sex)+age,data=twinstut,
response="binstut",id="tvparnr",var.link=1,
theta.formula=~-1+factor(zyg1))
summary(out)
## ----osdesign-----------------------------------------------------------------
# refers to zygosity of first subject in eash pair : zyg1
# could also use zyg2 (since zyg2=zyg1 within twinpair's))
desfs<-function(x,num1="zyg1",num2="zyg2")
c(x[num1]=="dz",x[num1]=="mz",x[num1]=="os")*1
margbinall <- glm(binstut~factor(sex)+age,data=twinsall,family=binomial())
out3 <- easy.binomial.twostage(binstut~factor(sex)+age,
data=twinsall,response="binstut",id="tvparnr",var.link=1,
theta.formula=desfs,desnames=c("dz","mz","os"))
summary(out3)
## -----------------------------------------------------------------------------
library(mets)
data(twinstut)
twinstut <- subset(twinstut,zyg%in%c("mz","dz"))
twinstut$binstut <- 1*(twinstut$stutter=="yes")
head(twinstut)
twinstut <- subset(twinstut,tvparnr < 2000)
## ----biprobit1----------------------------------------------------------------
b1 <- bptwin(binstut~sex,data=twinstut,id="tvparnr",zyg="zyg",DZ="dz",type="un")
summary(b1)
## ----bptwin1------------------------------------------------------------------
b1 <- bptwin(binstut~sex,data=twinstut,id="tvparnr",zyg="zyg",DZ="dz",type="ace")
summary(b1)
## ----bptwin2------------------------------------------------------------------
b0 <- bptwin(binstut~sex,data=twinstut,id="tvparnr",zyg="zyg",DZ="dz",type="ae")
summary(b0)
## ----addgamma1----------------------------------------------------------------
theta.des <- model.matrix( ~-1+factor(zyg),data=twinstut)
margbin <- glm(binstut~sex,data=twinstut,family=binomial())
bintwin <- binomial.twostage(margbin,data=twinstut,model="gamma",
clusters=twinstut$tvparnr,detail=0,theta=c(0.1)/1,var.link=1,
theta.des=theta.des)
summary(bintwin)
# test for same dependence in MZ and DZ
theta.des <- model.matrix( ~factor(zyg),data=twinstut)
margbin <- glm(binstut~sex,data=twinstut,family=binomial())
bintwin <- binomial.twostage(margbin,data=twinstut,model="gamma",
clusters=twinstut$tvparnr,detail=0,theta=c(0.1)/1,var.link=1,
theta.des=theta.des)
summary(bintwin)
## ----polygenic1---------------------------------------------------------------
out <- twin.polygen.design(twinstut,id="tvparnr",zygname="zyg",zyg="dz",type="ace")
head(cbind(out$des.rv,twinstut$tvparnr),10)
out$pardes
## ----polygenic2---------------------------------------------------------------
margbin <- glm(binstut~sex,data=twinstut,family=binomial())
bintwin1 <- binomial.twostage(margbin,data=twinstut,
clusters=twinstut$tvparnr,detail=0,theta=c(0.1)/1,var.link=0,
random.design=out$des.rv,theta.des=out$pardes)
summary(bintwin1)
## -----------------------------------------------------------------------------
concordanceTwinACE(bintwin1,type="ace")
## ----polygenic_ae-------------------------------------------------------------
out <- twin.polygen.design(twinstut,id="tvparnr",zygname="zyg",zyg="dz",type="ae")
bintwin <- binomial.twostage(margbin,data=twinstut,
clusters=twinstut$tvparnr,detail=0,theta=c(0.1)/1,var.link=0,
random.design=out$des.rv,theta.des=out$pardes)
summary(bintwin)
## -----------------------------------------------------------------------------
concordanceTwinACE(bintwin,type="ae")
## -----------------------------------------------------------------------------
sessionInfo()
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