library(SMARTAR)

#R code and results: Example 1
data(codiacs)

summary(codiacs)

head(codiacs)


#R code and results: Example 2
#Part 1
smartsize(delta=0.1213,df=5,global=TRUE,alpha=0.05,beta=0.20)        #input effect size of global test directly

#Part 2
#build sequence information matrix
SEQ=seq(1,8)
A1=c(0,0,0,0,1,1,1,1)
PI1=rep(0.5,8)
O2=c(0,0,1,1,0,0,1,1)
P2=c(0.7,0.7,0.3,0.3,0.6,0.6,0.4,0.4)
A2=c(0,1,0,1,0,1,0,1)
PI2=rep(0.5,8)
MEAN=c(1,8,11,10,9,6,20,12)
SD=rep(10,8)
SIMatrix=data.frame(SEQ,A1,PI1,O2,P2,A2,PI2,MEAN,SD)

SIMatrix
smartsize(sim=SIMatrix,global=TRUE,alpha=0.05,beta=0.20)             #input sequence-inforamtion matrix for powering by global test

#Part 3
smartsize(delta=0.90,global=FALSE,alpha=0.05,beta=0.20)              #power a SMART based on a pairwise comparison


#R code and results: Example 3
getncp(df=5,alpha=0.05,beta=0.20,d=0.0001,start=5)


#R code and results: Example 4
seqmeans(data=codiacs,family="gaussian",digits=2,plot="d",pch=c(19,15),
         legend=c("Intermediate evaluation”,“Stage-specific treatment"),
         xlab="stage-specific treatment/evalution",
         title="(A) Design diagram of CODIACS")

seqmeans(data=codiacs,family="gaussian",digits=2,plot="s",
         reference=TRUE,
         color="yellow",
         xlab="Treatment sequence",
         ylab="BDI reduction at 6 months",
         title="(B) Primary outcome by treatment sequence (A1,O2,A2)")


#R code and results: Example 5
atsmeans(data=codiacs,family="gaussian",method="Gest",conf=TRUE,digits=2,
         alpha=0.05,plot=TRUE,
         title="Estimated values of depression management strategy in CODIACS",
         xlab="Strategy",ylab="BDI reduction")


#R code and results: Example 6
smartest(data=codiacs,family="gaussian",method="Gest",digits=2,adjust="Bon")