inst/TestConstructor/CreateTest-logLikelihood.R
In rcqls/VAM: Virtual Age Models
# R script used to develop the testthat test for log-likelihood.R
# The number of the test
nbtest<-"TLeftCens3"
switch(nbtest,
TLeftCens3={
#Weibull + CM ABAO + PM ARAInf + mutlisystems + LeftCens
simData<-data.frame(System=c(rep(1,5),rep(2,4),rep(3,5),rep(4,4),rep(5,8)),Time=c(2.28,3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,1.57,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 1.95,2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,0,1, -1,-1,-1,0, 1,0,-1,-1,1, -1,1,1,0, 1,0,-1,1,-1,-1,1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ABAO() | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rhoMC<-0
rhoMP<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
c<-T[4]
T<-T[c(1:3,5:length(T))]
rho<-rhoMP
#Lcalc<--H(T[1])
#Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
#Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(c-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
c<-T[2]
T<-T[c(1,3:length(T))]
#Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(c-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
c<-T[2]
T<-T[c(1,3:length(T))]
#Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(c-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TLeftCens2={
#Weibull + CM ABAO + LeftCens + RightCens
simData<-data.frame(Time=c(2,3.36,4.04,4.97,5.16),Type=c(0,-1,-1,-1,0),row.names=1:5)
mle <- mle.vam(Time & Type ~ (ABAO() | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,2.5)
rho<-0
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[2:5]
c<-simData$Time[1]
Lcalc<-log(h(T[1]))-(H(T[1])-H(c))
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TLeftCens1={
#Weibull + CM ABAO + LeftCens
simData<-data.frame(Time=c(2,3.36,4.04,4.97,5.16),Type=c(0,-1,-1,-1,-1),row.names=1:5)
mle <- mle.vam(Time & Type ~ (ABAO() | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,2.5)
rho<-0
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[2:5]
c<-simData$Time[1]
Lcalc<-log(h(T[1]))-(H(T[1])-H(c))
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRGQR={
#Weibull + CM GQR-sqrt+PM GQR-ARA4-log
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,15)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78,15.2),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,2,1,-1,1,-1,0),row.names=1:23)
#simData<-simData[1:23,]
theta<-c(0.3,2.3,0.9,1.3,0.7)
mle <- mle.vam(System & Time & Type ~ (GQR(0.8|sqrt) | Weibull(0.001,2.5)) & (GQR_ARAm(1.2,0.9|log,2)+AGAN()),data=simData)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[5]
AMP<-theta[4]
T<-simData$Time[1:4]
iPM=0;iCM=0
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
A=1
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
iPM<-iPM+C;iCM<-iCM+0^C
C<-1;i<-1
V1=A*(1-rho)*(T[i])
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
iPM<-iPM+C;iCM<-iCM+0^C
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*A*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-3
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
T<-simData$Time[5:8]
iCM<-0;iPM<-0
C<-0
A<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-1
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
T<-simData$Time[9:23]
iCM<-0;iPM<-0
C<-1
A=1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-0;i<-4
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-5
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-9
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
i<-10
iPM<-0;iCM<-0
V5=0
V4=0
V3=0
V2=0
V1=0
A<-1
V=V1+V2+V3+V4+V5
C<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-11
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-12
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-13
V5=V4+V5
V4=V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-14
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARAm={
#Weibull + GQR_ARAm-m=3
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75,198.7,220.9,230),Type=c(-1,-1,-1,-1,-1,-1,0),row.names=1:7)
mle <- mle.vam(Time & Type ~ (GQR_ARAm(1.2,0.5|3) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,1.3,0.7)
rho<-theta[4]
rhoA<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-0
C<-0
V1=0;V2=0;V3=0;V4=0
A=1
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
C<-0;i<-1
V1=A*(1-rho)*(T[1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V4=V3+V4
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V4=V3+V4
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-i+1
V4=V3+V4
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_6={
#Weibull + CM ARAm-m=3 + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
#simData<-simData[1:4,]
theta<-c(0.3,1.8,0.3,0.7)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
mle <- mle.vam(System & Time & Type ~ (ARAm(0.3|2) | Weibull(0.001,2.5)) & (QR(0.6)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rho<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
A=1
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
#rho=rhoMP
A=A*rhoMP
C<-1;i<-1
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
#rho=rhoMP
A=A*rhoMP
C<-0;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-3
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[5:8]
C<-0
A<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
#rho=0
#A=rhoMC*A
C<-1;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-3
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[9:22]
C<-1
A=1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
A=A*rhoMP
C<-0;i<-1
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
#rho=0
#A=rhoMC*A
C<-1;i<-2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-3
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
#rho=0
#A=A*rhoMC
C<-0;i<-4
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-5
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-6
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-7
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-8
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-9
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-10
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-11
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-12
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-13
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_5={
#Weibull + CM QR + PM ARAm-m=3 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
#simData<-simData[1:4,]
theta<-c(0.3,1.8,1.3,0.7)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
mle <- mle.vam(System & Time & Type ~ (QR(0.3) | Weibull(0.001,2.5)) & (ARAm(0.6|2)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
A=1
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-1;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
C<-1;i<-3
V3=0
V2=0
V1=0
A=rhoMC*A
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[5:8]
C<-0
A<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=0
A=rhoMC*A
C<-1;i<-1
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[9:22]
C<-1
A=1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-0;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=rhoMC*A
C<-1;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-0;i<-4
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-5
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-9
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-10
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-11
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-12
V5=V4+V5
V4=V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-13
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_4={
#Weibull + CM ARAm-m=4 + PM ARAm-m=2 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
theta<-c(0.3,1.8,0.3,0.7)
mle <- mle.vam(System & Time & Type ~ (ARAm(0.3|4) | Weibull(0.001,2.5)) & (ARAm(0.6|2)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[5:8]
C<-0
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMC
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[9:22]
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-0;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-0;i<-4
V4=(1-rho)*V3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-5
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-9
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-10
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-11
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-12
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-13
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_3={
#Weibull + CM ARAm-m=2 + PM ARAm-m=4 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
theta<-c(0.3,1.8,0.3,0.7)
mle <- mle.vam(System & Time & Type ~ (ARAm(0.3|2) | Weibull(0.001,2.5)) & (ARAm(0.6|4)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[5:8]
C<-0
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMC
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[9:22]
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-0;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-0;i<-4
V4=V3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-5
V5=V4+V5
V4=V3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-9
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-10
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-11
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-12
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-13
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_2={
#Weibull + ARAm-m=4
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75,198.7,220.9),Type=c(-1,-1,-1,-1,-1,-1),row.names=1:6)
mle <- mle.vam(Time & Type ~ (ARAm(0.5|3) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
A<-rho*T[1]
Lcalc<-Lcalc+log(h(T[2]-A))-(H(T[2]-A)-H(T[1]-A))
i<-2
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-3
A<-rho*(T[i]+(1-rho)*T[i-1]+(1-rho)^2*T[i-2])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-4
A<-rho*(T[i]+(1-rho)*T[i-1]+(1-rho)^2*T[i-2])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-5
A<-rho*(T[i]+(1-rho)*T[i-1]+(1-rho)^2*T[i-2])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm={
#Weibull + ARAm-m=2
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75,198.7,220.9),Type=c(-1,-1,-1,-1,-1,-1),row.names=1:6)
mle <- mle.vam(Time & Type ~ (ARAm(0.5|2) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
A<-rho*T[1]
Lcalc<-Lcalc+log(h(T[2]-A))-(H(T[2]-A)-H(T[1]-A))
i<-2
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-3
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-4
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-5
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_5={
#Weibull + MC ARA1 + MP GQ_RARAInf-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (GQR_ARAInf(0.7,-1.3|log)),data=simData)
theta<-c(0.3,2.2,0.7,0.4,-0.9)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(3)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_4={
#Weibull + MC AGAN + MP GQ_RARA1-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,8)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.52),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,0),row.names=1:24)
#simData<-simData[1:24,]
mle <- mle.vam(System & Time & Type ~ (AGAN() | Weibull(0.001,2.5)) & (GQR_ARA1(0.7,-1.3|log)),data=simData)
theta<-c(0.3,2.2,0.4,-0.9)
#L<-logLik(mle,theta,TRUE,FALSE,FALSE)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMP<-theta[3]
rhoMP2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE)
alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_3={
#Weibull + MC ARA1 + MP GQ_RARA1-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (GQR_ARA1(0.7,-1.3|log)),data=simData)
theta<-c(0.3,2.2,0.7,0.4,-0.9)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_2={
#Weibull + GQR_ARAInf
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR_ARAInf(0.1,0.5) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7,-1.2)
rho<-theta[3]
rho2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
V<-(1-rho2)*T[1]
Lcalc<-Lcalc+log(rho^(1)*h(rho^(1)*(T[2]-T[1])+V))-(H(rho^(1)*(T[2]-T[1])+V)-H(V))
V<-(1-rho2)*(rho^(1)*(T[2]-T[1])+V )
Lcalc<-Lcalc+log(rho^(2)*h(rho^(2)*(T[3]-T[2])+V))-(H(rho^(2)*(T[3]-T[2])+V)-H(V))
V<-(1-rho2)*(rho^(2)*(T[3]-T[2])+V)
Lcalc<-Lcalc+log(rho^(3)*h(rho^(3)*(T[4]-T[3])+V))-(H(rho^(3)*(T[4]-T[3])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_1={
#Weibull + GQR_ARA1-log
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR_ARA1(0.7,-1.2|log) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7,-1.2)
rho<-theta[3]
rho2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
V<-(1-rho2)*T[1]
Lcalc<-Lcalc+log(rho^(log(2))*h(rho^(log(2))*(T[2]-T[1])+V))-(H(rho^(log(2))*(T[2]-T[1])+V)-H(V))
V<-rho^(log(2))*(T[2]-T[1])+V -rho2 *rho^(log(2))*(T[2]-T[1])
Lcalc<-Lcalc+log(rho^(log(3))*h(rho^(log(3))*(T[3]-T[2])+V))-(H(rho^(log(3))*(T[3]-T[2])+V)-H(V))
V<-rho^(log(3))*(T[3]-T[2])+V -rho2* rho^(log(3))*(T[3]-T[2])
Lcalc<-Lcalc+log(rho^(log(4))*h(rho^(log(4))*(T[4]-T[3])+V))-(H(rho^(log(4))*(T[4]-T[3])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQR3={
#Weibull + MC ARA1 + MP GQR-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (GQR(0.7|log)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(3)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQR2={
#Weibull + GQR-sqrt
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR(0.7|sqrt) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho^(sqrt(1))*h(rho^(sqrt(1))*(T[2]-T[1])))-(H(rho^(sqrt(1))*(T[2]-T[1]))-H(rho^(sqrt(1))*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^(sqrt(2))*h(rho^(sqrt(2))*(T[3]-T[2])))-(H(rho^(sqrt(2))*(T[3]-T[2]))-H(rho^(sqrt(2))*(T[2]-T[2])))
Lcalc<-Lcalc+log(rho^(sqrt(3))*h(rho^(sqrt(3))*(T[4]-T[3])))-(H(rho^(sqrt(3))*(T[4]-T[3]))-H(rho^(sqrt(3))*(T[3]-T[3])))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQR1={
#Weibull + GQR-log
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR(0.7|log) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho^(log(2))*h(rho^(log(2))*(T[2]-T[1])))-(H(rho^(log(2))*(T[2]-T[1]))-H(rho^(log(2))*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^(log(3))*h(rho^(log(3))*(T[3]-T[2])))-(H(rho^(log(3))*(T[3]-T[2]))-H(rho^(log(3))*(T[2]-T[2])))
Lcalc<-Lcalc+log(rho^(log(4))*h(rho^(log(4))*(T[4]-T[3])))-(H(rho^(log(4))*(T[4]-T[3]))-H(rho^(log(4))*(T[3]-T[3])))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR10={
#Weibull + CM ARAInf + PM QAGAN + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (QAGAN()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR9={
#Weibull + CM ARAInf + PM AGAP + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAP()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR8={
#Weibull + CM ARAInf + PM ABAO + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ABAO()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(A*(T[i+1]-T[i])+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(A*(T[i+1]-T[i])+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR7={
#Weibull + CM ARAInf + PM AGAN + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAN()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR6={
#Weibull + MC ARA1 + MP QR + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (QR(0.7)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR5={
#Weibull + MC QR + MP ARA1 + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (QR(0.2) | Weibull(0.001,2.5)) & (ARA1(0.7)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR4={
#Weibull + MC QR + MP ARAinf + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (QR(0.2) | Weibull(0.001,2.5)) & (ARAInf(0.7)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR3={
#Weibull + MC ARAInf + MP QR + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.2) | Weibull(0.001,2.5)) & (QR(0.7)),data=simData)
theta<-c(0.3,2.2,0.3,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-H(rho*(T[2]-T[1]))
Lcalc<-Lcalc-H(rho^2*(T[3]-T[2]))
Lcalc<-Lcalc-H(rho^3*(T[4]-T[3]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(rhoMP*h(rhoMP*(T[2]-T[1])))-H(rhoMP*(T[2]-T[1]))
V<-(1-rhoMC)*rhoMP*(T[2]-T[1])
Lcalc<-Lcalc+log(rhoMP*h(rhoMP*(T[3]-T[2])+V))-(H(rhoMP*(T[3]-T[2])+V)-H(V))
V<-(1-rhoMC)*(rhoMP*(T[3]-T[2])+V)
Lcalc<-Lcalc-(H(rhoMP*(T[4]-T[3])+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
Lcalc<-Lcalc-H(rhoMP*(T[3]-T[2]))
Lcalc<-Lcalc-H(rhoMP^2*(T[4]-T[3]))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(rhoMP*h(rhoMP*(T[2]-T[1])))-H(rhoMP*(T[2]-T[1]))
V<-(1-rhoMC)*rhoMP*(T[2]-T[1])
Lcalc<-Lcalc-(H(rhoMP*(T[3]-T[2])+V)-H(V))
Lcalc<-Lcalc+log(rhoMP^2*h(rhoMP^2*(T[4]-T[3])))-H(rhoMP^2*(T[4]-T[3]))
V<-(1-rhoMC)*rhoMP^2*(T[4]-T[3])
Lcalc<-Lcalc+log(rhoMP^2*h(rhoMP^2*(T[5]-T[4])+V))-(H(rhoMP^2*(T[5]-T[4])+V)-H(V))
V<-(1-rhoMC)*(rhoMP^2*(T[5]-T[4])+V)
Lcalc<-Lcalc-(H(rhoMP^2*(T[6]-T[5])+V)-H(V))
Lcalc<-Lcalc-H(rhoMP^3*(T[7]-T[6]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR2={
#Weibull + QR + MultiSystems + Censorship
simData<-data.frame(System=c(1,1,1,1,2,2,2,3),Time=c(18.09,52.07,95.71,145.75,15.02,45.1,82,20.1),Type=c(-1,-1,-1,0,-1,-1,-1,-1),row.names=1:8)
mle <- mle.vam(System & Time & Type ~ (QR(0.7) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[1:4]
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho*h(rho*(T[2]-T[1])))-(H(rho*(T[2]-T[1]))-H(rho*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^2*h(rho^2*(T[3]-T[2])))-(H(rho^2*(T[3]-T[2]))-H(rho^2*(T[2]-T[2])))
Lcalc<-Lcalc-(H(rho^3*(T[4]-T[3]))-H(rho^3*(T[3]-T[3])))
T<-simData$Time[5:7]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho*h(rho*(T[2]-T[1])))-(H(rho*(T[2]-T[1]))-H(rho*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^2*h(rho^2*(T[3]-T[2])))-(H(rho^2*(T[3]-T[2]))-H(rho^2*(T[2]-T[2])))
T<-simData$Time[8]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR={
#Weibull + QR
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (QR(0.7) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho*h(rho*(T[2]-T[1])))-(H(rho*(T[2]-T[1]))-H(rho*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^2*h(rho^2*(T[3]-T[2])))-(H(rho^2*(T[3]-T[2]))-H(rho^2*(T[2]-T[2])))
Lcalc<-Lcalc+log(rho^3*h(rho^3*(T[4]-T[3])))-(H(rho^3*(T[4]-T[3]))-H(rho^3*(T[3]-T[3])))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T01={
#Weibull + CM AGAN
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (AGAN() | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,1)
rho<-1
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T02={
#LogLinear + CM ABAO
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ABAO() | LogLinear(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,1)
rho<-0
h<-function(t) theta[1]*exp(theta[2]*t)
H<-function(t) theta[1]/theta[2]*(exp(theta[2]*t)-1)
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T03={
#Weibull3
simData<-data.frame(Time=c(3.36),Type=c(-1),row.names=1:1)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | Weibull3(0.001,2.5,5)),data=simData)
theta<-c(0.3,1.8,4,0.6)
c<-theta[3]
rho<-theta[4]
h<-function(t) theta[1]*theta[2]*(t+c)^(theta[2]-1)
H<-function(t) theta[1]*((t+c)^(theta[2])-c^(theta[2]))
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T1={
#Weibull
simData<-data.frame(Time=c(3.36),Type=c(-1),row.names=1:1)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T2={
#LogLinear
simData<-data.frame(Time=c(3.36),Type=c(-1),row.names=1:1)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | LogLinear(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*exp(theta[2]*t)
H<-function(t) theta[1]/theta[2]*(exp(theta[2]*t)-1)
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T3={
#Weibull + CM ARAInf
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T4={
#Weibull + CM ARA1
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]))-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T5={
#LogLinear + CM ARAInf
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | LogLinear(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*exp(theta[2]*t)
H<-function(t) theta[1]/theta[2]*(exp(theta[2]*t)-1)
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T6={
#Weibull + CM ARA1 + Censorship
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,0),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T7={
#Weibull + multiSystems
simData<-data.frame(System=c(1,2),Time=c(3.36,2.34),Type=c(-1,-1),row.names=1:2)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<-log(h(T[1]))-H(T[1])
T<-simData$Time[simData$System==2]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T8={
#Weibull + CM ARAInf + Censorship + multiSystems
simData<-data.frame(System=c(1,1,1,1,2,2,2,3),Time=c(3.36,4.04,4.97,5.16,2.34,3.46,5.02,4),Type=c(-1,-1,-1,0,-1,-1,-1,0),row.names=1:8)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T9={
#Weibull + CM ARAInf + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T91={
#Weibull + CM ARAInf + PM AGAN + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAN()),data=simData)
theta<-c(0.3,1.8,0.3)
rhoMC<-theta[3]
rhoMP<-1
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T92={
#Weibull + CM ARAInf + PM ABAO + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ABAO()),data=simData)
theta<-c(0.3,1.8,0.3)
rhoMC<-theta[3]
rhoMP<-0
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T93={
#Weibull + CM AGAN + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (AGAN() | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rhoMC<-1
rhoMP<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T94={
#Weibull + CM ABAO + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ABAO() | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rhoMC<-0
rhoMP<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T10={
#LogLinear + CM ARA1 + PM AR1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)) & (ARA1(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-V+(1-rhoMC)*(T[3]-T[2])
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3])+V
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4])+V
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T11={
#Weibull + CM ARA1 + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
#n<-11
#Data<-data.frame(System=simData$System[1:n],Time=simData$Time[1:n],Type=simData$Type[1:n])
#mle2 <- mle.vam(System & Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=Data)
#L2<-logLik(mle2,theta,c(TRUE,FALSE,FALSE))
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3])+V
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4])+V
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T12={
#Weibull + CM ARAInf + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ARA1(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T13={
#Weibull + CM ARAInf + PM ARAInf + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,10)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43),Type=c(1,2,2,1, -1,-1,-1,0, 1,-1,-1,2, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)+ARA1(-1)),data=simData)
theta<-c(0.3,1.8,0.3,0.8,-1)
rhoMC<-theta[3]
rhoMP1<-theta[4]
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMP1*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP1)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP2)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
V<-(1-rhoMP1)*(T[7]-T[6]+V)
Lcalc<-Lcalc-(H(T[8]-T[7]+V)-H(V))
V<-(1-rhoMP2)*(T[8]-T[7])+V
Lcalc<-Lcalc+log(h(T[9]-T[8]+V))-(H(T[9]-T[8]+V)-H(V))
V<-(1-rhoMC)*(T[9]-T[8]+V)
Lcalc<-Lcalc-(H(T[10]-T[9]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T14={
#Weibull + CM ARAInf + PM AGAN + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,10)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43),Type=c(1,2,2,1, -1,-1,-1,0, 1,-1,-1,2, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAN()+ARA1(-1)),data=simData)
theta<-c(0.3,1.8,0.3,-1)
rhoMC<-theta[3]
rhoMP1<-1
rhoMP2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMP1*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP1)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP2)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
V<-(1-rhoMP1)*(T[7]-T[6]+V)
Lcalc<-Lcalc-(H(T[8]-T[7]+V)-H(V))
V<-(1-rhoMP2)*(T[8]-T[7])+V
Lcalc<-Lcalc+log(h(T[9]-T[8]+V))-(H(T[9]-T[8]+V)-H(V))
V<-(1-rhoMC)*(T[9]-T[8]+V)
Lcalc<-Lcalc-(H(T[10]-T[9]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T15={
#Weibull3 + CM ARAInf + PM AGAN + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,10)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43),Type=c(1,2,2,1, -1,-1,-1,0, 1,-1,-1,2, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull3(0.001,2.5,3)) & (AGAN()+ARA1(-1)),data=simData)
theta<-c(0.3,1.8,4,0.3,-1)
c<-theta[3]
rhoMC<-theta[4]
rhoMP1<-1
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*(t+c)^(theta[2]-1)
H<-function(t) theta[1]*((t+c)^(theta[2])-(c)^(theta[2]))
T<-simData$Time[simData$System==1]
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMP1*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP1)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP2)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
V<-(1-rhoMP1)*(T[7]-T[6]+V)
Lcalc<-Lcalc-(H(T[8]-T[7]+V)-H(V))
V<-(1-rhoMP2)*(T[8]-T[7])+V
Lcalc<-Lcalc+log(h(T[9]-T[8]+V))-(H(T[9]-T[8]+V)-H(V))
V<-(1-rhoMC)*(T[9]-T[8]+V)
Lcalc<-Lcalc-(H(T[10]-T[9]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
)
L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
dL<-logLik(mle,theta,c(FALSE,TRUE,FALSE))
d2L<-logLik(mle,theta,c(FALSE,FALSE,TRUE))
C<-contrast(mle,theta,c(TRUE,FALSE,FALSE))
dC<-contrast(mle,theta,c(FALSE,TRUE,FALSE))
d2C<-contrast(mle,theta,c(FALSE,FALSE,TRUE))
epsilon<-0.000001
EstdL<-dL
EstdC<-dC
for(i in (1:length(dL))){
theta1<-theta
theta1[i]<-theta1[i]+epsilon
EstdL[i]<-(logLik(mle,theta1,c(TRUE,FALSE,FALSE))-logLik(mle,theta,c(TRUE,FALSE,FALSE)))/epsilon
}
for(i in (1:length(dC))){
theta1<-theta
theta1[i+1]<-theta1[i+1]+epsilon
EstdC[i]<-(contrast(mle,theta1,c(TRUE,FALSE,FALSE))-contrast(mle,theta,c(TRUE,FALSE,FALSE)))/epsilon
}
Estd2L<-d2L
Estd2C<-d2C
for(i in (1:(dim(d2L)[1]))){
theta1<-theta
theta1[i]<-theta1[i]+epsilon
Estd2L[i,]<-(logLik(mle,theta1,c(FALSE,TRUE,FALSE))-logLik(mle,theta,c(FALSE,TRUE,FALSE)))/epsilon
}
if(!(is.null(dim(d2C)))){
for(i in (1:(dim(d2C)[1]))){
theta1<-theta
theta1[i+1]<-theta1[i+1]+epsilon
Estd2C[i,]<-(contrast(mle,theta1,c(FALSE,TRUE,FALSE))-contrast(mle,theta,c(FALSE,TRUE,FALSE)))/epsilon
}
} else {
theta1<-theta
theta1[2]<-theta1[2]+epsilon
Estd2C<-(contrast(mle,theta1,c(FALSE,TRUE,FALSE))-contrast(mle,theta,c(FALSE,TRUE,FALSE)))/epsilon
}
print(L)
print(Lcalc)
print(C)
print(Ccalc)
print(dL)
print(EstdL)
print(dC)
print(EstdC)
print(d2L)
print(Estd2L)
print(d2C)
print(Estd2C)
print((L-Lcalc)/L)
print((C-Ccalc)/C)
print((dL-EstdL)/dL)
print((dC-EstdC)/dC)
print((d2L-Estd2L)/d2L)
print((d2C-Estd2C)/d2C)
ecrit<-function(aprinter,nl,nc){
res<-""
if((nl>0)&&(nc>0)){
for(i in 1:nc){
for(j in 1:nl){
res<-paste(res,aprinter[j,i],sep=',')
}
}}
else if((nl>0)||(nc>0)){
for(j in 1:max(nl,nc)){
res<-paste(res,aprinter[j],sep=',')
}
}
else res<-paste(res,aprinter,sep=',')
print(res)
}
ecrit(L,0,0)
ecrit(dL,0,length(dL))
ecrit(d2L,dim(d2L)[1],dim(d2L)[2])
ecrit(C,0,0)
ecrit(dC,0,length(dC))
if(!(is.null(dim(d2C)))){
ecrit(d2C,dim(d2C)[1],dim(d2C)[2])
} else {
ecrit(d2C,0,0)
}
rcqls/VAM documentation built on Jan. 14, 2024, 9:07 p.m.
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# R script used to develop the testthat test for log-likelihood.R
# The number of the test
nbtest<-"TLeftCens3"
switch(nbtest,
TLeftCens3={
#Weibull + CM ABAO + PM ARAInf + mutlisystems + LeftCens
simData<-data.frame(System=c(rep(1,5),rep(2,4),rep(3,5),rep(4,4),rep(5,8)),Time=c(2.28,3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,1.57,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 1.95,2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,0,1, -1,-1,-1,0, 1,0,-1,-1,1, -1,1,1,0, 1,0,-1,1,-1,-1,1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ABAO() | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rhoMC<-0
rhoMP<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
c<-T[4]
T<-T[c(1:3,5:length(T))]
rho<-rhoMP
#Lcalc<--H(T[1])
#Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
#Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(c-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
c<-T[2]
T<-T[c(1,3:length(T))]
#Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(c-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
c<-T[2]
T<-T[c(1,3:length(T))]
#Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(c-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TLeftCens2={
#Weibull + CM ABAO + LeftCens + RightCens
simData<-data.frame(Time=c(2,3.36,4.04,4.97,5.16),Type=c(0,-1,-1,-1,0),row.names=1:5)
mle <- mle.vam(Time & Type ~ (ABAO() | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,2.5)
rho<-0
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[2:5]
c<-simData$Time[1]
Lcalc<-log(h(T[1]))-(H(T[1])-H(c))
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TLeftCens1={
#Weibull + CM ABAO + LeftCens
simData<-data.frame(Time=c(2,3.36,4.04,4.97,5.16),Type=c(0,-1,-1,-1,-1),row.names=1:5)
mle <- mle.vam(Time & Type ~ (ABAO() | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,2.5)
rho<-0
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[2:5]
c<-simData$Time[1]
Lcalc<-log(h(T[1]))-(H(T[1])-H(c))
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRGQR={
#Weibull + CM GQR-sqrt+PM GQR-ARA4-log
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,15)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78,15.2),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,2,1,-1,1,-1,0),row.names=1:23)
#simData<-simData[1:23,]
theta<-c(0.3,2.3,0.9,1.3,0.7)
mle <- mle.vam(System & Time & Type ~ (GQR(0.8|sqrt) | Weibull(0.001,2.5)) & (GQR_ARAm(1.2,0.9|log,2)+AGAN()),data=simData)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[5]
AMP<-theta[4]
T<-simData$Time[1:4]
iPM=0;iCM=0
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
A=1
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
iPM<-iPM+C;iCM<-iCM+0^C
C<-1;i<-1
V1=A*(1-rho)*(T[i])
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
iPM<-iPM+C;iCM<-iCM+0^C
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*A*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-3
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
T<-simData$Time[5:8]
iCM<-0;iPM<-0
C<-0
A<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-1
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
T<-simData$Time[9:23]
iCM<-0;iPM<-0
C<-1
A=1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-0;i<-4
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-5
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-9
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
i<-10
iPM<-0;iCM<-0
V5=0
V4=0
V3=0
V2=0
V1=0
A<-1
V=V1+V2+V3+V4+V5
C<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-11
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-12
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=rhoMP
C<-0;i<-13
V5=V4+V5
V4=V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
rho=0
C<-1;i<-14
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
A=rhoMC^(sqrt(iCM))*AMP^(log(iPM+1))
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
iPM<-iPM+C;iCM<-iCM+0^C
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARAm={
#Weibull + GQR_ARAm-m=3
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75,198.7,220.9,230),Type=c(-1,-1,-1,-1,-1,-1,0),row.names=1:7)
mle <- mle.vam(Time & Type ~ (GQR_ARAm(1.2,0.5|3) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,1.3,0.7)
rho<-theta[4]
rhoA<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-0
C<-0
V1=0;V2=0;V3=0;V4=0
A=1
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
C<-0;i<-1
V1=A*(1-rho)*(T[1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V4=V3+V4
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-0;i<-i+1
V4=V3+V4
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-i+1
V4=V3+V4
V3=(1-rho)*V2
V2=(1-rho)*V1
V1=A*(1-rho)*(T[i]-T[i-1])
A=A*rhoA
V=V1+V2+V3+V4
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_6={
#Weibull + CM ARAm-m=3 + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
#simData<-simData[1:4,]
theta<-c(0.3,1.8,0.3,0.7)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
mle <- mle.vam(System & Time & Type ~ (ARAm(0.3|2) | Weibull(0.001,2.5)) & (QR(0.6)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rho<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
A=1
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
#rho=rhoMP
A=A*rhoMP
C<-1;i<-1
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
#rho=rhoMP
A=A*rhoMP
C<-0;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-3
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[5:8]
C<-0
A<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
#rho=0
#A=rhoMC*A
C<-1;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-3
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[9:22]
C<-1
A=1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
A=A*rhoMP
C<-0;i<-1
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
#rho=0
#A=rhoMC*A
C<-1;i<-2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-3
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
#rho=0
#A=A*rhoMC
C<-0;i<-4
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-5
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-6
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-1;i<-7
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-8
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-9
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-10
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-11
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
A=A*rhoMP
C<-0;i<-12
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
C<-1;i<-13
V3=V2+V3
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_5={
#Weibull + CM QR + PM ARAm-m=3 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
#simData<-simData[1:4,]
theta<-c(0.3,1.8,1.3,0.7)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
mle <- mle.vam(System & Time & Type ~ (QR(0.3) | Weibull(0.001,2.5)) & (ARAm(0.6|2)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
A=1
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-1;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
C<-1;i<-3
V3=0
V2=0
V1=0
A=rhoMC*A
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[5:8]
C<-0
A<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=0
A=rhoMC*A
C<-1;i<-1
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-simData$Time[9:22]
C<-1
A=1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-0;i<-1
V1=A*(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=rhoMC*A
C<-1;i<-2
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-0;i<-4
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-5
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-9
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-10
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-11
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=rhoMP
C<-0;i<-12
V5=V4+V5
V4=V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=A*(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
rho=0
A=A*rhoMC
C<-1;i<-13
V5=0
V4=0
V3=0
V2=0
V1=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_4={
#Weibull + CM ARAm-m=4 + PM ARAm-m=2 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
theta<-c(0.3,1.8,0.3,0.7)
mle <- mle.vam(System & Time & Type ~ (ARAm(0.3|4) | Weibull(0.001,2.5)) & (ARAm(0.6|2)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[5:8]
C<-0
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMC
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[9:22]
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-0;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-0;i<-4
V4=(1-rho)*V3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-5
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-9
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-10
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-11
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-12
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-13
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_3={
#Weibull + CM ARAm-m=2 + PM ARAm-m=4 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,1,-1,1,-1,1,-1,0),row.names=1:22)
theta<-c(0.3,1.8,0.3,0.7)
mle <- mle.vam(System & Time & Type ~ (ARAm(0.3|2) | Weibull(0.001,2.5)) & (ARAm(0.6|4)),data=simData)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
T<-simData$Time[1:4]
Lcalc<-0
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[5:8]
C<-0
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMC
C<-1;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
T<-simData$Time[9:22]
C<-1
V1=0;V2=0;V3=0;V4=0;V5=0
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[1]))-H(T[1])
rho=rhoMP
C<-0;i<-1
V1=(1-rho)*(T[i])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-3
V3=(1-rho)*V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-0;i<-4
V4=V3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-5
V5=V4+V5
V4=V3
V3=V2
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-6
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-1;i<-7
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-8
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-9
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-10
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-11
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMP
C<-0;i<-12
V5=V4+V5
V4=(1-rho)*V3
V3=(1-rho)*(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
rho=rhoMC
C<-1;i<-13
V5=V4+V5
V4=V3
V3=(V2)
V2=(1-rho)*(V1)
V1=(1-rho)*(T[i]-T[i-1])
V=V1+V2+V3+V4+V5
Lcalc<-Lcalc+(1-C)*log(h(T[i+1]-T[i]+V))-(H(T[i+1]-T[i]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm_2={
#Weibull + ARAm-m=4
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75,198.7,220.9),Type=c(-1,-1,-1,-1,-1,-1),row.names=1:6)
mle <- mle.vam(Time & Type ~ (ARAm(0.5|3) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
A<-rho*T[1]
Lcalc<-Lcalc+log(h(T[2]-A))-(H(T[2]-A)-H(T[1]-A))
i<-2
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-3
A<-rho*(T[i]+(1-rho)*T[i-1]+(1-rho)^2*T[i-2])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-4
A<-rho*(T[i]+(1-rho)*T[i-1]+(1-rho)^2*T[i-2])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-5
A<-rho*(T[i]+(1-rho)*T[i-1]+(1-rho)^2*T[i-2])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TARAm={
#Weibull + ARAm-m=2
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75,198.7,220.9),Type=c(-1,-1,-1,-1,-1,-1),row.names=1:6)
mle <- mle.vam(Time & Type ~ (ARAm(0.5|2) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
A<-rho*T[1]
Lcalc<-Lcalc+log(h(T[2]-A))-(H(T[2]-A)-H(T[1]-A))
i<-2
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-3
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-4
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
i<-5
A<-rho*(T[i]+(1-rho)*T[i-1])
Lcalc<-Lcalc+log(h(T[i+1]-A))-(H(T[i+1]-A)-H(T[i]-A))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_5={
#Weibull + MC ARA1 + MP GQ_RARAInf-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (GQR_ARAInf(0.7,-1.3|log)),data=simData)
theta<-c(0.3,2.2,0.7,0.4,-0.9)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(3)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i])+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_4={
#Weibull + MC AGAN + MP GQ_RARA1-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,8)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.52),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,1,0),row.names=1:24)
#simData<-simData[1:24,]
mle <- mle.vam(System & Time & Type ~ (AGAN() | Weibull(0.001,2.5)) & (GQR_ARA1(0.7,-1.3|log)),data=simData)
theta<-c(0.3,2.2,0.4,-0.9)
#L<-logLik(mle,theta,TRUE,FALSE,FALSE)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMP<-theta[3]
rhoMP2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-1; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE)
alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_3={
#Weibull + MC ARA1 + MP GQ_RARA1-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (GQR_ARA1(0.7,-1.3|log)),data=simData)
theta<-c(0.3,2.2,0.7,0.4,-0.9)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(3)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-rhoMP2)*(A*(T[i+1]-T[i]))+V; A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_2={
#Weibull + GQR_ARAInf
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR_ARAInf(0.1,0.5) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7,-1.2)
rho<-theta[3]
rho2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
V<-(1-rho2)*T[1]
Lcalc<-Lcalc+log(rho^(1)*h(rho^(1)*(T[2]-T[1])+V))-(H(rho^(1)*(T[2]-T[1])+V)-H(V))
V<-(1-rho2)*(rho^(1)*(T[2]-T[1])+V )
Lcalc<-Lcalc+log(rho^(2)*h(rho^(2)*(T[3]-T[2])+V))-(H(rho^(2)*(T[3]-T[2])+V)-H(V))
V<-(1-rho2)*(rho^(2)*(T[3]-T[2])+V)
Lcalc<-Lcalc+log(rho^(3)*h(rho^(3)*(T[4]-T[3])+V))-(H(rho^(3)*(T[4]-T[3])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQRARA_1={
#Weibull + GQR_ARA1-log
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR_ARA1(0.7,-1.2|log) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7,-1.2)
rho<-theta[3]
rho2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
V<-(1-rho2)*T[1]
Lcalc<-Lcalc+log(rho^(log(2))*h(rho^(log(2))*(T[2]-T[1])+V))-(H(rho^(log(2))*(T[2]-T[1])+V)-H(V))
V<-rho^(log(2))*(T[2]-T[1])+V -rho2 *rho^(log(2))*(T[2]-T[1])
Lcalc<-Lcalc+log(rho^(log(3))*h(rho^(log(3))*(T[3]-T[2])+V))-(H(rho^(log(3))*(T[3]-T[2])+V)-H(V))
V<-rho^(log(3))*(T[3]-T[2])+V -rho2* rho^(log(3))*(T[3]-T[2])
Lcalc<-Lcalc+log(rho^(log(4))*h(rho^(log(4))*(T[4]-T[3])+V))-(H(rho^(log(4))*(T[4]-T[3])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQR3={
#Weibull + MC ARA1 + MP GQR-log + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (GQR(0.7|log)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(3)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(2)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(3)); C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(log(4)); C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQR2={
#Weibull + GQR-sqrt
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR(0.7|sqrt) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho^(sqrt(1))*h(rho^(sqrt(1))*(T[2]-T[1])))-(H(rho^(sqrt(1))*(T[2]-T[1]))-H(rho^(sqrt(1))*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^(sqrt(2))*h(rho^(sqrt(2))*(T[3]-T[2])))-(H(rho^(sqrt(2))*(T[3]-T[2]))-H(rho^(sqrt(2))*(T[2]-T[2])))
Lcalc<-Lcalc+log(rho^(sqrt(3))*h(rho^(sqrt(3))*(T[4]-T[3])))-(H(rho^(sqrt(3))*(T[4]-T[3]))-H(rho^(sqrt(3))*(T[3]-T[3])))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TGQR1={
#Weibull + GQR-log
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (GQR(0.7|log) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho^(log(2))*h(rho^(log(2))*(T[2]-T[1])))-(H(rho^(log(2))*(T[2]-T[1]))-H(rho^(log(2))*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^(log(3))*h(rho^(log(3))*(T[3]-T[2])))-(H(rho^(log(3))*(T[3]-T[2]))-H(rho^(log(3))*(T[2]-T[2])))
Lcalc<-Lcalc+log(rho^(log(4))*h(rho^(log(4))*(T[4]-T[3])))-(H(rho^(log(4))*(T[4]-T[3]))-H(rho^(log(4))*(T[3]-T[3])))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR10={
#Weibull + CM ARAInf + PM QAGAN + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (QAGAN()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR9={
#Weibull + CM ARAInf + PM AGAP + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAP()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR8={
#Weibull + CM ARAInf + PM ABAO + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ABAO()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(A*(T[i+1]-T[i])+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(A*(T[i+1]-T[i])+V); A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-A*(T[i+1]-T[i])+V; A<-A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR7={
#Weibull + CM ARAInf + PM AGAN + PM QR + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,14)),Time=c(3.36,4.04,4.97,5.16, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43,10.2,11.5,12,13.78),Type=c(1,2,2,1, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,1,2,2,1,0),row.names=1:22)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAN()+QR(0.7)),data=simData)
theta<-c(0.3,1.8,0.3,0.7)
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-0*(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i])+V)); A<-1+0*rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR6={
#Weibull + MC ARA1 + MP QR + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARA1(0.2) | Weibull(0.001,2.5)) & (QR(0.7)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-(1-C)*((1-rhoMC)*(A*(T[i+1]-T[i]))+V); A<-rhoMP^(C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR5={
#Weibull + MC QR + MP ARA1 + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (QR(0.2) | Weibull(0.001,2.5)) & (ARA1(0.7)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*((1-rhoMP)*(A*(T[i+1]-T[i]))+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR4={
#Weibull + MC QR + MP ARAinf + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (QR(0.2) | Weibull(0.001,2.5)) & (ARAInf(0.7)),data=simData)
theta<-c(0.3,2.2,0.7,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
Lcalc<-0
T<-c(0,simData$Time[simData$System==1])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==2])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==3])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==4])
V<-0; C<-0; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
T<-c(0,simData$Time[simData$System==5])
V<-0; C<-1; A<-1; i<-1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-0; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
V<-C*(1-rhoMP)*(A*(T[i+1]-T[i])+V); A<-rhoMC^(1-C)*A; C<-1; i<-i+1
Lcalc<-Lcalc+(1-C)*log(A*h(A*(T[i+1]-T[i])+V))-(H(A*(T[i+1]-T[i])+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR3={
#Weibull + MC ARAInf + MP QR + MultiSystems + Censorship
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
#simData<-simData[1:12,]
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.2) | Weibull(0.001,2.5)) & (QR(0.7)),data=simData)
theta<-c(0.3,2.2,0.3,0.4)
#L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-H(rho*(T[2]-T[1]))
Lcalc<-Lcalc-H(rho^2*(T[3]-T[2]))
Lcalc<-Lcalc-H(rho^3*(T[4]-T[3]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(rhoMP*h(rhoMP*(T[2]-T[1])))-H(rhoMP*(T[2]-T[1]))
V<-(1-rhoMC)*rhoMP*(T[2]-T[1])
Lcalc<-Lcalc+log(rhoMP*h(rhoMP*(T[3]-T[2])+V))-(H(rhoMP*(T[3]-T[2])+V)-H(V))
V<-(1-rhoMC)*(rhoMP*(T[3]-T[2])+V)
Lcalc<-Lcalc-(H(rhoMP*(T[4]-T[3])+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
Lcalc<-Lcalc-H(rhoMP*(T[3]-T[2]))
Lcalc<-Lcalc-H(rhoMP^2*(T[4]-T[3]))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(rhoMP*h(rhoMP*(T[2]-T[1])))-H(rhoMP*(T[2]-T[1]))
V<-(1-rhoMC)*rhoMP*(T[2]-T[1])
Lcalc<-Lcalc-(H(rhoMP*(T[3]-T[2])+V)-H(V))
Lcalc<-Lcalc+log(rhoMP^2*h(rhoMP^2*(T[4]-T[3])))-H(rhoMP^2*(T[4]-T[3]))
V<-(1-rhoMC)*rhoMP^2*(T[4]-T[3])
Lcalc<-Lcalc+log(rhoMP^2*h(rhoMP^2*(T[5]-T[4])+V))-(H(rhoMP^2*(T[5]-T[4])+V)-H(V))
V<-(1-rhoMC)*(rhoMP^2*(T[5]-T[4])+V)
Lcalc<-Lcalc-(H(rhoMP^2*(T[6]-T[5])+V)-H(V))
Lcalc<-Lcalc-H(rhoMP^3*(T[7]-T[6]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR2={
#Weibull + QR + MultiSystems + Censorship
simData<-data.frame(System=c(1,1,1,1,2,2,2,3),Time=c(18.09,52.07,95.71,145.75,15.02,45.1,82,20.1),Type=c(-1,-1,-1,0,-1,-1,-1,-1),row.names=1:8)
mle <- mle.vam(System & Time & Type ~ (QR(0.7) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[1:4]
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho*h(rho*(T[2]-T[1])))-(H(rho*(T[2]-T[1]))-H(rho*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^2*h(rho^2*(T[3]-T[2])))-(H(rho^2*(T[3]-T[2]))-H(rho^2*(T[2]-T[2])))
Lcalc<-Lcalc-(H(rho^3*(T[4]-T[3]))-H(rho^3*(T[3]-T[3])))
T<-simData$Time[5:7]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho*h(rho*(T[2]-T[1])))-(H(rho*(T[2]-T[1]))-H(rho*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^2*h(rho^2*(T[3]-T[2])))-(H(rho^2*(T[3]-T[2]))-H(rho^2*(T[2]-T[2])))
T<-simData$Time[8]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
TQR={
#Weibull + QR
simData<-data.frame(Time=c(18.09,52.07,95.71,145.75),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (QR(0.7) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.03,2.4,0.7)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(rho*h(rho*(T[2]-T[1])))-(H(rho*(T[2]-T[1]))-H(rho*(T[1]-T[1])))
Lcalc<-Lcalc+log(rho^2*h(rho^2*(T[3]-T[2])))-(H(rho^2*(T[3]-T[2]))-H(rho^2*(T[2]-T[2])))
Lcalc<-Lcalc+log(rho^3*h(rho^3*(T[4]-T[3])))-(H(rho^3*(T[4]-T[3]))-H(rho^3*(T[3]-T[3])))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T01={
#Weibull + CM AGAN
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (AGAN() | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,1)
rho<-1
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T02={
#LogLinear + CM ABAO
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ABAO() | LogLinear(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,1)
rho<-0
h<-function(t) theta[1]*exp(theta[2]*t)
H<-function(t) theta[1]/theta[2]*(exp(theta[2]*t)-1)
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T03={
#Weibull3
simData<-data.frame(Time=c(3.36),Type=c(-1),row.names=1:1)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | Weibull3(0.001,2.5,5)),data=simData)
theta<-c(0.3,1.8,4,0.6)
c<-theta[3]
rho<-theta[4]
h<-function(t) theta[1]*theta[2]*(t+c)^(theta[2]-1)
H<-function(t) theta[1]*((t+c)^(theta[2])-c^(theta[2]))
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T1={
#Weibull
simData<-data.frame(Time=c(3.36),Type=c(-1),row.names=1:1)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T2={
#LogLinear
simData<-data.frame(Time=c(3.36),Type=c(-1),row.names=1:1)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | LogLinear(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*exp(theta[2]*t)
H<-function(t) theta[1]/theta[2]*(exp(theta[2]*t)-1)
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T3={
#Weibull + CM ARAInf
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T4={
#Weibull + CM ARA1
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]))-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T5={
#LogLinear + CM ARAInf
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,-1),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARAInf(0.4) | LogLinear(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*exp(theta[2]*t)
H<-function(t) theta[1]/theta[2]*(exp(theta[2]*t)-1)
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc+log(h(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T6={
#Weibull + CM ARA1 + Censorship
simData<-data.frame(Time=c(3.36,4.04,4.97,5.16),Type=c(-1,-1,-1,0),row.names=1:4)
mle <- mle.vam(Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,0.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T7={
#Weibull + multiSystems
simData<-data.frame(System=c(1,2),Time=c(3.36,2.34),Type=c(-1,-1),row.names=1:2)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<-log(h(T[1]))-H(T[1])
T<-simData$Time[simData$System==2]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T8={
#Weibull + CM ARAInf + Censorship + multiSystems
simData<-data.frame(System=c(1,1,1,1,2,2,2,3),Time=c(3.36,4.04,4.97,5.16,2.34,3.46,5.02,4),Type=c(-1,-1,-1,0,-1,-1,-1,0),row.names=1:8)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rho<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<-log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T9={
#Weibull + CM ARAInf + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T91={
#Weibull + CM ARAInf + PM AGAN + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAN()),data=simData)
theta<-c(0.3,1.8,0.3)
rhoMC<-theta[3]
rhoMP<-1
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T92={
#Weibull + CM ARAInf + PM ABAO + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ABAO()),data=simData)
theta<-c(0.3,1.8,0.3)
rhoMC<-theta[3]
rhoMP<-0
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T93={
#Weibull + CM AGAN + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (AGAN() | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rhoMC<-1
rhoMP<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T94={
#Weibull + CM ABAO + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ABAO() | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.6)
rhoMC<-0
rhoMP<-theta[3]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T10={
#LogLinear + CM ARA1 + PM AR1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)) & (ARA1(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-V+(1-rhoMC)*(T[3]-T[2])
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3])+V
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4])+V
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T11={
#Weibull + CM ARA1 + PM ARAInf + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
#n<-11
#Data<-data.frame(System=simData$System[1:n],Time=simData$Time[1:n],Type=simData$Type[1:n])
#mle2 <- mle.vam(System & Time & Type ~ (ARA1(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)),data=Data)
#L2<-logLik(mle2,theta,c(TRUE,FALSE,FALSE))
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]))-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-rhoMC*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-T[1])+T[1]-rhoMP*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3])+V
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4])+V
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5]+V)
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T12={
#Weibull + CM ARAInf + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,7)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98),Type=c(1,1,1,1, -1,-1,-1,0, 1,-1,-1,1, -1,1,1,0, 1,-1,1,-1,-1,1,0),row.names=1:23)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ARA1(0.5)),data=simData)
theta<-c(0.3,1.8,0.3,0.8)
rhoMC<-theta[3]
rhoMP<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
rho<-rhoMP
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc-(H(T[3]-rho*T[2])-H(T[2]-rho*T[2]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3])-H(T[3]-rho*T[3]))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP*T[1]))-(H(T[2]-rhoMP*T[1])-H(T[1]-rhoMP*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP)*(T[3]-T[2])+V
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T13={
#Weibull + CM ARAInf + PM ARAInf + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,10)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43),Type=c(1,2,2,1, -1,-1,-1,0, 1,-1,-1,2, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (ARAInf(0.5)+ARA1(-1)),data=simData)
theta<-c(0.3,1.8,0.3,0.8,-1)
rhoMC<-theta[3]
rhoMP1<-theta[4]
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMP1*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP1)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP2)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
V<-(1-rhoMP1)*(T[7]-T[6]+V)
Lcalc<-Lcalc-(H(T[8]-T[7]+V)-H(V))
V<-(1-rhoMP2)*(T[8]-T[7])+V
Lcalc<-Lcalc+log(h(T[9]-T[8]+V))-(H(T[9]-T[8]+V)-H(V))
V<-(1-rhoMC)*(T[9]-T[8]+V)
Lcalc<-Lcalc-(H(T[10]-T[9]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T14={
#Weibull + CM ARAInf + PM AGAN + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,10)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43),Type=c(1,2,2,1, -1,-1,-1,0, 1,-1,-1,2, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull(0.001,2.5)) & (AGAN()+ARA1(-1)),data=simData)
theta<-c(0.3,1.8,0.3,-1)
rhoMC<-theta[3]
rhoMP1<-1
rhoMP2<-theta[4]
h<-function(t) theta[1]*theta[2]*t^(theta[2]-1)
H<-function(t) theta[1]*t^(theta[2])
T<-simData$Time[simData$System==1]
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMP1*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP1)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP2)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
V<-(1-rhoMP1)*(T[7]-T[6]+V)
Lcalc<-Lcalc-(H(T[8]-T[7]+V)-H(V))
V<-(1-rhoMP2)*(T[8]-T[7])+V
Lcalc<-Lcalc+log(h(T[9]-T[8]+V))-(H(T[9]-T[8]+V)-H(V))
V<-(1-rhoMC)*(T[9]-T[8]+V)
Lcalc<-Lcalc-(H(T[10]-T[9]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
T15={
#Weibull3 + CM ARAInf + PM AGAN + PM ARA1 + mutlisystems
simData<-data.frame(System=c(rep(1,4),rep(2,4),rep(3,4),rep(4,4),rep(5,10)),Time=c(3.36,4.04,4.97,5.16, 2.34,3.46,5.02,5.45, 1.18,2.22,3.14,4.83, 0.78,2.36,4.05,4.97, 2.45,2.78,3.56,4.23,5.32,6.43,6.98,7.51,8.02,9.43),Type=c(1,2,2,1, -1,-1,-1,0, 1,-1,-1,2, -1,2,2,0, 1,-1,1,-1,-1,2,1,2,-1,0),row.names=1:26)
mle <- mle.vam(System & Time & Type ~ (ARAInf(0.4) | Weibull3(0.001,2.5,3)) & (AGAN()+ARA1(-1)),data=simData)
theta<-c(0.3,1.8,4,0.3,-1)
c<-theta[3]
rhoMC<-theta[4]
rhoMP1<-1
rhoMP2<-theta[5]
h<-function(t) theta[1]*theta[2]*(t+c)^(theta[2]-1)
H<-function(t) theta[1]*((t+c)^(theta[2])-(c)^(theta[2]))
T<-simData$Time[simData$System==1]
Lcalc<--H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMP1*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==2]
rho<-rhoMC
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rho*T[1]))-(H(T[2]-rho*T[1])-H(T[1]-rho*T[1]))
Lcalc<-Lcalc+log(h(T[3]-rho*T[2]-rho*(1-rho)*T[1]))-(H(T[3]-rho*T[2]-rho*(1-rho)*T[1])-H(T[2]-rho*T[2]-rho*(1-rho)*T[1]))
Lcalc<-Lcalc-(H(T[4]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1])-H(T[3]-rho*T[3]-rho*(1-rho)*T[2]-rho*(1-rho)^2*T[1]))
T<-simData$Time[simData$System==3]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc+log(h(T[3]-T[2]+V))-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMC)*(T[3]-T[2]+V)
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==4]
Lcalc<-Lcalc+log(h(T[1]))-H(T[1])
Lcalc<-Lcalc-(H(T[2]-rhoMC*T[1])-H(T[1]-rhoMC*T[1]))
V<-(1-rhoMP2)*(T[2]-T[1])+T[1]-rhoMC*T[1]
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP2)*(T[3]-T[2])+V
Lcalc<-Lcalc-(H(T[4]-T[3]+V)-H(V))
T<-simData$Time[simData$System==5]
Lcalc<-Lcalc-H(T[1])
Lcalc<-Lcalc+log(h(T[2]-rhoMP1*T[1]))-(H(T[2]-rhoMP1*T[1])-H(T[1]-rhoMP1*T[1]))
V<-(1-rhoMC)*(T[2]-rhoMP1*T[1])
Lcalc<-Lcalc-(H(T[3]-T[2]+V)-H(V))
V<-(1-rhoMP1)*(T[3]-T[2]+V)
Lcalc<-Lcalc+log(h(T[4]-T[3]+V))-(H(T[4]-T[3]+V)-H(V))
V<-(1-rhoMC)*(T[4]-T[3]+V)
Lcalc<-Lcalc+log(h(T[5]-T[4]+V))-(H(T[5]-T[4]+V)-H(V))
V<-(1-rhoMC)*(T[5]-T[4]+V)
Lcalc<-Lcalc-(H(T[6]-T[5]+V)-H(V))
V<-(1-rhoMP2)*(T[6]-T[5])+V
Lcalc<-Lcalc-(H(T[7]-T[6]+V)-H(V))
V<-(1-rhoMP1)*(T[7]-T[6]+V)
Lcalc<-Lcalc-(H(T[8]-T[7]+V)-H(V))
V<-(1-rhoMP2)*(T[8]-T[7])+V
Lcalc<-Lcalc+log(h(T[9]-T[8]+V))-(H(T[9]-T[8]+V)-H(V))
V<-(1-rhoMC)*(T[9]-T[8]+V)
Lcalc<-Lcalc-(H(T[10]-T[9]+V)-H(V))
fix<-rep(TRUE,length(theta))
fix[1]=FALSE
run(mle,fixed=fix,verbose=FALSE);alpha_Est<-coef(mle)[1]
Ccalc<-contrast(mle,c(alpha_Est,theta[2:length(theta)]))
},
)
L<-logLik(mle,theta,c(TRUE,FALSE,FALSE))
dL<-logLik(mle,theta,c(FALSE,TRUE,FALSE))
d2L<-logLik(mle,theta,c(FALSE,FALSE,TRUE))
C<-contrast(mle,theta,c(TRUE,FALSE,FALSE))
dC<-contrast(mle,theta,c(FALSE,TRUE,FALSE))
d2C<-contrast(mle,theta,c(FALSE,FALSE,TRUE))
epsilon<-0.000001
EstdL<-dL
EstdC<-dC
for(i in (1:length(dL))){
theta1<-theta
theta1[i]<-theta1[i]+epsilon
EstdL[i]<-(logLik(mle,theta1,c(TRUE,FALSE,FALSE))-logLik(mle,theta,c(TRUE,FALSE,FALSE)))/epsilon
}
for(i in (1:length(dC))){
theta1<-theta
theta1[i+1]<-theta1[i+1]+epsilon
EstdC[i]<-(contrast(mle,theta1,c(TRUE,FALSE,FALSE))-contrast(mle,theta,c(TRUE,FALSE,FALSE)))/epsilon
}
Estd2L<-d2L
Estd2C<-d2C
for(i in (1:(dim(d2L)[1]))){
theta1<-theta
theta1[i]<-theta1[i]+epsilon
Estd2L[i,]<-(logLik(mle,theta1,c(FALSE,TRUE,FALSE))-logLik(mle,theta,c(FALSE,TRUE,FALSE)))/epsilon
}
if(!(is.null(dim(d2C)))){
for(i in (1:(dim(d2C)[1]))){
theta1<-theta
theta1[i+1]<-theta1[i+1]+epsilon
Estd2C[i,]<-(contrast(mle,theta1,c(FALSE,TRUE,FALSE))-contrast(mle,theta,c(FALSE,TRUE,FALSE)))/epsilon
}
} else {
theta1<-theta
theta1[2]<-theta1[2]+epsilon
Estd2C<-(contrast(mle,theta1,c(FALSE,TRUE,FALSE))-contrast(mle,theta,c(FALSE,TRUE,FALSE)))/epsilon
}
print(L)
print(Lcalc)
print(C)
print(Ccalc)
print(dL)
print(EstdL)
print(dC)
print(EstdC)
print(d2L)
print(Estd2L)
print(d2C)
print(Estd2C)
print((L-Lcalc)/L)
print((C-Ccalc)/C)
print((dL-EstdL)/dL)
print((dC-EstdC)/dC)
print((d2L-Estd2L)/d2L)
print((d2C-Estd2C)/d2C)
ecrit<-function(aprinter,nl,nc){
res<-""
if((nl>0)&&(nc>0)){
for(i in 1:nc){
for(j in 1:nl){
res<-paste(res,aprinter[j,i],sep=',')
}
}}
else if((nl>0)||(nc>0)){
for(j in 1:max(nl,nc)){
res<-paste(res,aprinter[j],sep=',')
}
}
else res<-paste(res,aprinter,sep=',')
print(res)
}
ecrit(L,0,0)
ecrit(dL,0,length(dL))
ecrit(d2L,dim(d2L)[1],dim(d2L)[2])
ecrit(C,0,0)
ecrit(dC,0,length(dC))
if(!(is.null(dim(d2C)))){
ecrit(d2C,dim(d2C)[1],dim(d2C)[2])
} else {
ecrit(d2C,0,0)
}
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