-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathModelInImputedDatasets.R
231 lines (216 loc) · 12.7 KB
/
ModelInImputedDatasets.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
###############################################################################################################
##################### Run the Bayesian model to each one of the imputed datasets #####################
##############################################################################################################
#give the data for imputed dataset 1
jagsdataSMSC1 <- list(
Nobservations=nrow(imp.list[[1]]),
outcome=as.numeric(factor(imp.list[[1]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[1]]$patient.id)),
subj=as.integer(factor(imp.list[[1]]$patient.id)),
age=imp.list[[1]]$age-mean(imp.list[[1]]$age),
disease.duration=imp.list[[1]]$disease.duration-mean(imp.list[[1]]$disease.duration),
edss=imp.list[[1]]$edss-mean(imp.list[[1]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[1]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[1]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[1]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[1]]$months.since.last.relapse-mean(imp.list[[1]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[1]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[1]]$gender),
treatment.during.cycle=as.factor(imp.list[[1]]$treatment.during.cycle)
)
#give the data for imputed dataset 1
jagsdataSMSC2<- list(
Nobservations=nrow(imp.list[[2]]),
outcome=as.numeric(factor(imp.list[[2]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[2]]$patient.id)),
subj=as.integer(factor(imp.list[[2]]$patient.id)),
age=imp.list[[2]]$age-mean(imp.list[[2]]$age),
disease.duration=imp.list[[2]]$disease.duration-mean(imp.list[[2]]$disease.duration),
edss=imp.list[[2]]$edss-mean(imp.list[[2]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[2]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[2]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[2]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[2]]$months.since.last.relapse-mean(imp.list[[2]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[2]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[2]]$gender),
treatment.during.cycle=as.factor(imp.list[[2]]$treatment.during.cycle)
)
#give the data for imputed dataset 3
jagsdataSMSC3<- list(
Nobservations=nrow(imp.list[[3]]),
outcome=as.numeric(factor(imp.list[[3]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[3]]$patient.id)),
subj=as.integer(factor(imp.list[[3]]$patient.id)),
age=imp.list[[3]]$age-mean(imp.list[[3]]$age),
disease.duration=imp.list[[3]]$disease.duration-mean(imp.list[[3]]$disease.duration),
edss=imp.list[[3]]$edss-mean(imp.list[[3]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[3]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[3]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[3]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[3]]$months.since.last.relapse-mean(imp.list[[3]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[3]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[3]]$gender),
treatment.during.cycle=as.factor(imp.list[[3]]$treatment.during.cycle)
)
#give the data for imputed dataset 4
jagsdataSMSC4<- list(
Nobservations=nrow(imp.list[[4]]),
outcome=as.numeric(factor(imp.list[[4]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[4]]$patient.id)),
subj=as.integer(factor(imp.list[[4]]$patient.id)),
age=imp.list[[4]]$age-mean(imp.list[[4]]$age),
disease.duration=imp.list[[4]]$disease.duration-mean(imp.list[[4]]$disease.duration),
edss=imp.list[[4]]$edss-mean(imp.list[[4]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[4]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[4]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[4]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[4]]$months.since.last.relapse-mean(imp.list[[4]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[4]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[4]]$gender),
treatment.during.cycle=as.factor(imp.list[[4]]$treatment.during.cycle)
)
#give the data for imputed dataset 5
jagsdataSMSC5<- list(
Nobservations=nrow(imp.list[[5]]),
outcome=as.numeric(factor(imp.list[[5]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[5]]$patient.id)),
subj=as.integer(factor(imp.list[[5]]$patient.id)),
age=imp.list[[5]]$age-mean(imp.list[[5]]$age),
disease.duration=imp.list[[5]]$disease.duration-mean(imp.list[[5]]$disease.duration),
edss=imp.list[[5]]$edss-mean(imp.list[[5]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[5]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[5]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[5]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[5]]$months.since.last.relapse-mean(imp.list[[5]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[5]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[5]]$gender),
treatment.during.cycle=as.factor(imp.list[[5]]$treatment.during.cycle)
)
#give the data for imputed dataset 6
jagsdataSMSC6<- list(
Nobservations=nrow(imp.list[[6]]),
outcome=as.numeric(factor(imp.list[[6]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[6]]$patient.id)),
subj=as.integer(factor(imp.list[[6]]$patient.id)),
age=imp.list[[6]]$age-mean(imp.list[[6]]$age),
disease.duration=imp.list[[6]]$disease.duration-mean(imp.list[[6]]$disease.duration),
edss=imp.list[[6]]$edss-mean(imp.list[[6]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[6]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[6]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[6]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[6]]$months.since.last.relapse-mean(imp.list[[6]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[6]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[6]]$gender),
treatment.during.cycle=as.factor(imp.list[[6]]$treatment.during.cycle)
)
#give the data for imputed dataset 7
jagsdataSMSC7<- list(
Nobservations=nrow(imp.list[[7]]),
outcome=as.numeric(factor(imp.list[[7]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[7]]$patient.id)),
subj=as.integer(factor(imp.list[[7]]$patient.id)),
age=imp.list[[7]]$age-mean(imp.list[[7]]$age),
disease.duration=imp.list[[7]]$disease.duration-mean(imp.list[[7]]$disease.duration),
edss=imp.list[[7]]$edss-mean(imp.list[[7]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[7]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[7]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[7]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[7]]$months.since.last.relapse-mean(imp.list[[7]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[7]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[7]]$gender),
treatment.during.cycle=as.factor(imp.list[[7]]$treatment.during.cycle)
)
#give the data for imputed dataset 8
jagsdataSMSC8<- list(
Nobservations=nrow(imp.list[[8]]),
outcome=as.numeric(factor(imp.list[[8]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[8]]$patient.id)),
subj=as.integer(factor(imp.list[[8]]$patient.id)),
age=imp.list[[8]]$age-mean(imp.list[[8]]$age),
disease.duration=imp.list[[8]]$disease.duration-mean(imp.list[[8]]$disease.duration),
edss=imp.list[[8]]$edss-mean(imp.list[[8]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[8]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[8]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[8]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[8]]$months.since.last.relapse-mean(imp.list[[8]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[8]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[8]]$gender),
treatment.during.cycle=as.factor(imp.list[[8]]$treatment.during.cycle)
)
#give the data for imputed dataset 9
jagsdataSMSC9<- list(
Nobservations=nrow(imp.list[[9]]),
outcome=as.numeric(factor(imp.list[[9]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[9]]$patient.id)),
subj=as.integer(factor(imp.list[[9]]$patient.id)),
age=imp.list[[9]]$age-mean(imp.list[[9]]$age),
disease.duration=imp.list[[9]]$disease.duration-mean(imp.list[[9]]$disease.duration),
edss=imp.list[[9]]$edss-mean(imp.list[[9]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[9]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[9]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[9]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[9]]$months.since.last.relapse-mean(imp.list[[9]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[9]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[9]]$gender),
treatment.during.cycle=as.factor(imp.list[[9]]$treatment.during.cycle)
)
#give the data for imputed dataset 10
jagsdataSMSC10<- list(
Nobservations=nrow(imp.list[[10]]),
outcome=as.numeric(factor(imp.list[[10]]$outcome))-1,
npf=10,
npid=length(unique(imp.list[[10]]$patient.id)),
subj=as.integer(factor(imp.list[[10]]$patient.id)),
age=imp.list[[10]]$age-mean(imp.list[[10]]$age),
disease.duration=imp.list[[10]]$disease.duration-mean(imp.list[[10]]$disease.duration),
edss=imp.list[[10]]$edss-mean(imp.list[[10]]$edss),
nr.Gd.enhanced.lesions=as.factor(imp.list[[10]]$nr.Gd.enhanced.lesions),
nr.relapses.2y.prior.study1=as.factor(imp.list[[10]]$nr.relapses.2y.prior.study1),
nr.relapses.2y.prior.study2=as.factor(imp.list[[10]]$nr.relapses.2y.prior.study2),
months.since.last.relapse=imp.list[[10]]$months.since.last.relapse-mean(imp.list[[10]]$months.since.last.relapse),
treatment.naive.prior.visit=as.factor(imp.list[[10]]$treatment.naive.prior.visit),
gender=as.factor(imp.list[[10]]$gender),
treatment.during.cycle=as.factor(imp.list[[10]]$treatment.during.cycle)
)
jags.inits <- function(){
list("b"=c(0,0,0,0,0,0,0,0,0,0,0),"sigma"=0.02,"rho"=0.4)
}
set.seed(2000)
SMSCjagsResults1 <- jags.parallel(data = jagsdataSMSC1 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults2 <- jags.parallel(data = jagsdataSMSC2 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults3 <- jags.parallel(data = jagsdataSMSC3 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults4 <- jags.parallel(data = jagsdataSMSC4 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults5 <- jags.parallel(data = jagsdataSMSC5 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults6 <- jags.parallel(data = jagsdataSMSC6 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults7 <- jags.parallel(data = jagsdataSMSC7 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults8 <- jags.parallel(data = jagsdataSMSC8 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults9 <- jags.parallel(data = jagsdataSMSC9 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)
set.seed(2000)
SMSCjagsResults10 <- jags.parallel(data = jagsdataSMSC10 ,inits=jags.inits,parameters.to.save = c('b','sigma', 'rho' ),model.file = jagsmodelSMSC,
n.chains=2,n.iter = 50000,n.burnin = 10000,n.thin = 10)