Hi there, I encountered a weird problem using cph()
with Design package in S-Plus:
I have 2 datasets, say "dat1" and "dat2", both data
frames with 3 columns "time","status" and "scores",
all numeric
If I run the following:
dd<-datadist(dat1)
options(datadist='dd')
dd
time status scores
Low:effect 37.0 0 -6.018
Adjust to 88.0 0 11.252
High:effect 109.0 1 33.267
Low:prediction 11.0 0 -34.419
High:prediction 147.5 1 88.218
Low 5.0 0 -72.072
High 171.0 1 154.678
fit <- cph(Surv(time,status) ~ scores,
data=dat1,surv=T, x=T, y=T)
fit
Cox Proportional Hazards Model
cph(formula = Surv(time, status) ~ scores, data = xx,
x = T, y = T, surv = T)
Obs Events Model L.R. d.f. P Score Score P R2
171 64 10.65 1 0.0011 12.01 0.0005 0.062
so everything is ok.
However, if I run the following with the second
dataset:
dd<-datadist(dat2)
options(datadist='dd')
dd
time status scores
Low:effect 68.10 0 -16.036
Adjust to 91.75 0 9.068
High:effect 119.03 1 42.447
Low:prediction 21.75 0 -48.103
High:prediction 120.00 1 96.661
Low 6.90 0 -75.392
High 120.00 1 141.524
fit <- cph(Surv(time,status) ~ scores,
data=dat2,surv=T, x=T, y=T)
fit
Problem: Object "fit" not found, while calling
subroutine S_agsurv2
Use traceback() to see the call stack
traceback()
4: eval(action, sys.parent())
3: doErrorAction("Problem: Object \"fit\" not found,
while calling subroutine S_agsurv2", 1000)
2: eval(expression(fit))
1:
Message: Problem: Object "fit" not found, while
calling subroutine S_agsurv2
so it didn't work with the second dataset. The 2
dataset is very similar in terms of column data type.
With the second dataset, I also tried subsets: cph()
worked until the first 106 rows and started to stop
working when the 107th row was added:
xx<-dat2[1:106,]
dd<-datadist(xx)
options(datadist='dd')
fit <- cph(Surv(time,status) ~ scores,
data=xx,surv=T, x=T, y=T)
fit
Cox Proportional Hazards Model
cph(formula = Surv(time, status) ~ scores, data = xx,
x = T, y = T, surv = T)
Obs Events Model L.R. d.f. P Score Score P R2
106 22 15.31 1 0.0001 17.92 0 0.159
coef se(coef) z p
scores 0.017 0.00418 4.07 0.000047
xx<-dat2[1:107,]
dd<-datadist(xx)
options(datadist='dd')
fit <- cph(Surv(time,status) ~ scores,
data=xx,surv=T, x=T, y=T)
fit
Problem: Object "fit" not found, while calling
subroutine S_agsurv2
Use traceback() to see the call stack
The data between 105th and 107th rows are:
time status scores
105 104.4 0 32.48
106 109.1 0 -38.76
107 99.9 0 74.96
any suggestions?
Many thanks
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