[R] using survreg() in survival package with "long" data

[Göran Broström]

Dear John,

I think you are missing that 'survreg' does not handle left truncated
data. With that you should use the 'eha' package, for a PH model the
function 'phreg', and for an AFT model the function 'aftreg' (you didn't
tell which model you want to fit).

Your attempt with the 'survreg' function implies that you are satisfied 
with a Weibull baseline distribution, in which case you could choose 
either model.

Göran


On 08/29/2015 07:06 PM, Fox, John wrote:
> Dear list members,
>
> I'm unable to fit a parametric survival regression using survreg() in
> the survival package with data in "counting-process" ("long") form.
>
> To illustrate using a scaled-down problem with 10 subjects (with data
> placed on the web):
>
> --------------- snip ------------
>> library(survival) RW <-
>> read.table("http://socserv.mcmaster.ca/jfox/.Pickup/RW.txt") RL <-
>> read.table("http://socserv.mcmaster.ca/jfox/.Pickup/RL.txt")
>
>> RW # "wide" data
> week arrest age 1    20      1  27 2    17      1  18 3    25      1
> 19 4    52      0  23 5    52      0  19 6    52      0  24 7    23
> 1  25 8    52      0  21 9    52      0  22 10   52      0  20
>
>> head(RL, 20) # "long" data, counting-process form
> start stop arrest.time age 1.1      0    1           0  27 1.2      1
> 2           0  27 1.3      2    3           0  27 1.4      3    4
> 0  27 1.5      4    5           0  27 1.6      5    6           0
> 27 1.7      6    7           0  27 1.8      7    8           0  27
> 1.9      8    9           0  27 1.10     9   10           0  27 1.11
> 10   11           0  27 1.12    11   12           0  27 1.13    12
> 13           0  27 1.14    13   14           0  27 1.15    14   15
> 0  27 1.16    15   16           0  27 1.17    16   17           0
> 27 1.18    17   18           0  27 1.19    18   19           0  27
> 1.20    19   20           1  27
>
> --------------- snip ------------
>
> I have no trouble fitting a Cox model to both the wide and long forms
> of the data, obtaining (as should be the case) identical results:
>
> --------------- snip ------------
>
>> coxph(Surv(week, arrest) ~ age, data=RW)  # works
> Call: coxph(formula = Surv(week, arrest) ~ age, data = RW)
>
>
> coef exp(coef) se(coef)    z    p age 0.0963    1.1011   0.2073 0.46
> 0.64
>
> Likelihood ratio test=0.21  on 1 df, p=0.643 n= 10, number of events=
> 4
>> coxph(Surv(start, stop, arrest.time) ~ age,  data=RL) # works,
>> same
> Call: coxph(formula = Surv(start, stop, arrest.time) ~ age, data =
> RL)
>
>
> coef exp(coef) se(coef)    z    p age 0.0963    1.1011   0.2073 0.46
> 0.64
>
> Likelihood ratio test=0.21  on 1 df, p=0.643 n= 397, number of
> events= 4
>
> --------------- snip ------------
>
> But when I try to fit a parametric survival regression with
> survreg(), I get an error with the long form of the data:
>
> --------------- snip ------------
>
>> survreg(Surv(week, arrest) ~ age, data=RW) # works
> Call: survreg(formula = Surv(week, arrest) ~ age, data = RW)
>
> Coefficients: (Intercept)         age 6.35386771 -0.08982624
>
> Scale= 0.7363196
>
> Loglik(model)= -22.1   Loglik(intercept only)= -22.2 Chisq= 0.3 on 1
> degrees of freedom, p= 0.58 n= 10
>
>> survreg(Surv(start, stop, arrest.time) ~ age,  data=RL) # fails
> Error in survreg(Surv(start, stop, arrest.time) ~ age, data = RL) :
> Invalid survival type
>
> --------------- snip ------------
>
> I expect that there's something about survreg() that I'm missing. I
> first noted this problem quite some time ago but didn't look into it
> carefully because I didn't really need to use survreg().
>
> Any help would be appreciated.
>
> Thanks, John ----------------------------- John Fox, Professor
> McMaster University Hamilton, Ontario Canada L8S 4M4 Web:
> socserv.mcmaster.ca/jfox
>
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