[R] error in survival analysis
David Winsemius
dwinsemius at comcast.net
Tue Jul 26 15:01:11 CEST 2011
On Jul 26, 2011, at 8:43 AM, Terry Therneau wrote:
> There is something very odd about your data to give se values that are
> so very large. Usually, this means that the data is deterministic:
> some
> combination of predictors is able to separate a subset with no events
> from all the others. This leads to a problem where the log-likelihood
> is maximum at infinity.
> I expect that both the warning messages you see are completely
> correct.
>
> Terry Therneau
You might also consider investigating with a tablular examination of
your data:
The variable "DODamen" looks suspiciously like a date-of-death
variable, unless it is a Department of Defense variable, and as such
would not be expected to be on the RHS of a survival formula. If that
guess is wrong on my part, and DODamen is a legitimate predictor, then
since it is NA'ed, you should look at:
with(test1, table(Depart, DODamen) )
And then also look at:
with(test1, table(Depart, DOLoomis, DOI55) )
--
David.
>
> ---- begin included message ---
> This is a simple R program that I have been trying to run. I keep
> running into the "singular matrix" error. I end up with no sensible
> results. Can anyone suggest any changes or a way around this?
>
> I am a total rookie when working with R.
>
> Thanks,
> Rasika
>
>> library(survival)
> Loading required package: splines
>> args(coxph)
> function (formula, data, weights, subset, na.action, init, control,
> method = c("efron", "breslow", "exact"), singular.ok = TRUE,
> robust = FALSE, model = FALSE, x = FALSE, y = TRUE, tt, ...)
> NULL
>>
> test1<-read.table("S:/FISHDO/03_Phase_I_Field_Work/Data_6_28_2011/
> Working Folder/R_files/4SondesJuly24.csv", header=T, sep=",")
>> sondes<-coxph(Surv(Start, Stop, Depart)~DOLoomis + DOI55 + DODamen,
> data=test1)
> Warning messages:
> 1: In fitter(X, Y, strats, offset, init, control, weights =
> weights, :
> Loglik converged before variable 1,2 ; beta may be infinite.
> 2: In coxph(Surv(Start, Stop, + DODamen, :
> X matrix deemed to be singular; variable 3
>> summary(sondes)
> Call:
> coxph(formula = Surv(Start, Stop, Depart) ~ DOLoomis + DOI55 +
> DODamen, data = test1)
>
> n= 1737, number of events= 58
> (1 observation deleted due to missingness)
>
> coef exp(coef) se(coef) z Pr(>|z|)
> DOLoomis -2.152e+00 1.163e-01 1.161e+05 0 1
> DOI55 4.560e-01 1.578e+00 3.755e+04 0 1
> DODamen NA NA 0.000e+00 NA NA
>
> exp(coef) exp(-coef) lower .95 upper .95
> DOLoomis 0.1163 8.5995 0 Inf
> DOI55 1.5777 0.6338 0 Inf
> DODamen NA NA NA NA
>
> Concordance= 0.5 (se = 0 )
> Rsquare= 0 (max possible= 0.01 )
> Likelihood ratio test= 0 on 2 df, p=1
> Wald test = 0 on 2 df, p=1
> Score (logrank) test = 0 on 2 df, p=1
>
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David Winsemius, MD
West Hartford, CT
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