[R] error in survival analysis

[Rasika Gawde]

DODamen represents the dissolved oxygen values and is a valid predictor.  I'm not sure how the with(test1, table(Depart, DODamen)) helps. It does show that the DODamen column is populated and in use since it lists out a table of relation between the Depart and DODamen columns.

Thanks for the help so far guys. I guess it shows that I am completely out of my depth here.

Rasika
 

-----Original Message-----
From: David Winsemius [mailto:dwinsemius at comcast.net] 
Sent: Tuesday, July 26, 2011 9:01 AM
To: Rasika Gawde
Cc: r-help at r-project.org R; Terry Therneau
Subject: Re: [R] error in survival analysis


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