Dear R-helpers,
To get curves for a pseudo cohort other than the one centered at the mean of
the covariates, I have been trying to use the newdata argument to survfit
with no success. Here is my model statement, the newdata and the ensuing
error. What am I doing wrong?

> summary(fit)
Call:
coxph(formula = Surv(Start, Stop, Event, type = "counting") ~ 
    Week + LagAOO + Prior.f + cluster(interaction(Station, Year)), 
    data = data8, method = "breslow", x = T, y = T)

  n= 1878 
            coef exp(coef) se(coef) robust se     z       p
Week     0.00582      1.01   0.0323    0.0239 0.244 8.1e-01
LagAOO   0.71929      2.05   0.1238    0.1215 5.918 3.3e-09
Prior.f2 0.12927      1.14   0.4402    0.4025 0.321 7.5e-01
Prior.f3 0.79082      2.21   0.5484    0.4460 1.773 7.6e-02
Prior.f4 2.04189      7.71   0.6008    0.4685 4.358 1.3e-05
Prior.f5 1.20450      3.34   0.6423    0.5481 2.198 2.8e-02

         exp(coef) exp(-coef) lower .95 upper .95
Week          1.01      0.994     0.960      1.05
LagAOO        2.05      0.487     1.618      2.61
Prior.f2      1.14      0.879     0.517      2.50
Prior.f3      2.21      0.453     0.920      5.29
Prior.f4      7.71      0.130     3.076     19.30
Prior.f5      3.34      0.300     1.139      9.76

Rsquare= 0.047   (max possible= 0.25 )
Likelihood ratio test= 91  on 6 df,   p=0
Wald test            = 209  on 6 df,   p=0
Score (logrank) test = 142  on 6 df,   p=0,   Robust = 17.4  p=0.00803

  (Note: the likelihood ratio and score tests assume independence of
     observations within a cluster, the Wald and robust score tests do not).
>
newdat
      Week   LagAOO Prior.f2 Prior.f3 Prior.f4 Prior.f5
1 17.55218 1.191693        1        0        0        0
2 17.55218 1.191693        0        0        0        0

> survfit(fit,newdata=newdat)
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  : 
        variable lengths differ
In addition: Warning message: 
'newdata' had 2 rows but variable(s) found have 1878 rows 

Regards,
Alex


Alex Hanke
Department of Fisheries and Oceans
St. Andrews Biological Station
531 Brandy Cove Road
St. Andrews, NB
Canada
E5B 2L9



	[[alternative HTML version deleted]]


