[R] Coxph and ordered factors
Florent Baty
florent.baty at unibas.ch
Tue Feb 27 12:10:09 CET 2007
Dear Terry,
Thanks for your answer. I realised that depending on whether or not I am
using an ordered factor I have some substantial changes in the output of
function coxph:
Here is the output I obtain when using variable 'stage2' as an ordered
factor:
Call:
coxph(formula = Surv(survTime, status) ~ stage2, data = survData)
coef exp(coef) se(coef) z p
stage2.L 2.3430 10.413 0.709 3.3033 0.00096
stage2.Q -0.0498 0.951 0.629 -0.0792 0.94000
stage2.C -0.0468 0.954 0.541 -0.0866 0.93000
Likelihood ratio test=30.2 on 3 df, p=1.25e-06 n= 61
Here is the output when using 'stage2' without ordering:
Call:
coxph(formula = Surv(survTime, status) ~ stage2, data = survData)
coef exp(coef) se(coef) z p
stage22 1.06 2.87 1.16 0.914 0.3600
stage23 2.17 8.73 1.10 1.975 0.0480
stage24 3.12 22.70 1.03 3.037 0.0024
Likelihood ratio test=30.2 on 3 df, p=1.25e-06 n= 61
Finally here is the output when coding 'stage2' as a numerical variable:
Call:
coxph(formula = Surv(survTime, status) ~ stage2, data = survData)
coef exp(coef) se(coef) z p
stage2 1.03 2.79 0.226 4.53 5.8e-06
Likelihood ratio test=30.2 on 1 df, p=3.94e-08 n= 61
It seems that when using ordered factors a model with linear, quadratic
and cubic terms is fitted. Is that something expected? Can't we
specifically focus on a simpler model including only linear terms? I am
not sure to have a full understanding of what is actually done when
factors are ordered.
Best wishes,
Florent
--
--------------------------------------------------
Dr Florent BATY
Pulmonary Gene Research, Universitätsspital Basel
Petersgraben 4, CH-4031 Basel, Switzerland
tel: +41 61 265 57 27 - fax: +41 61 265 45 87
More information about the R-help
mailing list