[R] Cox PH Warning Message

[Mayeul KAUFFMANN]

sorry for late answer.

"This is the output. I think it means that there is a problem with
project$pluralgpTriplet???
Neil"

Yes.
definitely. there are probably no triplet, or all triplet are coded as
twins too (and there are no real twins). Or the only triplet is the first
individual that dies (in fact, the latter should rather give an infinite
exp(coef), I think).
You also seem to use many qualitative variable. If a combination of two of
the other variables is identical to  "pluralgpTriplet", R drops the
variable. (This is true for any regression model.)
To find out which combination, you may regress pluralgpTriplet on all
other variables with lm(). You'll probably have R²=1 and some very low
p-values.

If the number of triplet is very small, I advise you group them with
twins, except if it is a major variable in your model.



Cheers,
Mayeul KAUFFMANN
Université Pierre Mendès France
Grenoble - France

 > fm.CPH
Call:
coxph(formula = Surv(age_at_death, death) ~ project$pluralgp +
     project$yrborn + project$private + project$pcdead + project$mheight
+
     project$ga2 + project$apgcode + project$apgar5 + project$VLBWgp +
     project$PEBW + project$LBWgp + project$LBWcat + project$totadm +
     project$totlos + project$sex + teen + project$DS + project$pcsborn +
     project$disadv + project$ecores + project$edoccu)


                                 coef exp(coef) se(coef)       z       p
project$pluralgpTwin       -0.509203     0.601  0.74415 -0.6843 4.9e-01
project$pluralgpTriplet           NA        NA  0.00000      NA      NA
project$yrborn1988-1992    -0.083348     0.920  0.22553 -0.3696 7.1e-01
project$private             0.260465     1.298  0.12384  2.1032 3.5e-02
project$pcdead             -0.058200     0.943  0.49418 -0.1178 9.1e-01
project$mheight             0.016361     1.016  0.01745  0.9378 3.5e-01
project$ga2                 0.104246     1.110  0.10162  1.0258 3.0e-01
project$apgcode4-7         -0.266885     0.766  0.50211 -0.5315 6.0e-01
project$apgcode1-3         -1.704620     0.182  1.12545 -1.5146 1.3e-01
project$apgar5             -0.427139     0.652  0.14099 -3.0296 2.4e-03
project$VLBWgp=>1500 grams  0.046203     1.047  0.65494  0.0705 9.4e-01
project$PEBW                0.015297     1.015  0.01356  1.1281 2.6e-01
project$LBWgp=>2500 grams  -0.257472     0.773  0.42496 -0.6059 5.4e-01
project$LBWcat             -0.222823     0.800  0.23938 -0.9308 3.5e-01
project$totadm              0.005836     1.006  0.01536  0.3800 7.0e-01
project$totlos              0.007342     1.007  0.00176  4.1664 3.1e-05
project$sexFemale          -0.016431     0.984  0.22803 -0.0721 9.4e-01
teen                        0.286282     1.331  0.34807  0.8225 4.1e-01
project$DSDown syndrome     1.193727     3.299  0.27227  4.3844 1.2e-05
project$pcsborn            -0.704743     0.494  0.75943 -0.9280 3.5e-01
project$disadv             -0.000573     0.999  0.00250 -0.2296 8.2e-01
project$ecores             -0.001588     0.998  0.00249 -0.6392 5.2e-01
project$edoccu              0.000590     1.001  0.00193  0.3054 7.6e-01