Dear R users,

Here is the coxme output I obtain on my survival dataset having 3 strains
and 2 infection status (i: infected, ni: non infected)

coxme(Surv(lay) ~ infection*strain, data=datalay, random= ~1 |block)

Cox mixed-effects model fit by maximum likelihood

Data: datalay
 n= 1194
 Iterations= 3 77
                    NULL Integrated Penalized
Log-likelihood -7270.028  -7223.859 -7218.175

 Penalized loglik: chisq= 103.71 on 10.24 degrees of freedom, p= 0
 Integrated loglik: chisq= 92.34 on 6 degrees of freedom, p= 0

Fixed effects: Surv(lay) ~ infection * strain


coef                  exp(coef)          se(coef)                z
p

(line1)     infection_ni                       -0.6482079         0.5229822
        0.1481232    -4.38    1.2e-05
(line2)     strainB                              -0.8797408
0.4148904          0.1091490    -8.06   7.8e-16
(line3)     strainC                             -0.7378955
0.4781191          0.1045977    -7.05   1.7e-12
(line4 )    infection_ni:strainB        0.7631418
2.1450049          0.1462481    5.22    1.8e-07
(line5 )    infection_ni:strainC        0.5358302
1.7088664           0.1431092   3.74   1.8e-04

Random effects: ~1 | block

                block
Variance: 0.02493629

I'm not sure I understand properly what are the hazard ratios in the *exp(coef)
column* for the two interaction terms. In the R book of Mick Crawley is
explained that you should be able to calculate these figures approximatively
using the mean survival as below:

tapply(datalay$lay,datalay$strain:datalay$infection,mean)

A:i                  A:ni              B:i                 B:ni
C:i                C:ni
1.864865   2.888372    3.586826  3.253394   3.296296    3.52073

For example, the exp(coef) value in (line 1) of my model output
representsthe ratio between the mean survival of genotype A infected
(i), with mean
survival of genotype A (ni):1.86/2.88 =  0.64, not too far from what the
model gives.

Following the same reasoning, (line 2) is ratio between "B infected" and "A
infected", and (line 3) the ratio between C (i) and A (i).

My question is very simple: *what are the hazard ratios for the interaction
terms stated (line 4) and (line 5), and how are they calculated ?*

Thanks a lot in advance,
Julien.

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