# # Data from CA McGilchrist, CW Aisbett (1991), Regression with frailty in # survival analysis. _Biometrics_ *47*, 461-66. # # Recurrence times to catheter infection in # patients using portable # dialysis equipment. Catheters may be removed for reasons other # than infection, in which case the observation is censored. Each # patient has exactly 2 observations. # # BUGs example of Weibull frailty Sib-pair # regression: chains=4 burn=1000 # burnin=1000 iterations=10000 iterations=50000 # # par mean SD MC-SE # alpha -4.529 0.9036 0.0624 4.4571 0.8687 0.0638 # GN 0.1265 0.5679 0.0186 -0.0397 0.5219 0.0138 # AN 0.5995 0.5781 0.0220 -0.5586 0.5146 0.0118 # PKD -1.198 0.8483 0.0315 1.2897 0.7660 0.0225 # Female -1.945 0.5019 0.0280 1.9924 0.4931 0.0254 # r 1.205 0.1711 0.0125 1.1903 # sigma 0.6367 0.3802 0.0316 0.6201 0.2489 0.0173 # # # Results from survreg(Surv(time, status) ~ age + sex + disease + # frailty.gaussian(id), data = kidney) # # coef se(coef) se2 Chisq DF p # (Intercept) 2.11528 0.7612 0.36962 7.72 1.0 5.5e-03 # age -0.00301 0.0127 0.00595 0.06 1.0 8.1e-01 # sex 1.56195 0.3518 0.17657 19.71 1.0 9.0e-06 # diseaseGN -0.15705 0.4563 0.22798 0.12 1.0 7.3e-01 # diseaseAN -0.55862 0.4565 0.22832 1.50 1.0 2.2e-01 # diseasePKD 0.63778 0.6346 0.32905 1.01 1.0 3.1e-01 # frailty.gaussian(id) 58.62 22.5 4.6e-05 # # Scale= 0.55 # # Iterations: 6 outer, 28 Newton-Raphson # Variance of random effect= 0.628 # Degrees of freedom for terms= 0.2 0.2 0.3 0.8 22.5 0.9 # Likelihood ratio test=81.7 on 22.8 df, p=1.53e-08 n= 76 # # # And survreg(Surv(time, status)~ age + sex + disease + # frailty.gaussian(id, method="aic", caic=T), kidney)) # # Value Std. Error z p # (Intercept) 2.06991 0.6667 3.105 1.90e-03 # age -0.00277 0.0105 -0.264 7.92e-01 # sex 1.59980 0.3108 5.147 2.65e-07 # diseaseGN -0.08882 0.3840 -0.231 8.17e-01 # diseaseAN -0.53129 0.3788 -1.403 1.61e-01 # diseasePKD 0.96965 0.5749 1.686 9.17e-02 # Log(scale) -0.31929 0.1263 -2.527 1.15e-02 # # Scale= 0.727 # # Weibull distribution # Loglik(model)= -314 Loglik(intercept only)= -340.9 # Chisq= 53.81 on 12.7 degrees of freedom, p= 5.2e-07 # Number of Newton-Raphson Iterations: 8 32 # set loc time qua . recurrence times to catheter infection set loc status qua . set loc age qua . in years set loc disease qua . 1=Other 2=GN 2=AN 3=PKD set loc frail qua . frailty estimate from McGilchrist 1991 set loc GN aff . set loc AN aff . set loc PKD aff . read pedigree inline # id obs sex time status age disease frail GN AN PKD 1 1 x x 1 8 y 28 1 2.3 n n n 1 2 x x 1 16 y 28 1 2.3 n n n 2 3 x x 2 23 y 48 2 1.9 y n n 2 4 x x 2 13 n 48 2 1.9 y n n 3 5 x x 1 22 y 32 1 1.2 n n n 3 6 x x 1 28 y 32 1 1.2 n n n 4 7 x x 2 447 y 31 1 0.5 n n n 4 8 x x 2 318 y 32 1 0.5 n n n 5 9 x x 1 30 y 10 1 1.5 n n n 5 10 x x 1 12 y 10 1 1.5 n n n 6 11 x x 2 24 y 16 1 1.1 n n n 6 12 x x 2 245 y 17 1 1.1 n n n 7 13 x x 1 7 y 51 2 3 y n n 7 14 x x 1 9 y 51 2 3 y n n 8 15 x x 2 511 y 55 2 0.5 y n n 8 16 x x 2 30 y 56 2 0.5 y n n 9 17 x x 2 53 y 69 3 0.7 n y n 9 18 x x 2 196 y 69 3 0.7 n y n 10 19 x x 1 15 y 51 2 0.4 y n n 10 20 x x 1 154 y 52 2 0.4 y n n 11 21 x x 2 7 y 44 3 0.6 n y n 11 22 x x 2 333 y 44 3 0.6 n y n 12 23 x x 2 141 y 34 1 1.2 n n n 12 24 x x 2 8 n 34 1 1.2 n n n 13 25 x x 2 96 y 35 3 1.4 n y n 13 26 x x 2 38 y 35 3 1.4 n y n 14 27 x x 2 149 n 42 3 0.4 n y n 14 28 x x 2 70 n 42 3 0.4 n y n 15 29 x x 2 536 y 17 1 0.4 n n n 15 30 x x 2 25 n 17 1 0.4 n n n 16 31 x x 1 17 y 60 3 1.1 n y n 16 32 x x 1 4 n 60 3 1.1 n y n 17 33 x x 2 185 y 60 1 0.8 n n n 17 34 x x 2 177 y 60 1 0.8 n n n 18 35 x x 2 292 y 43 1 0.8 n n n 18 36 x x 2 114 y 44 1 0.8 n n n 19 37 x x 2 22 n 53 2 0.5 y n n 19 38 x x 2 159 n 53 2 0.5 y n n 20 39 x x 2 15 y 44 1 1.3 n n n 20 40 x x 2 108 n 44 1 1.3 n n n 21 41 x x 1 152 y 46 4 0.2 n n y 21 42 x x 1 562 y 47 4 0.2 n n y 22 43 x x 2 402 y 30 1 0.6 n n n 22 44 x x 2 24 n 30 1 0.6 n n n 23 45 x x 2 13 y 62 3 1.7 n y n 23 46 x x 2 66 y 63 3 1.7 n y n 24 47 x x 2 39 y 42 3 1 n y n 24 48 x x 2 46 n 43 3 1 n y n 25 49 x x 1 12 y 43 3 0.7 n y n 25 50 x x 1 40 y 43 3 0.7 n y n 26 51 x x 2 113 n 57 3 0.5 n y n 26 52 x x 2 201 y 58 3 0.5 n y n 27 53 x x 2 132 y 10 2 1.1 y n n 27 54 x x 2 156 y 10 2 1.1 y n n 28 55 x x 2 34 y 52 3 1.8 n y n 28 56 x x 2 30 y 52 3 1.8 n y n 29 57 x x 1 2 y 53 2 1.5 y n n 29 58 x x 1 25 y 53 2 1.5 y n n 30 59 x x 2 130 y 54 2 1.5 y n n 30 60 x x 2 26 y 54 2 1.5 y n n 31 61 x x 2 27 y 56 3 1.7 n y n 31 62 x x 2 58 y 56 3 1.7 n y n 32 63 x x 2 5 n 50 3 1.3 n y n 32 64 x x 2 43 y 51 3 1.3 n y n 33 65 x x 2 152 y 57 4 2.9 n n y 33 66 x x 2 30 y 57 4 2.9 n n y 34 67 x x 2 190 y 44 2 0.7 y n n 34 68 x x 2 5 n 45 2 0.7 y n n 35 69 x x 2 119 y 22 1 2.2 n n n 35 70 x x 2 8 y 22 1 2.2 n n n 36 71 x x 2 54 n 42 1 0.7 n n n 36 72 x x 2 16 n 42 1 0.7 n n n 37 73 x x 2 6 n 52 4 2.1 n n y 37 74 x x 2 78 y 52 4 2.1 n n y 38 75 x x 1 63 y 60 4 1.2 n n y 38 76 x x 1 8 n 60 4 1.2 n n y ;;;; run set loc fem aff fem=female reg time = age fem GN AN PKD weibull status set iter 5000 set chains 4 fpm time lik weibull cens status nqtl 0 c cov age + fem + GN + AN + PKD