Restricted mean for stratified Kaplan-Meier or Cox model with martingale standard errors
Source:R/phreg.R
resmean.phreg.RdRestricted mean for stratified Kaplan-Meier or stratified Cox with martingale standard error. Standard error is computed using linear interpolation between standard errors at jump-times. Plots gives restricted mean at all times. Years lost can be computed based on this and decomposed into years lost for different causes using the cif.yearslost function that is based on integrating the cumulative incidence functions. One particular feature of these functions are that the restricted mean and years-lost are computed for all event times as functions and can be plotted/viewed. When times are given and beyond the last event time withn a strata the curves are extrapolated using the estimates of cumulative incidence.
resmean.phreg(x, times = NULL, covs = NULL, ...)Arguments
Examples
data(bmt); bmt$time <- bmt$time+runif(408)*0.001
out1 <- phreg(Surv(time,cause!=0)~strata(tcell,platelet),data=bmt)
rm1 <- resmean.phreg(out1,times=10*(1:6))
summary(rm1)
#> strata times rmean se.rmean years.lost
#> tcell.0..platelet.0 0 10 5.863335 0.2565971 4.136665
#> tcell.0..platelet.1 1 10 7.631973 0.3423832 2.368027
#> tcell.1..platelet.0 2 10 7.277572 0.7092852 2.722428
#> tcell.1..platelet.1 3 10 7.670164 0.5624534 2.329836
#> tcell.0..platelet.0.1 0 20 9.888950 0.5393857 10.111050
#> tcell.0..platelet.1.1 1 20 13.506463 0.8000204 6.493537
#> tcell.1..platelet.0.1 2 20 12.102970 1.5545626 7.897030
#> tcell.1..platelet.1.1 3 20 12.787746 1.4675818 7.212254
#> tcell.0..platelet.0.2 0 30 13.602940 0.8315420 16.397060
#> tcell.0..platelet.1.2 1 30 18.901294 1.2693245 11.098706
#> tcell.1..platelet.0.2 2 30 16.191143 2.4006207 13.808857
#> tcell.1..platelet.1.2 3 30 17.766101 2.4422016 12.233899
#> tcell.0..platelet.0.3 0 40 17.159951 1.1235967 22.840049
#> tcell.0..platelet.1.3 1 40 23.883707 1.7372982 16.116293
#> tcell.1..platelet.0.3 2 40 19.549215 3.2030980 20.450785
#> tcell.1..platelet.1.3 3 40 22.433310 3.3838363 17.566690
#> tcell.0..platelet.0.4 0 50 20.482466 1.4110541 29.517534
#> tcell.0..platelet.1.4 1 50 28.330744 2.1961702 21.669256
#> tcell.1..platelet.0.4 2 50 22.746018 4.0537116 27.253982
#> tcell.1..platelet.1.4 3 50 26.115616 4.2306828 23.884384
#> tcell.0..platelet.0.5 0 60 23.741474 1.7038102 36.258526
#> tcell.0..platelet.1.5 1 60 32.771271 2.6865715 27.228729
#> tcell.1..platelet.0.5 2 60 25.942822 4.9476044 34.057178
#> tcell.1..platelet.1.5 3 60 29.671584 5.1599164 30.328416
par(mfrow=c(1,2))
plot(rm1,se=1)
plot(rm1,years.lost=TRUE,se=1)
## years.lost decomposed into causes
drm1 <- cif.yearslost(Event(time,cause)~strata(tcell,platelet),data=bmt,times=10*(1:6))
par(mfrow=c(1,2)); plot(drm1,cause=1,se=1); plot(drm1,cause=2,se=1);
summary(drm1)
#> strata times intF11 intF12 se.intF11 se.intF12
#> tcell.0..platelet.0 0 10 3.117729 1.0189359 0.2487178 0.1703643
#> tcell.0..platelet.1 1 10 1.710893 0.6571334 0.3238355 0.1870577
#> tcell.1..platelet.0 2 10 1.876139 0.8462887 0.6339031 0.4726389
#> tcell.1..platelet.1 3 10 1.358613 0.9712227 0.5303130 0.3617332
#> tcell.0..platelet.0.1 0 20 7.517571 2.5934794 0.5441136 0.3861264
#> tcell.0..platelet.1.1 1 20 4.230923 2.2626139 0.7414037 0.5327583
#> tcell.1..platelet.0.1 2 20 4.568447 3.3285831 1.4876765 1.1718408
#> tcell.1..platelet.1.1 3 20 3.569497 3.6427573 1.3003045 1.1906597
#> tcell.0..platelet.0.2 0 30 12.105134 4.2919265 0.8508105 0.6161437
#> tcell.0..platelet.1.2 1 30 6.884157 4.2145481 1.1740966 0.9057017
#> tcell.1..platelet.0.2 2 30 7.260755 6.5481018 2.3532864 1.9703466
#> tcell.1..platelet.1.2 3 30 5.780382 6.4535180 2.0925012 2.0815185
#> tcell.0..platelet.0.3 0 40 16.718645 6.1214041 1.1626278 0.8509979
#> tcell.0..platelet.1.3 1 40 9.727977 6.3883168 1.6094938 1.2998314
#> tcell.1..platelet.0.3 2 40 9.953062 10.4977225 3.2212048 2.8144174
#> tcell.1..platelet.1.3 3 40 8.302412 9.2642786 2.8717935 2.9840842
#> tcell.0..platelet.0.4 0 50 21.367829 8.1497050 1.4766462 1.0945192
#> tcell.0..platelet.1.4 1 50 12.979220 8.6900356 2.0475113 1.7124389
#> tcell.1..platelet.0.4 2 50 12.645370 14.6086116 4.0899622 3.7302664
#> tcell.1..platelet.1.4 3 50 11.809345 12.0750393 3.6736885 3.8902170
#> tcell.0..platelet.0.5 0 60 26.017013 10.2415133 1.7930407 1.3471498
#> tcell.0..platelet.1.5 1 60 16.236975 10.9917545 2.5097367 2.1389877
#> tcell.1..platelet.0.5 2 60 15.337678 18.7195007 4.9591177 4.6873882
#> tcell.1..platelet.1.5 3 60 15.442616 14.8858000 4.5899675 4.7978962
#> total.years.lost
#> tcell.0..platelet.0 4.136665
#> tcell.0..platelet.1 2.368027
#> tcell.1..platelet.0 2.722428
#> tcell.1..platelet.1 2.329836
#> tcell.0..platelet.0.1 10.111050
#> tcell.0..platelet.1.1 6.493537
#> tcell.1..platelet.0.1 7.897030
#> tcell.1..platelet.1.1 7.212254
#> tcell.0..platelet.0.2 16.397060
#> tcell.0..platelet.1.2 11.098706
#> tcell.1..platelet.0.2 13.808857
#> tcell.1..platelet.1.2 12.233899
#> tcell.0..platelet.0.3 22.840049
#> tcell.0..platelet.1.3 16.116293
#> tcell.1..platelet.0.3 20.450785
#> tcell.1..platelet.1.3 17.566690
#> tcell.0..platelet.0.4 29.517534
#> tcell.0..platelet.1.4 21.669256
#> tcell.1..platelet.0.4 27.253982
#> tcell.1..platelet.1.4 23.884384
#> tcell.0..platelet.0.5 36.258526
#> tcell.0..platelet.1.5 27.228729
#> tcell.1..platelet.0.5 34.057178
#> tcell.1..platelet.1.5 30.328416