Summary method for an object of class 'msfit'. It prints a selection of the estimated cumulative transition intensities, and, if requested, also of the (co)variances.
# S3 method for msfit summary( object, times, transitions, variance = TRUE, conf.int = 0.95, conf.type = c("log", "none", "plain"), extend = FALSE, ... )
| object | Object of class 'msfit', containing estimated cumulative transition intensities for all transitions in a multi-state model |
|---|---|
| times | Time points at which to evaluate the cumulative transition hazards |
| transitions | The transition for which to summarize the cumulative transition hazards |
| variance | Whether or not the standard errors of the estimated
cumulative transition intensities should be printed; default is |
| conf.int | The proportion to be covered by the confidence intervals, default is 0.95 |
| conf.type | The type of confidence interval, one of "log", "none", or "plain". Defaults to "log" |
| extend | logical value: if |
| ... | Further arguments to summary |
Function summary.msfit returns an object of class
"summary.msfit", which is a list (for each from state) of cumulative
transition hazaards at the specified (or all) time points. The print
method of a summary.probtrans doesn't return a value.
Hein Putter H.Putter@lumc.nl
# Start with example from msfit tmat <- trans.illdeath() tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) tglong <- expand.covs(tglong,c("x1","x2")) cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) # Default, all transitions, with SE summary(msf)#> #> Transition 1 : #> time Haz seHaz lower upper #> 1 1 0.06204689 0.08871763 0.003763839 1.022843 #> 2 5 0.06204689 0.08871763 0.003763839 1.022843 #> 3 6 0.33333333 0.33333333 0.046954498 2.366357 #> 4 7 0.33333333 0.33333333 0.046954498 2.366357 #> 5 8 0.33333333 0.33333333 0.046954498 2.366357 #> 6 9 1.33333333 1.05409255 0.283142349 6.278742 #> 7 12 1.33333333 1.05409255 0.283142349 6.278742 #> #> Transition 2 : #> time Haz seHaz lower upper #> 8 1 0.007971491 0.03134544 3.584681e-06 17.726731 #> 9 5 0.007971491 0.03134544 3.584681e-06 17.726731 #> 10 6 0.007971491 0.03134544 3.584681e-06 17.726731 #> 11 7 0.007971491 0.03134544 3.584681e-06 17.726731 #> 12 8 0.305921143 0.36774138 2.900000e-02 3.227164 #> 13 9 0.305921143 0.36774138 2.900000e-02 3.227164 #> 14 12 0.305921143 0.36774138 2.900000e-02 3.227164 #> #> Transition 3 : #> time Haz seHaz lower upper #> 15 1 0.0 0.000000 0.0000000 0.000000 #> 16 5 1.0 1.000000 0.1408635 7.099071 #> 17 6 1.0 1.000000 0.1408635 7.099071 #> 18 7 1.5 1.118034 0.3480512 6.464567 #> 19 8 1.5 1.118034 0.3480512 6.464567 #> 20 9 2.5 1.500000 0.7712925 8.103282 #> 21 12 3.5 1.802776 1.2753583 9.605144#> #> Transition 1 : #> time Haz seHaz lower upper #> 1 1 0.06204689 0.08871763 0 0.2359302 #> 2 5 0.06204689 0.08871763 0 0.2359302 #> 3 6 0.33333333 0.33333333 0 0.9866547 #> 4 7 0.33333333 0.33333333 0 0.9866547 #> 5 8 0.33333333 0.33333333 0 0.9866547 #> 6 9 1.33333333 1.05409255 0 3.3993168 #> 7 12 1.33333333 1.05409255 0 3.3993168 #> #> Transition 2 : #> time Haz seHaz lower upper #> 8 1 0.007971491 0.03134544 0 0.06940743 #> 9 5 0.007971491 0.03134544 0 0.06940743 #> 10 6 0.007971491 0.03134544 0 0.06940743 #> 11 7 0.007971491 0.03134544 0 0.06940743 #> 12 8 0.305921143 0.36774138 0 1.02668100 #> 13 9 0.305921143 0.36774138 0 1.02668100 #> 14 12 0.305921143 0.36774138 0 1.02668100 #> #> Transition 3 : #> time Haz seHaz lower upper #> 15 1 0.0 0.000000 0 0.000000 #> 16 5 1.0 1.000000 0 2.959964 #> 17 6 1.0 1.000000 0 2.959964 #> 18 7 1.5 1.118034 0 3.691306 #> 19 8 1.5 1.118034 0 3.691306 #> 20 9 2.5 1.500000 0 5.439946 #> 21 12 3.5 1.802776 0 7.033375#> #> Transition 1 : #> time Haz seHaz lower upper #> 1 1 0.06204689 0.08871763 0.003763839 1.022843 #> 2 5 0.06204689 0.08871763 0.003763839 1.022843 #> 3 6 0.33333333 0.33333333 0.046954498 2.366357 #> 4 7 0.33333333 0.33333333 0.046954498 2.366357 #> 5 8 0.33333333 0.33333333 0.046954498 2.366357 #> 6 9 1.33333333 1.05409255 0.283142349 6.278742 #> 7 12 1.33333333 1.05409255 0.283142349 6.278742 #> #> Transition 3 : #> time Haz seHaz lower upper #> 15 1 0.0 0.000000 0.0000000 0.000000 #> 16 5 1.0 1.000000 0.1408635 7.099071 #> 17 6 1.0 1.000000 0.1408635 7.099071 #> 18 7 1.5 1.118034 0.3480512 6.464567 #> 19 8 1.5 1.118034 0.3480512 6.464567 #> 20 9 2.5 1.500000 0.7712925 8.103282 #> 21 12 3.5 1.802776 1.2753583 9.605144#> #> Transition 1 : #> time Haz seHaz lower upper #> 1 1 0.06204689 0.08871763 0.00590618 0.6518284 #> 2 5 0.06204689 0.08871763 0.00590618 0.6518284 #> 3 6 0.33333333 0.33333333 0.06434694 1.7267505 #> 4 7 0.33333333 0.33333333 0.06434694 1.7267505 #> 5 8 0.33333333 0.33333333 0.06434694 1.7267505 #> 6 9 1.33333333 1.05409255 0.36324095 4.8942108 #> 7 12 1.33333333 1.05409255 0.36324095 4.8942108 #> #> Transition 2 : #> time Haz seHaz lower upper #> 8 1 0.007971491 0.03134544 1.237582e-05 5.134584 #> 9 5 0.007971491 0.03134544 1.237582e-05 5.134584 #> 10 6 0.007971491 0.03134544 1.237582e-05 5.134584 #> 11 7 0.007971491 0.03134544 1.237582e-05 5.134584 #> 12 8 0.305921143 0.36774138 4.235487e-02 2.209610 #> 13 9 0.305921143 0.36774138 4.235487e-02 2.209610 #> 14 12 0.305921143 0.36774138 4.235487e-02 2.209610 #> #> Transition 3 : #> time Haz seHaz lower upper #> 15 1 0.0 0.000000 0.0000000 0.000000 #> 16 5 1.0 1.000000 0.1930408 5.180252 #> 17 6 1.0 1.000000 0.1930408 5.180252 #> 18 7 1.5 1.118034 0.4401955 5.111366 #> 19 8 1.5 1.118034 0.4401955 5.111366 #> 20 9 2.5 1.500000 0.9318146 6.707343 #> 21 12 3.5 1.802776 1.5001031 8.166106#> #> Transition 1 : #> time Haz #> 1 1 0.06204689 #> 2 5 0.06204689 #> 3 6 0.33333333 #> 4 7 0.33333333 #> 5 8 0.33333333 #> 6 9 1.33333333 #> 7 12 1.33333333 #> #> Transition 2 : #> time Haz #> 8 1 0.007971491 #> 9 5 0.007971491 #> 10 6 0.007971491 #> 11 7 0.007971491 #> 12 8 0.305921143 #> 13 9 0.305921143 #> 14 12 0.305921143 #> #> Transition 3 : #> time Haz #> 15 1 0.0 #> 16 5 1.0 #> 17 6 1.0 #> 18 7 1.5 #> 19 8 1.5 #> 20 9 2.5 #> 21 12 3.5#> #> Transition 1 : #> times Haz seHaz lower upper #> 1 0 0.06204689 0.08871763 0.003763839 1.022843 #> 2 3 0.06204689 0.08871763 0.003763839 1.022843 #> 3 6 0.33333333 0.33333333 0.046954498 2.366357 #> 4 9 1.33333333 1.05409255 0.283142349 6.278742 #> 5 12 1.33333333 1.05409255 0.283142349 6.278742 #> #> Transition 2 : #> times Haz seHaz lower upper #> 1 0 0.007971491 0.03134544 3.584681e-06 17.726731 #> 2 3 0.007971491 0.03134544 3.584681e-06 17.726731 #> 3 6 0.007971491 0.03134544 3.584681e-06 17.726731 #> 4 9 0.305921143 0.36774138 2.900000e-02 3.227164 #> 5 12 0.305921143 0.36774138 2.900000e-02 3.227164 #> #> Transition 3 : #> times Haz seHaz lower upper #> 1 0 0.0 0.000000 0.0000000 0.000000 #> 2 3 0.0 0.000000 0.0000000 0.000000 #> 3 6 1.0 1.000000 0.1408635 7.099071 #> 4 9 2.5 1.500000 0.7712925 8.103282 #> 5 12 3.5 1.802776 1.2753583 9.605144# Last specified time point is larger than last observed, not printed # Use extend=TRUE as in summary.survfit summary(msf, times=seq(0, 15, by=3), extend=TRUE)#> #> Transition 1 : #> times Haz seHaz lower upper #> 1 0 0.06204689 0.08871763 0.003763839 1.022843 #> 2 3 0.06204689 0.08871763 0.003763839 1.022843 #> 3 6 0.33333333 0.33333333 0.046954498 2.366357 #> 4 9 1.33333333 1.05409255 0.283142349 6.278742 #> 5 12 1.33333333 1.05409255 0.283142349 6.278742 #> 6 15 1.33333333 1.05409255 0.283142349 6.278742 #> #> Transition 2 : #> times Haz seHaz lower upper #> 1 0 0.007971491 0.03134544 3.584681e-06 17.726731 #> 2 3 0.007971491 0.03134544 3.584681e-06 17.726731 #> 3 6 0.007971491 0.03134544 3.584681e-06 17.726731 #> 4 9 0.305921143 0.36774138 2.900000e-02 3.227164 #> 5 12 0.305921143 0.36774138 2.900000e-02 3.227164 #> 6 15 0.305921143 0.36774138 2.900000e-02 3.227164 #> #> Transition 3 : #> times Haz seHaz lower upper #> 1 0 0.0 0.000000 0.0000000 0.000000 #> 2 3 0.0 0.000000 0.0000000 0.000000 #> 3 6 1.0 1.000000 0.1408635 7.099071 #> 4 9 2.5 1.500000 0.7712925 8.103282 #> 5 12 3.5 1.802776 1.2753583 9.605144 #> 6 15 3.5 1.802776 1.2753583 9.605144# Different types of confidence intervals, default is log summary(msf, times=seq(0, 15, by=3), conf.type="plain")#> #> Transition 1 : #> times Haz seHaz lower upper #> 1 0 0.06204689 0.08871763 0 0.2359302 #> 2 3 0.06204689 0.08871763 0 0.2359302 #> 3 6 0.33333333 0.33333333 0 0.9866547 #> 4 9 1.33333333 1.05409255 0 3.3993168 #> 5 12 1.33333333 1.05409255 0 3.3993168 #> #> Transition 2 : #> times Haz seHaz lower upper #> 1 0 0.007971491 0.03134544 0 0.06940743 #> 2 3 0.007971491 0.03134544 0 0.06940743 #> 3 6 0.007971491 0.03134544 0 0.06940743 #> 4 9 0.305921143 0.36774138 0 1.02668100 #> 5 12 0.305921143 0.36774138 0 1.02668100 #> #> Transition 3 : #> times Haz seHaz lower upper #> 1 0 0.0 0.000000 0 0.000000 #> 2 3 0.0 0.000000 0 0.000000 #> 3 6 1.0 1.000000 0 2.959964 #> 4 9 2.5 1.500000 0 5.439946 #> 5 12 3.5 1.802776 0 7.033375#> #> Transition 1 : #> times Haz seHaz #> 1 0 0.06204689 0.08871763 #> 2 3 0.06204689 0.08871763 #> 3 6 0.33333333 0.33333333 #> 4 9 1.33333333 1.05409255 #> 5 12 1.33333333 1.05409255 #> #> Transition 2 : #> times Haz seHaz #> 1 0 0.007971491 0.03134544 #> 2 3 0.007971491 0.03134544 #> 3 6 0.007971491 0.03134544 #> 4 9 0.305921143 0.36774138 #> 5 12 0.305921143 0.36774138 #> #> Transition 3 : #> times Haz seHaz #> 1 0 0.0 0.000000 #> 2 3 0.0 0.000000 #> 3 6 1.0 1.000000 #> 4 9 2.5 1.500000 #> 5 12 3.5 1.802776# When the number of time points specified is larger than 12, head and tail is shown x <- summary(msf, times=seq(5, 8, by=0.25)) x#> #> Transition 1 (head and tail): #> times Haz seHaz lower upper #> 1 5.00 0.06204689 0.08871763 0.003763839 1.022843 #> 2 5.25 0.06204689 0.08871763 0.003763839 1.022843 #> 3 5.50 0.06204689 0.08871763 0.003763839 1.022843 #> 4 5.75 0.06204689 0.08871763 0.003763839 1.022843 #> 5 6.00 0.33333333 0.33333333 0.046954498 2.366357 #> 6 6.25 0.33333333 0.33333333 0.046954498 2.366357 #> #> ... #> times Haz seHaz lower upper #> 8 6.75 0.3333333 0.3333333 0.0469545 2.366357 #> 9 7.00 0.3333333 0.3333333 0.0469545 2.366357 #> 10 7.25 0.3333333 0.3333333 0.0469545 2.366357 #> 11 7.50 0.3333333 0.3333333 0.0469545 2.366357 #> 12 7.75 0.3333333 0.3333333 0.0469545 2.366357 #> 13 8.00 0.3333333 0.3333333 0.0469545 2.366357 #> #> Transition 2 (head and tail): #> times Haz seHaz lower upper #> 1 5.00 0.007971491 0.03134544 3.584681e-06 17.72673 #> 2 5.25 0.007971491 0.03134544 3.584681e-06 17.72673 #> 3 5.50 0.007971491 0.03134544 3.584681e-06 17.72673 #> 4 5.75 0.007971491 0.03134544 3.584681e-06 17.72673 #> 5 6.00 0.007971491 0.03134544 3.584681e-06 17.72673 #> 6 6.25 0.007971491 0.03134544 3.584681e-06 17.72673 #> #> ... #> times Haz seHaz lower upper #> 8 6.75 0.007971491 0.03134544 3.584681e-06 17.726731 #> 9 7.00 0.007971491 0.03134544 3.584681e-06 17.726731 #> 10 7.25 0.007971491 0.03134544 3.584681e-06 17.726731 #> 11 7.50 0.007971491 0.03134544 3.584681e-06 17.726731 #> 12 7.75 0.007971491 0.03134544 3.584681e-06 17.726731 #> 13 8.00 0.305921143 0.36774138 2.900000e-02 3.227164 #> #> Transition 3 (head and tail): #> times Haz seHaz lower upper #> 1 5.00 1 1 0.1408635 7.099071 #> 2 5.25 1 1 0.1408635 7.099071 #> 3 5.50 1 1 0.1408635 7.099071 #> 4 5.75 1 1 0.1408635 7.099071 #> 5 6.00 1 1 0.1408635 7.099071 #> 6 6.25 1 1 0.1408635 7.099071 #> #> ... #> times Haz seHaz lower upper #> 8 6.75 1.0 1.000000 0.1408635 7.099071 #> 9 7.00 1.5 1.118034 0.3480512 6.464567 #> 10 7.25 1.5 1.118034 0.3480512 6.464567 #> 11 7.50 1.5 1.118034 0.3480512 6.464567 #> 12 7.75 1.5 1.118034 0.3480512 6.464567 #> 13 8.00 1.5 1.118034 0.3480512 6.464567