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.
Arguments
- 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
TRUE- 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
TRUE, prints information for all specified times, even if there are no subjects left at the end of the specified times. This is only valid if the times argument is present- ...
Further arguments to summary
Value
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.
Author
Hein Putter H.Putter@lumc.nl
Examples
# 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
summary(msf, conf.type="plain")
#>
#> 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
# Only transitions 1 and 3
summary(msf, tra=c(1, 3))
#>
#> 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
# Default is 95% confidence interval, change here to 90%
summary(msf, conf.int=0.90)
#>
#> 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
# Do not show variances (nor confidence intervals)
summary(msf, variance=FALSE)
#>
#> 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
# Cumulative hazards only at specified time points
summary(msf, times=seq(0, 15, by=3))
#>
#> 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
summary(msf, times=seq(0, 15, by=3), conf.type="no")
#>
#> 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