mstate: summary.probtrans – R documentation

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summary.probtrans

Summary method for a probtrans object

Description

Summary method for an object of class 'probtrans'. It prints a selection of the estimated transition probabilities, and, if requested, also of the variances.

Usage

## S3 method for class 'probtrans'
summary(
  object,
  times,
  from = 1,
  to = 0,
  variance = TRUE,
  conf.int = 0.95,
  conf.type = c("log", "none", "plain"),
  extend = FALSE,
  ...
)

Arguments

`object`	Object of class 'probtrans', containing estimated transition probabilities from and to all states in a multi-state model
`times`	Time points at which to evaluate the transition probabilites
`from`	Specifies from which state the transition probabilities are to be printed. Should be subset of 1:S, with S the number of states in the multi-state model. Default is print from state 1 only. User can specify from=0 to print transition probabilities from all states
`to`	Specifies the transition probabilities to which state are to be printed. User can specify to=0 to print transition probabilities to all states. This is also the default
`variance`	Whether or not the standard errors of the estimated transition probabilities 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 print

Value

Function summary.probtrans returns an object of class "summary.probtrans", which is a list (for each from state) of transition probabilities at the specified (or all) time points. The print method of a summary.probtrans doesn't return a value.

Author(s)

Hein Putter H.Putter@lumc.nl

Examples

# First run the example of probtrans
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)
HvH <- msfit(cx,newdata,trans=tmat)
pt <- probtrans(HvH,predt=0)

# Default, prediction from state 1
summary(pt)
# Only from states 1 and 3
summary(pt, from=c(1, 3))
# Use from=0 for prediction from all states
summary(pt, from=0)
# Only to states 1 and 2
summary(pt, to=1:2)
# Default is 95% confidence interval, change here to 90% 
summary(pt, to=1:2, conf.int=0.90)
# Do not show variances (nor confidence intervals)
summary(pt, to=1:2, variance=FALSE)
# Transition probabilities only at specified time points
summary(pt, times=seq(0, 15, by=3))
# Last specified time point is larger than last observed, not printed
# Use extend=TRUE as in summary.survfit
summary(pt, times=seq(0, 15, by=3), extend=TRUE)
# Different types of confidence intervals, default is log
summary(pt, times=seq(0, 15, by=3), conf.type="plain")
summary(pt, times=seq(0, 15, by=3), conf.type="no")
# When the number of time points specified is larger than 12, head and tail is shown
x <- summary(pt, times=seq(5, 8, by=0.25))
x

mstate

Data Preparation, Estimation and Prediction in Multi-State Models

v0.3.1

GPL (>= 2)

Authors

Hein Putter [aut, cre], Liesbeth C. de Wreede [aut], Marta Fiocco [aut], Ronald B. Geskus [ctb], Edouard F. Bonneville [ctb], Damjan Manevski [ctb]

Initial release

2020-12-17