presmoothedTP (version 0.1.0)

unsmoothTP: This function implements unsmoothed estimates of from the Aalen-Johansen estimator (AJ) and landmark Aalen-Johansen method of Putter & Spitoni (2016) for non-parametric estimation of transition probabilities in non-Markov multi-state models.

Description

This function is used to obtain nonparametric unsmoothed estimates of the transition probabilities. The methods used to compute the transition probabilities are ”AJ” and ”LM” which can be also applied for any type of multistate model, including models that allow for reversible transitions, and potencially non-Markovian seetings.

Usage

unsmoothTP(data, s, from, to, method = "LM", trans = trans)

Value

Nonparametric estimates of transition probabilities in general multi-state models using the AJ and the LMAJ estimators.

Arguments

data

A data frame in the long format containing the subject id; from corresponding to the starting state; the receiving state, to; the transition number, trans; the starting time of the transition given by Tstart; the stopping time of the transition, Tstop, and status for the status variable, with 1 indicating an event (transition), 0 a censoring.

s

The first time for obtaining estimates for the transition.

from

The starting state of the transition probabilities.

to

The last receiving state considered for the estimation of the transition probabilities.

method

The method used to compute the transition probabilities. Possible options are "AJ" and "LM".

trans

The transition matrix for multi-state model.

Examples

data("ebmt4")
db_wide <- ebmt4
positions<-list(c(2, 3, 5, 6), c(4, 5, 6), c(4, 5, 6), c(5, 6), c(6), c())
states.names = c("Tx", "Rec", "AE", "Rec+AE", "Rel", "Death")
trans<-transTP(positions, states.names)
times.names = c(NA, "rec", "ae","recae", "rel", "srv")
status.names=c(NA, "rec.s", "ae.s", "recae.s", "rel.s", "srv.s")
data.long<-prepTP(data=db_wide, trans, times.names, status.names)

res1<-unsmoothTP(data.long, s = 100, from = 1, to = 1, method = 'AJ', 
trans=trans)
head(res1)
res2<-unsmoothTP(data.long, s = 100, from = 1, to = 1, method = 'LM', 
trans=trans)
head(res2)
plot(res1, type='s', xlim=c(0,3000), ylim=c(0.6,1), ylab=c('p11(100,t)'))
lines(res2, type='s', col=2)
legend("topright", legend = c("AJ","LM"), lwd = 0.3, col = c(1,2), cex=0.7,
lty=c(1, 1))

res3<-unsmoothTP(data.long, s = 1000, from = 2, to = 6, method = 'AJ', 
trans=trans)
res4<-unsmoothTP(data.long, s = 1000, from = 2, to = 6, method = 'LM', 
trans=trans)

plot(res3, type='s', xlim=c(1000,3000), ylim=c(0,0.12), ylab=c('p26(100,t)'))
lines(res4, type='s', col=2)
legend("topright", legend = c("AJ","LM"), lwd = 0.3, col = c(1,2), cex=0.7,
lty=c(1, 1))