presmTP: Methods for estimation of transition probabilities in the...

In presmTP: Methods for Transition Probabilities

Description

This function is used to obtain unsmoothed and presmoothed estimates of the transition probabilities in the illness-death model.

Usage

presmTP(data, s, method = "uns", estimand = "S",
  bw.selec = "plug-in", fixed.bw = NULL, bound = "none")

Arguments

data	A numeric value to be squared
s	The first time for obtaining estimates for the transition probabilities.
method	The method used to compute the transition probabilities. Possible options are "uns", "np" "logit", "logit.gam", "probit" and "cauchit". Defaults to "uns".
estimand	An optional character string identifying the function to estimate: "S" for survival function and "H" for cumulative hazard function. Defaults to "S".
bw.selec	An optional (partially matched) character string specifying the method of bandwidth selection. "fixed" if no bandwidth selection is done, in which case the bandwidth(s) given by the fixed.bw argument is (are) used, "plug-in" for plug-in bandwidth selection and "bootstrap" for bootstrap bandwidth selection. Defaults to "fixed".
fixed.bw	An optional numeric vector with the fixed bandwidth(s) used when the value of the bw.selec argument is "fixed". It must be of length 1 for estimating survival and cumulative hazard functions, and of length 2 for density and hazard functions (in this case, the first element is the presmoothing bandwidth).
bound	An optional numeric vector with the fixed bandwidth(s) used when the value of the bw.selec argument is "fixed". It must be of length 1 for estimating survival and cumulative hazard functions, and of length 2 for density and hazard functions (in this case, the first element is the presmoothing bandwidth).

Value

An object of class "pstp" and one of the following classes: "uns", "np", "logit", "logit.gam", "probit" and "cauchit". Objects are implemented as a list with elements:

est0	data.frame with estimates of the transition probabilities 0->0, 0->1 and 0->2.
est1	data.frame with estimates of the transition probabilities 1->1 and 1->2.
s	The first time for obtaining estimates for the transition probabilities.
callp	The expression of the estimated probability.
call	A call object.

Author(s)

Gustavo Soutinho, Luis Meira-Machado, Pedro Oliveira.

References

Aalen O. O., Johansen S. (1978) An Empirical Transition Matrix for Nonhomogeneous Markov Chains Based on Censored Observations. Scandinavian Journal of Statistics 5(3), 141–150.

Cao, R., Lopez-de-Ullibarri, I., Janssen, P. and Veraverbeke, N. (2005). Presmoothed Kaplan-Meier and Nelson-Aalen estimators, Journal of Nonparametric Statistics, 17, 31-56.

Meira-Machado L. F., de Una-Alvarez J. and Cadarso-Suarez C. (2006). Nonparametric estimation of transition probabilities in a non-Markov illness-death model. Lifetime Data Anal 12(3), 325–344.

Lopez-de-Ullibarri, I and Jacome, M. A. (2013). survPresmooth: An R Package for Presmoothed Estimation in Survival Analysis, Journal of Statistical Software, 54(11), 1-26. URL: http://www.jstatsoft.org/v54/i11/. de Una-Alvarez J. and Meira-Machado L. (2015). Nonparametric estimation of transition probabilities in a non-Markov illness-death model: a comparative study. Biometrics 71, 364–375.

Meira-Machado, L. (2016). Smoothed landmark estimators of the transition probabilities, SORT-Statistics and Operations Research Transactions, 40, 375-398.

Examples

#Unsmoothed
res1<- presmTP(data = colonIDM, s = 365,method = "uns" )
res1$est0$t
res1$est0$p02
res1$est1$t
summary(res1, state_ini=1, time=365*1:5)
plot(res1)
res1$call
class(res1)
#Nonparametric
res2<- presmTP(data = colonIDM, s = 365,method = "np" )
res3<- presmTP(data = colonIDM, s = 365,method = "np", estimand="S")
res4<- presmTP(data = colonIDM, s = 365,method = "np", estimand="H")
res5<- presmTP(data = colonIDM, s = 365,method = "np", 
               bw.selec="fixed", fixed.bw=30)
#Presmoothed - Logit
res6<- presmTP(data = colonIDM, s = 365,method = "logit" )
summary(res6, state_ini=1, time=365*1:5)
#Presmoothed - Logit GAM
res7<- presmTP(data = colonIDM, s = 365,method = "logit.gam" )

presmTP documentation built on Nov. 1, 2019, 7:45 p.m.