| Title: | Methods for Transition Probabilities |
|---|---|
| Description: | Provides a function for estimating the transition probabilities in an illness-death model. The transition probabilities can be estimated from the unsmoothed landmark estimators developed by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>. Presmoothed estimates can also be obtained through the use of a parametric family of binary regression curves, such as logit, probit or cauchit. The additive logistic regression model and nonparametric regression are also alternatives which have been implemented. The idea behind the presmoothed landmark estimators is to use the presmoothing techniques developed by Cao et al. (2005) <doi:10.1007/s00180-007-0076-6> in the landmark estimation of the transition probabilities. |
| Authors: | Gustavo Soutinho, Luis Meira-Machado and Pedro Oliveira |
| Maintainer: | Gustavo Soutinho <[email protected]> |
| License: | GPL-3 |
| Version: | 1.1.0 |
| Built: | 2024-11-16 02:47:38 UTC |
| Source: | https://github.com/cran/presmTP |
These are data from one of the first successful trials of adjuvant chemotherapy for colon cancer. Levamisole is a low-toxicity compound previously used to treat worm infestations in animals; 5-FU is a moderately toxic (as these things go) chemotherapy agent.
data("colonIDM")data("colonIDM")
A data frame with 929 observations on the following 15 variables. Below a brief description is given for some of these variables.
Time to recurrence/censoring/death, whichever occurs first.
Recurrence/censoring indicator (recurrence=1, alive=0).
Time to censoring/death, whichever occurs first.
Death/censoring indicator (death=1, alive=0).
Treatment - Obs(ervation), Lev(amisole), Lev(amisole)+5-FU.
Sex indicator (male=1, female=0).
Age in years.
Obstruction of colon by tumour.
Perforation of colon.
Adherence to nearby organs.
Number of lymph nodes with detectable cancer.
Differentiation of tumour (1=well, 2=moderate, 3=poor).
Extent of local spread (1=submucosa, 2=muscle, 3=serosa, 4=contiguous structures).
Time from surgery to registration (0=short, 1=long).
More than 4 positive lymph nodes.
The study is originally described in Laurie (1989).The main report is found in Moertel (1990). This data set is closest to that of the final report in Moertel (1991). A version of the data with less follow-up time was used in the paper by Lin (1994).
JA Laurie, CG Moertel, TR Fleming, HS Wieand, JE Leigh, J Rubin, GW McCormack, JB Gerstner, JE Krook and J Malliard. Surgical adjuvant therapy of large-bowel carcinoma: An evaluation of levamisole and the combination of levamisole and fluorouracil: The North Central Cancer Treatment Group and the Mayo Clinic. Journal of Clinical Oncology, 7:1447-1456, 1989.
DY Lin. Cox regression analysis of multivariate failure time data: the marginal approach. Statistics in Medicine, 13:2233-2247, 1994.
CG Moertel, TR Fleming, JS MacDonald, DG Haller, JA Laurie, PJ Goodman, JS Ungerleider, WA Emerson, DC Tormey, JH Glick, MH Veeder and JA Maillard. Levamisole and fluorouracil for adjuvant therapy of resected colon carcinoma. New England Journal of Medicine, 332:352-358, 1990.
CG Moertel, TR Fleming, JS MacDonald, DG Haller, JA Laurie, CM Tangen, JS Ungerleider, WA Emerson, DC Tormey, JH Glick, MH Veeder and JA Maillard. Fluorouracil plus Levamisole as and effective adjuvant therapy after resection of stage II colon carcinoma: a final report. Annals of Internal Medicine, 122:321-326, 1991.
data(colonIDM) head(colonIDM)data(colonIDM) head(colonIDM)
It draws the estimated probabilities.
## S3 method for class 'pstp' plot(x = object, state_ini = 0, ...)## S3 method for class 'pstp' plot(x = object, state_ini = 0, ...)
x |
A fitted pstp object as produced by presmTP. |
state_ini |
Initial state of the transition. Defaults to state_ini=0 |
... |
For future methods. |
No value is returned.
Gustavo Soutinho, Luis Meira-Machado, Pedro Oliveira.
res<- presmTP(data = colonIDM, s = 365,method = "uns") plot(res)res<- presmTP(data = colonIDM, s = 365,method = "uns") plot(res)
This function is used to obtain unsmoothed and presmoothed estimates of the transition probabilities in the illness-death model.
presmTP(data, s, method = "uns", estimand = "S", bw.selec = "plug-in", fixed.bw = NULL, bound = "none")presmTP(data, s, method = "uns", estimand = "S", bw.selec = "plug-in", fixed.bw = NULL, bound = "none")
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 |
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). |
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. |
Gustavo Soutinho, Luis Meira-Machado, Pedro Oliveira.
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.
#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$call class(res1) #Nonparametric res2<- presmTP(data = colonIDM, s = 365,method = "np" ) res3<- presmTP(data = colonIDM, s = 365,method = "np", estimand="S") res4<- presmTP(data = colonIDM, s = 365,method = "np", estimand="H") res5<- presmTP(data = colonIDM, s = 365,method = "np", bw.selec="fixed", fixed.bw=30) #Presmoothed - Logit res6<- presmTP(data = colonIDM, s = 365,method = "logit" ) summary(res6, state_ini=1, time=365*1:5) #Presmoothed - Logit GAM res7<- presmTP(data = colonIDM, s = 365,method = "logit.gam" )#Unsmoothed res1<- presmTP(data = colonIDM, s = 365,method = "uns" ) res1$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" )
Returns a a data.frame or list containing the estimates of the probabilities.
## S3 method for class 'pstp' summary(object, state_ini = 0, times = NULL, ...)## S3 method for class 'pstp' summary(object, state_ini = 0, times = NULL, ...)
object |
A fitted pstp object as produced by presmTP. |
state_ini |
Initial state of the transition. Defaults to state_ini=0. |
times |
Vector of times; the returned data frame will contain 1 row for each time. |
... |
For future methods. |
A data frame or a list containing the estimates of the probability.
Gustavo Soutinho, Luis Meira-Machado, Pedro Oliveira.
res<- presmTP(data = colonIDM, s = 365, method = "uns") summary(res, state_ini=1, times=365*1:5)res<- presmTP(data = colonIDM, s = 365, method = "uns") summary(res, state_ini=1, times=365*1:5)