However, in the context of survival trees, a further difficulty arises when time—varying effects are included. Hence, we feel that the interpretation of covariate effects with tree ensembles in general is still mainly unsolved and should attract future research.
I believe that the major use for tree-based models for survival data will be to deal with very large data sets. The following code pulls out the survival data from the three model objects and puts them into a data frame for ggplot. For this data set, I would put my money on a carefully constructed Cox model that takes into account the time varying coefficients.
I suspect that there are neither enough observations nor enough explanatory variables for the ranger model to do better. This four-package excursion only hints at the Survival Analysis tools that are available in R, but it does illustrate some of the richness of the R platform, which has been under continuous development and improvement for nearly twenty years. The ranger package, which suggests the survival package, and ggfortify , which depends on ggplot2 and also suggests the survival package, illustrate how open-source code allows developers to build on the work of their predecessors.
For a very nice, basic tutorial on survival analysis, have a look at the Survival Analysis in R  and the OIsurv package produced by the folks at OpenIntro. For an elementary treatment of evaluating the proportional hazards assumption that uses the veterans data set, see the text by Kleinbaum and Klein .
Feature selection FS is very useful, especially in the medical area, as it reduces the time needed and the effort made by physicians to measure irrelevant and redundant features. Journal of Applied Econometrics, 4 , — Google Scholar. Singh R, Mukhopadhyay K. The prodlim package implements a fast algorithm and some features not included in survival. Data mining. New York: Wiley.
See the paper  by Intrator and Kooperberg for an early review of using classification and regression trees to study survival data. Cambridge University Press, 2nd ed. Wiley, pp. Non-parametric estimation from incomplete observations , J American Stats Assn. Regression models and life-tables with discussion , Journal of the Royal Statistical Society B 34, pp.
Statistics in Medicine, Vol 15 , pp. A review of survival trees Statistics Surveys Vol. Terry Therneau. He observed that the Cox Portional Hazards Model fitted in that post did not properly account for the time varying covariates. This revised post makes use of a different data set, and points to resources for addressing time varying covariates.
Many thanks to Dr.
Any errors that remain are mine. You may leave a comment below or discuss the post in the forum community.
Load the data This first block of code loads the required packages, along with the veteran dataset from the survival package that contains data from a two-treatment, randomized trial for lung cancer. Kaplan Meier Analysis The first thing to do is to use Surv to build the standard survival object. The data sets are documented and sources acknowledged in Lesson 1. All the data sets are contained in a single zip file: dta. See section 7. Users with version 8. Covariates may include regressor variables summarizing observed differences between persons either fixed or time-varying , and variables summarizing the duration dependence of the hazard rate.
SUMMARY. We present a model and semiparametric estimation procedures for analyzis of survival data with cross- effects (CE) of survival functions. Biostatistics. Jul;5(3) Analysis of survival data with cross-effects of survival functions. Bagdonavicius V(1), Hafdi MA, Nikulin M. Author information.
With suitable definition of covariates, models with a fully non-parametric specification for duration dependence may be estimated; so too may parametric specifications. Your data must be suitably organised before using the model: see the help file after installation, the STB article, or Lesson 3. The program is used in Lesson 8. Note: the likelihood ratio test of whether the gamma variance is equal to zero that pgmhaz reports does not take account of the fact that the null distribution is not the usual chi-squared d.
See Gutierrez et al. In the meantime, note that the LR test statistic is correct, but the correct p-value for the test is half the reported p-value. The correct statistic is reported by pgmhaz8. Discrete time hazard models with Normally distributed unobserved heterogeneity rather than Gamma can be now estimated in Stata. Those kinds of repeated observations have nothing to do with panel data.
Panel data arises, for instance, when individuals are from different countries and it was believed that country affects survival. In that case, in a panel-data model, there would be a random effect or, if you prefer, an unobserved latent effect for each country. We can, however, write models in which the random effect occurs at the individual level if we have repeated failure events for them. Panel-data random effects are similar to frailty, a survival-analysis concept.
In frailty, related observations individuals are grouped and viewed as sharing a latent component. Stata allows for frailty; see the manual entries [ST] streg and [ST] stcox. Panel-data random effects are assumed to be normally distributed and that is a selling point of this model. Frailty is assumed to be gamma distributed, and that is mainly for computational rather than substantive reasons.
Panel-data's normal random effects are a more plausible assumption. They are equivalent to lognormal frailties, if you care. Panel-data normally distributed random effects are available only with the parametric survival estimators. Examples of survival outcomes in panel data are the number of years until a new recession occurs for a group of countries that belong to different regions, or weeks unemployed for individuals who might experience multiple unemployment episodes. We want to study the duration of job position for a group of people.
We have observations in our data, meaning roughly three job positions per person. In these data, the end of a job position could mean the end of employment, but usually it means moving to a new job, whether in the same firm or a new firm.
Our outcome is time to the "end" of a job variable tend , and variable failure indicates whether that time corresponds to censoring or the job position having ended. These are real data.
To use Stata's new xtstreg , we must first stset and xtset our data because xtstreg is both an st and xt command. We model the time to end of job position as being determined by highest level of education attained, whether college degree was attained, number of previous jobs or job positions, prestige of the job, and gender. We use a Weibull distribution for survival times. The number of previous jobs and the prestige of the current job both increase survival time in the current job or, said differently, reduce current job mobility.
In addition, women and those with higher levels of education are more mobile.
The variance of the random effect reported is 0. Also new to Stata 14 is mestreg , which will fit the same models as the new and just demonstrated xtstreg , and more besides. Among the additional features, mestreg will allow more than one nesting level. Another additional feature is that it will fit random intercepts and random coefficients.