Bibliography

Sources for the models implemented in gen_surv.

Foundational papers

Cox (1972) Cox, D. R. (1972). Regression Models and Life-Tables. Journal of the Royal Statistical Society: Series B, 34(2), 187–220. → Cox proportional hazards

Kaplan and Meier (1958) Kaplan, E. L., & Meier, P. (1958). Nonparametric Estimation from Incomplete Observations. Journal of the American Statistical Association, 53(282), 457–481. → the estimator behind plot_survival_curve

Farewell (1982) Farewell, V. T. (1982). The Use of Mixture Models for the Analysis of Survival Data with Long-Term Survivors. Biometrics, 38(4), 1041–1046. → Mixture cure

Fine and Gray (1999) Fine, J. P., & Gray, R. J. (1999). A Proportional Hazards Model for the Subdistribution of a Competing Risk. Journal of the American Statistical Association, 94(446), 496–509. → Competing risks, and why subdistribution coefficients differ from the cause-specific ones

Books

Andersen, Borgan, Gill and Keiding (1993) Statistical Models Based on Counting Processes. Springer. → the counting-process formulation used by CMM

Fleming and Harrington (1991) Counting Processes and Survival Analysis. Wiley.

Kalbfleisch and Prentice (2002) The Statistical Analysis of Failure Time Data. Wiley. → AFT parameterisations, competing risks

Klein and Moeschberger (2003) Survival Analysis: Techniques for Censored and Truncated Data. Springer. → censoring mechanisms

Therneau and Grambsch (2000) Modeling Survival Data: Extending the Cox Model. Springer. → time-dependent covariates and the (start, stop] layout

Cook and Lawless (2007) The Statistical Analysis of Recurrent Events. Springer.

Collett (2015) Modelling Survival Data in Medical Research. CRC Press.

Kleinbaum and Klein (2012) Survival Analysis: A Self-Learning Text. Springer. → a gentler entry point than the others

Zucchini, MacDonald and Langrock (2017) Hidden Markov Models for Time Series. Chapman and Hall/CRC. → background on Markov chains; note that THMM is an observed-state model, not a hidden one

Software

genSurv (R) cran.r-project.org/package=genSurv — the package gen_surv is a port of. genCMM and genTHMM are the origin of the two illness-death layouts.

lifelines lifelines.readthedocs.io — Kaplan-Meier, Cox and AFT fitting; a hard dependency here.

scikit-survival scikit-survival.readthedocs.io — machine-learning survival models; optional, see Interoperability.