@article{flexsurv,
  title        = "{flexsurv}: A Platform for Parametric Survival Modeling in {R}",
  author       = "Jackson, C.",
  journal      = "Journal of Statistical Software",
  year         = "2016",
  volume       = "70",
  number       = "8",
  pages        = "1--33",
  doi          = "10.18637/jss.v070.i08",
}
                  
@Manual{R,
  title = {\proglang{R}: A Language and Environment for Statistical Computing},
  author = {{\proglang{R} Core Team}},
  organization = {\proglang{R} Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2014},
  url = {http://www.R-project.org/},
}

@article{stgenreg,
  title={\pkg{stgenreg}: A \proglang{Stata} Package for General Parametric Survival Analysis},
  author={Crowther, M. J. and Lambert, P. C.},
  journal={Journal of Statistical Software},
  volume={53},
  pages={1--17},
  year={2013}
}

@article{reid:cox:conversation,
  title={A Conversation with Sir David Cox},
  author={Reid, N.},
  journal={Statistical Science},
  pages={439--455},
  volume={9},
  number={3},
  year={1994},
  publisher={JSTOR}
}

@article{latimer2013survival,
  title={Survival Analysis for Economic Evaluations Alongside Clinical Trials --- Extrapolation with Patient-Level Data, Inconsistencies, Limitations, and a Practical Guide},
  author={Latimer, N. R.},
  journal={Medical Decision Making},
  volume={33},
  number={6},
  pages={743--754},
  year={2013},
  publisher={SAGE Publications}
}

@Misc{therneau:survival,
  OPTkey = 	 {},
  author =	 {Therneau, T.},
  title =	 {A Package for Survival Analysis in \proglang{S}},
  howpublished = {\proglang{R} package version 2.37-7. \url{http://CRAN.R-project.org/package=survival}},
  OPTmonth = 	 {},
  year =	 {2014},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Book{kalbfleisch:prentice,
  author =	 {Kalbfleisch, J. D. and Prentice, R. L.},
  ALTeditor = 	 {},
  title = 	 {The Statistical Analysis of Failure Time Data},
  publisher = 	 {John Wiley \& Sons},
  year = 	 {2002},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  address =	 {New York},
  edition =	 {Second},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{polyhazard,
  author = 	 {Louzada-Neto, F.},
  title = 	 {Polyhazard Models for Lifetime Data},
  journal = 	 {Biometrics},
  year = 	 {1999},
  OPTkey = 	 {},
  volume =	 {55},
  pages =	 {1281-1285},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{prentice:loggamma,
  title={A Log Gamma Model and its Maximum Likelihood Estimation},
  author={Prentice, R. L.},
  journal={Biometrika},
  volume={61},
  number={3},
  pages={539-544},
  year={1974},
  publisher={Biometrika Trust}
}

@Article{prentice:genf,
  author = 	 {Prentice, R. L.},
  title = 	 {Discrimination Among Some Parametric Models},
  journal = 	 {Biometrika},
  year = 	 {1975},
  OPTkey = 	 {},
  volume =	 {62},
  number =	 {3},
  pages =	 {607--614},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{ccox:taxonomy:hazards,
  author = 	 {Cox, C. and Chu, H. and Schneider, M. F. and Muñoz, A.},
  title = 	 {Parametric Survival Analysis and Taxonomy of Hazard Functions for the Generalized Gamma Distribution},
  journal = 	 {Statistics in Medicine},
  year = 	 {2007}, 
  OPTkey = 	 {},
  volume =	 {26},
  OPTnumber = 	 {},
  pages =	 {4352-4374},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{ccox:genf,
  author = 	 {Cox, C.},
  title = 	 {The Generalized {F} Distribution: An Umbrella for Parametric Survival Analysis},
  journal = 	 {Statistics in Medicine},
  year = 	 {2008},
  OPTkey = 	 {},
  volume =	 {27},
  number =	 {21},
  pages =	 {4301-4312},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{stacy:gengamma,
  author = 	 {Stacy, E. W.},
  title = 	 {A Generalization of the Gamma Distribution.},
  journal = 	 {The Annals of Mathematical Statistics},
  year = 	 {1962},
  OPTkey = 	 {},
  volume =	 {33},
  number =	 {3},
  pages =	 {1187-92},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@book{nash,
  title={Compact Numerical Methods for Computers: Linear Algebra and Function Minimisation},
  author={Nash, J. C.},
  year={1990},
  publisher={CRC Press}
}

@Article{royston:parmar,
  author = 	 {Royston, P. and Parmar, M.},
  title = 	 {Flexible Parametric Proportional-Hazards and Proportional-Odds Models for Censored Survival Data, with Application to Prognostic Modelling and Estimation of Treatment Effects  },
  journal = 	 {Statistics in Medicine},
  year = 	 {2002},
  OPTkey = 	 {},
  volume =	 {21},
  number =	 {1},
  pages =	 {2175--2197},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{stpm:update,
  title={Flexible Parametric Alternatives to the Cox Model: Update},
  author={Royston, P.},
  journal={The \proglang{Stata} Journal},
  volume={4},
  number={1},
  pages={98--101},
  year={2004}
}

@article{stpm:orig,
  title={Flexible Parametric Alternatives to the Cox Model, and More},
  author={Royston, P.},
  journal={\proglang{Stata} Journal},
  volume={1},
  number={1},
  pages={1--28},
  year={2001}
}

@article{stpm2,
  title={Further Development of Flexible Parametric Models for Survival Analysis},
  author={Lambert, P. C. and Royston, P.},
  journal={\proglang{Stata} Journal},
  volume={9},
  number={2},
  pages={265},
  year={2009}
}

@Article{kalbfleisch:lawless,
  author = 	 {Kalbfleisch, J.D. and Lawless, J.F.},
  title = 	 {The Analysis of Panel Data under a {M}arkov Assumption},
  journal = 	 {Journal of the American Statistical Association},
  year = 	 {1985},
  OPTkey = 	 {},
  volume =	 {80},
  number =	 {392},
  pages =	 {863-871},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}


@Article{putter:mstate,
  author = 	 {Putter, H. and Fiocco, M. and Geskus, R. B.},
  title = 	 {Tutorial in Biostatistics: Competing Risks and Multi-State Models},
  journal = 	 {Statistics in Medicine},
  year = 	 {2007},
  OPTkey = 	 {},
  volume =	 {26},
  number =	 {8},
  pages =	 {2389-2430},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{mstate:cmpb,
  title={The \pkg{mstate} Package for Estimation and Prediction in Non-and Semi-Parametric Multi-State and Competing Risks Models},
  author={de Wreede, L.C. and Fiocco, M. and Putter, H.},
  journal={Computer Methods and Programs in Biomedicine},
  volume={99},
  number={3},
  pages={261--274},
  year={2010},
  publisher={Elsevier}
}

@article{mstate:jss,
  title={\pkg{mstate}: An \proglang{R} Package for the Analysis of Competing Risks and Multi-State Models},
  author={de Wreede, L. C. and Fiocco, M. and Putter, H.},
  journal={Journal of Statistical Software},
  volume={38},
  pages={1--30},
  year={2011}
}

@Manual{eha,
    title = {\pkg{eha}: Event History Analysis},
    author = {G{\"o}ran Brostr{\"o}m},
    year = {2014},
    note = {\proglang{R} package version 2.4-1},
    url = {http://CRAN.R-project.org/package=eha},
}

@article{yee:wild,
  title={Vector Generalized Additive Models},
  author={Yee, T. W. and Wild, C. J.},
  journal={Journal of the Royal Statistical Society B},
  volume={58},
  number={3},
  pages={481--493},
  year={1996},
  publisher={JSTOR}
}

@article{actudistns,
  title={A New \proglang{R} Package for Actuarial Survival Models},
  author={Nadarajah, S. and Bakar, S. A. A.},
  journal={Computational Statistics},
  volume={28},
  number={5},
  pages={2139--2160},
  year={2013},
  publisher={Springer-Verlag}
}

@article{sauerbrei1999building,
  title={Building Multivariable Prognostic and Diagnostic Models: Transformation of the Predictors by Using Fractional Polynomials},
  author={Sauerbrei, W. and Royston, P.},
  journal={Journal of the Royal Statistical Society A},
  volume={162},
  number={1},
  pages={71--94},
  year={1999},
  publisher={Wiley Online Library}
}

@article{royston1994regression,
  title={Regression Using Fractional Polynomials of Continuous Covariates: Parsimonious Parametric Modelling},
  author={Royston, P. and Altman, D. G.},
  journal={Journal of the Royal Statistical Society C},
  pages={429--467},
  volume={43},
  number={3},
  year={1994},
  publisher={JSTOR}
}

@article{sauerbrei2007selection,
  title={Selection of Important Variables and Determination of Functional Form for Continuous Predictors in Multivariable Model Building},
  author={Sauerbrei, Willi and Royston, Patrick and Binder, Harald},
  journal={Statistics in Medicine},
  volume={26},
  number={30},
  pages={5512--5528},
  year={2007},
  publisher={Wiley Online Library}
}

@Article{mueller:wang,
  author = 	 {Mueller, H. G. and Wang, J. L.},
  title = 	 {Hazard Rates Estimation Under Random Censoring with Varying Kernels and Bandwidths},
  journal = 	 {Biometrics},
  year = 	 {1994},
  OPTkey = 	 {},
  volume =	 {50},
  OPTnumber =	 {},
  pages =	 {61-76},
  month =	 {March},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

  @Manual{muhaz,
    title = {\pkg{muhaz}: Hazard Function Estimation in Survival Analysis},
    author = {Hess, K.},
    year = {2010},
    note = {\proglang{R} package version 1.2.5, \proglang{S} original by K. Hess and \proglang{R} port by R. Gentleman},
    url = {http://CRAN.R-project.org/package=muhaz},
  }

  @Article{actuar,
    title = {\pkg{actuar}: An \proglang{R} Package for Actuarial Science},
    author = {Dutang, C. and Goulet, V. and Pigeon, M.},
    journal = {Journal of Statistical Software},
    year = {2008},
    volume = {25},
    number = {7},
    pages = {38},
    url = {http://www.jstatsoft.org/v25/i07},
  }

@article{demiris2011survival,
  title={Survival Extrapolation Using the Poly-Weibull Model},
  author={Demiris, N. and Lunn, D. and Sharples, L.D.},
  journal={Statistical Methods in Medical Research},
  year={2011},
  note={early view, DOI: 10.1177/0962280211419645},
  publisher={SAGE Publications}
}


@Article{heng:paper,
  author = 	 {Heng, D. and Sharples, L. and McNeil, K. and Stewart, S. and Wreghitt, T. and Wallwork, J.},
  title = 	 {Bronchiolitis {O}bliterans {S}yndrome: Incidence, Natural History, Prognosis, and Risk Factors},
  journal = 	 {The Journal of Heart and Lung Transplantation},
  year = 	 {1998},
  OPTkey = 	 {},
  volume =	 {17},
  number =	 {12},
  pages =	 {1255-1263},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{titman:nonhomog,
  title={Flexible Nonhomogeneous Markov Models for Panel Observed Data},
  author={Titman, A. C},
  journal={Biometrics},
  volume={67},
  number={3},
  pages={780--787},
  year={2011},
  publisher={Wiley Online Library}
}

@article{cook:lawless,
  title={Statistical Issues in Modeling Chronic Disease in Cohort Studies},
  author={Cook, R. J. and Lawless, J. F.},
  journal={Statistics in Biosciences},
  volume={6},
  number={1},
  pages={127--161},
  year={2014},
  publisher={Springer-Verlag}
}

@manual{stan-manual:2014,
  author = {\proglang{Stan} Development Team},
  year = {2014},
  title = {\proglang{Stan} Modeling Language Users Guide and Reference Manual,
           Version 2.4},
  url = {http://mc-stan.org/}
}

@book{bugs:book,
  title={The \proglang{BUGS} Book: A Practical Introduction to Bayesian Analysis},
  author={Lunn, D. and Jackson, C. and Best, N. and Thomas, A. and Spiegelhalter, D.},
  year={2012},
  publisher={CRC Press}
}

@article{crowther2014multilevel,
  title={Multilevel Mixed Effects Parametric Survival Models Using Adaptive Gauss--Hermite Quadrature With Application to Recurrent Events and Individual Participant Data Meta-Analysis},
  author={Crowther, M. J. and Look, M. P. and Riley, R. D.},
  journal={Statistics In Medicine},
  volume={33},
  number={22},
  year={2014},
  pages={3844-3858},
  publisher={Wiley Online Library}
}

@article{hougaard1995frailty,
  title={Frailty Models for Survival Data},
  author={Hougaard, P.},
  journal={Lifetime Data Analysis},
  volume={1},
  number={3},
  pages={255--273},
  year={1995},
  publisher={Springer-Verlag}
}

@article{royston:lambert:book,
  title={Flexible Parametric Survival Analysis Using \proglang{Stata}: Beyond the Cox Model},
  author={Royston, P. and Lambert, P. C.},
  journal={\proglang{Stata} Press books},
  year={2011},
  publisher={Statacorp Lp}
}

@article{nelson:relative:survival,
  title={Flexible Parametric Models for Relative Survival, With Application in Coronary Heart Disease},
  author={Nelson, C. P. and Lambert, P. C. and Squire, I. B. and Jones, D. R.},
  journal={Statistics in Medicine},
  volume={26},
  number={30},
  pages={5486--5498},
  year={2007},
  publisher={Wiley Online Library}
}

  @Article{gamlss,
    title = {Generalized Additive Models for Location, Scale and Shape (with discussion)},
    journal = {Journal of the Royal Statistical Society C},
    volume = {54},
    number = {3},
    pages = {507-554},
    year = {2005},
    author = {Rigby, R. A.  and Stasinopoulos, D. M.},
  }

@Article{msmjss,
  author = 	 {Jackson, C. H.},
  title = 	 {Multi-State Models for Panel Data: The \pkg{msm} Package for \proglang{R}},
  journal = 	 {Journal of Statistical Software},
  year = 	 {2011},
  OPTkey = 	 {},
  volume =	 {38},
  number =	 {8},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Book{cox:miller,
  author = 	 {Cox, D. R. and Miller, H. D.},
  ALTeditor = 	 {},
  title = 	 {The Theory of Stochastic Processes},
  publisher = 	 {Chapman and Hall},
  year = 	 {1965},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@book{aalen:process,
  title={Survival and Event History Analysis: A Process Point of View},
  author={Aalen, Odd and Borgan, Ornulf and Gjessing, Hakon},
  year={2008},
  publisher={Springer-Verlag}
}

@Book{andersen,
  author =	 {Andersen, P. K. and Borgan, O. and Gill, R. D. and Keiding, N.},
  ALTeditor = 	 {},
  title = 	 {Statistical Models Based On Counting Processes},
  publisher = 	 {Springer-Verlag},
  year = 	 {1993},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{fiocco:mstatepred,
  title={Reduced-rank Proportional Hazards Regression and Simulation-Based Prediction for Multi-State Models},
  author={Fiocco, Marta and Putter, Hein and van Houwelingen, Hans C},
  journal={Statistics in Medicine},
  volume={27},
  number={21},
  pages={4340--4358},
  year={2008},
  publisher={Wiley Online Library}
}

@article{mandel:simci,
  title={Simulation-Based Confidence Intervals for Functions with Complicated Derivatives},
  author={Mandel, Micha},
  journal={The American Statistician},
  volume={67},
  number={2},
  pages={76--81},
  year={2013},
  publisher={Taylor \& Francis}
}

  @Article{deSolve,
    title = {Solving Differential Equations in \proglang{R}: Package \pkg{deSolve}},
    author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
    journal = {Journal of Statistical Software},
    volume = {33},
    number = {9},
    pages = {1--25},
    year = {2010},
    coden = {JSSOBK},
    issn = {1548-7660},
    url = {http://www.jstatsoft.org/v33/i09},
    keywords = {ordinary differential equations, partial differential
    equations, differential algebraic equations, initial value problems,
    R, FORTRAN, C},
  }  

@Article{crowther:general,
  author = 	 {Crowther, M. J. and Lambert, P. C.},
  title = 	 {A General Framework for Parametric Survival Analysis},
  journal = 	 {Statistics in Medicine},
  year = 	 {2014},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  note =	 {early view, DOI: 10.1002/sim.6300},
  OPTannote = 	 {}
}

@article{andersen:keiding,
  title={Multi-state models for event history analysis},
  author={Andersen, P. K. and Keiding, N.},
  journal={Statistical Methods in Medical Research},
  volume={11},
  number={2},
  pages={91--115},
  year={2002},
  publisher={SAGE Publications}
}

@Manual{TH.data,
  title = {TH.data: TH's Data Archive},
  author = {Torsten Hothorn},
  year = {2015},
  note = {R package version 1.0-6},
  url = {http://CRAN.R-project.org/package=TH.data},
}

@Article{francesca:smmr,
  author = 	 {Ieva, F. and Jackson, C. H. and Sharples, L. D.},
  title = 	 {Multi-State modelling of repeated hospitalisation and death in patients with Heart Failure: the use of large administrative databases in clinical epidemiology},
  journal={Statistical Methods in Medical Research},
  year = 	 {2015},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  note =	 {Early view},
  OPTannote = 	 {}
}

@Article{survextrap:tatiana,
  author = 	 {Benaglia, T. and Jackson, C. H. and Sharples, L. D.},
  title = 	 {Survival Extrapolation in the Presence of Cause Specific Hazards},
  journal = 	 {Statistics in Medicine},
  year = 	 {2014},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  note =	 {In press.},
  OPTannote = 	 {}
}

@article{larson1985mixture,
  title={A mixture model for the regression analysis of competing risks data},
  author={Larson, M. G. and Dinse, G. E.},
  journal={Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  volume={34},
  number={3},
  pages={201--211},
  year={1985},
  annote = {} , 
  publisher={Wiley Online Library}
}


@article{cox1959analysis,
  title={The analysis of exponentially distributed life-times with two types of failure},
  author={Cox, D. R.},
  journal={Journal of the Royal Statistical Society: Series B (Methodological)},
  volume={21},
  number={2},
  pages={411--421},
  year={1959},
  publisher={Wiley Online Library}
}


@article{aalen:johansen,
  title={An empirical transition matrix for non-homogeneous Markov chains based on censored observations},
  author={Aalen, O. O. and Johansen, S.},
  journal={Scandinavian Journal of Statistics},
  pages={141--150},
  year={1978},
  publisher={JSTOR}
}


@article{lambert2017flexible,
  title={Flexible parametric modelling of the cause-specific cumulative incidence function},
  author={Lambert, P. C. and Wilkes, S. R. and Crowther, M. J.},
  journal={Statistics in Medicine},
  volume={36},
  number={9},
  pages={1429--1446},
  year={2017},
  publisher={Wiley Online Library}
}

@article{fine1999proportional,
  title={A proportional hazards model for the subdistribution of a competing risk},
  author={Fine, J. P. and Gray, R. J.},
  journal={Journal of the American Statistical Association},
  volume={94},
  number={446},
  pages={496--509},
  year={1999},
  publisher={Taylor \& Francis}
}


@article{nicolaie2010vertical,
  title={Vertical modeling: a pattern mixture approach for competing risks modeling},
  author={Nicolaie, M. A. and van Houwelingen, H. C. and Putter, H.},
  journal={Statistics in Medicine},
  volume={29},
  number={11},
  pages={1190--1205},
  year={2010},
  publisher={Wiley Online Library}
}