

@article{Sewak_Hothorn_2023,
  author = {Ainesh Sewak and Torsten Hothorn},
  title = {Estimating Transformations for Evaluating 
           Diagnostic Tests with Covariate Adjustment},
  year = 2023,
  journal = {Statistical Methods in Medical Research},
  doi = {10.1177/09622802231176030},
  volume = 32,
  number = 7,
  pages = {1403--1419}
}


@article{Barbanti_Hothorn_2023,
  author = {Luisa Barbanti and Torsten Hothorn},
  title = {A Transformation Perspective on Marginal and Conditional Models},
  year = 2024,
  page = {kxac048},
  journal = {Biostatistics},
  volume = 25, 
  number = 2, 
  pages = {402--428},
  doi = {10.1093/biostatistics/kxac048},
}

@manual{Barbanti_Hothorn_mtram, 
author =  {Luisa Barbanti and Torsten Hothorn}, 
title = {Some Applications of Marginally Interpretable Linear Transformation
  Models for Clustered Observations},
note = {\proglang{R}~package vignette, version~1.3-0},
year = {2025}, 
url = {https://doi.org/10.32614/CRAN.package.tram}
}

@article{Siegfried_Kook_Hothorn_2023,
  author = {Sandra Siegfried and Lucas Kook and Torsten Hothorn},
  title = {Distribution-Free Location-Scale Regression},
  journal = {The American Statistician},
  volume = {77},
  number = {4},
  pages = {345--356},
  year  = {2023},
  publisher = {Taylor & Francis},
  doi = {10.1080/00031305.2023.2203177},
}

@article{Tamasi_Crowther_Puhan_2022,
  author = {B{\'a}lint Tam{\'a}si and Michael Crowther and Milo Alan Puhan and
            Ewout Steyerberg and Torsten Hothorn},
  title = {Individual Participant Data Meta-Analysis with 
           Mixed-Effects Transformation Models},
  journal = {Biostatistics},
  volume = 23,
  number = 4,
  pages = {1083--1098},
  year = 2022,
  doi = {10.1093/biostatistics/kxab045}
}

@manual{Tamasi_Hothorn_2023, 
  author =  {B{\'a}lint Tam{\'a}si and Torsten Hothorn}, 
  title = {Flexible Regression for Correlated and Censored Ecological Data with
Mixed-Effects Additive Transformation Models},
  note = {\proglang{R}~package vignette, version~1.0.5},
  year = {2023}, 
  url = {https://CRAN.R-project.org/web/packages/tramME/vignettes/mixed-effects-additive-models.pdf},
  }
  
  @article{Klein_Hothorn_Barbanti_2020,
  author = {Nadja Klein and Torsten Hothorn and Luisa Barbanti 
            and Thomas Kneib},
  title = {Multivariate Conditional Transformation Models},
  journal = {Scandinavian Journal of Statistics},
  year = 2022,
  volume = 49,
  pages = {116--142},
  doi = {10.1111/sjos.12501}
}

@article{Siegfried_Bopp_Guenthard_2021,
  author = {Sandra Siegfried and Matthias Bopp and Huldrych F. G\"unthard
            and Olivia Keiser and Caroline E. Weibull and Michael J. Crowther 
            and Torsten Hothorn},
  title = {Assessing Relative {COVID-19} Mortality During the 
           Second Wave: A Prospective Swiss Population-based Study},
  year = 2021,
  journal = {BMJ Open},
  volume = {11},
  number = {10},
  pages = {e051164},
  doi = {10.1136/bmjopen-2021-051164}
}

@article{Tamasi_Hothorn_2021,
  author = {B{\'a}lint Tam{\'a}si and Torsten Hothorn},
  title = {\textbf{tramME}: Mixed-Effects Transformation Models Using
           Template Model Builder},
  year = 2021,
  volume = 13,
  number = 1,
  pages = {581--594},
  journal = {The \proglang{R}~Journal},
  doi = {10.32614/RJ-2021-075}
}

@article{Tamasi_2025,
  author = {B{\'a}lint Tam{\'a}si},
  doi={10.18637/jss.v114.i11},
  title = {Mixed-Effects Additive Transformation Models with the \textsf{R} Package \textbf{tramME}},
  journal = {Journal of Statistical Software},
  volume = {114},
  number = {11},
  year = {2025}
}

@article{Kook_Hothorn_2021,
  author = {Lucas Kook and Torsten Hothorn},
  title = {Regularized Transformation Models: The \textbf{tramnet} Package},
  year = {2021},
  journal = {The \proglang{R}~Journal},
  doi = {10.32614/RJ-2021-054},
  pages = {581--594},
  volume = {13},
  number = {1},
}

@article{Yuqi_Hothorn_Li_2020,
author = {Tian, Yuqi and Hothorn, Torsten and Li, Chun and Harrell Jr., Frank E. and Shepherd, Bryan E.},
title = {An Empirical Comparison of Two Novel Transformation Models},
journal = {Statistics in Medicine},
volume = {39},
number = {5},
pages = {562--576},
doi = {10.1002/sim.8425},
year = {2020}
}

@Article{	  matic_radoicic_2018,
  author	= {Ivan Mati{\'c} and Rado{\^s} Radoi{\^c}i{\'c} and Dan
		  Stefanica},
  title		= {A Sharp P{\'o}lya-Based Approximation to the Normal CDF},
  year		= 2018,
  journal	= {Applied Mathematics and Computation},
  volume	= 322,
  pages		= {111--122},
  doi           = {10.2139/ssrn.2842681}
}

@Article{	  heiss_winschel_2008,
  author	= {Florian Heiss and Viktor Winschel},
  title		= {Likelihood Approximation by Numerical Integration on
		  Sparse Grids},
  journal	= {Journal of Econometrics},
  volume	= 144,
  number	= 1,
  year		= 2008,
  pages		= {62--80},
  doi		= {10.1016/j.jeconom.2007.12.004}
}

@Article{	  pkg:lme4,
  title		= {Fitting Linear Mixed-Effects Models Using {lme4}},
  author	= {Douglas Bates and Martin M{\"a}chler and Ben Bolker and
		  Steve Walker},
  journal	= {Journal of Statistical Software},
  year		= {2015},
  volume	= {67},
  number	= {1},
  pages		= {1--48},
  doi		= {10.18637/jss.v067.i01}
}

@Article{         Pollet2009,
  author        = {Thomas V. Pollet and Daniel Nettle},
  title         = {Partner Wealth Predicts Self-Reported Orgasm Frequency in a Sample of Chinese Women},
  journal       = {Evolution and Human Behavior},
  year          = 2009,
  volume        = 30,  
  pages         = {146--151}
}

@Article{	  herberich+hothorn+nettle+pollet2010,
  author	= {Esther Herberich and Torsten Hothorn and Daniel Nettle and
		  Thomas V. Pollet},
  title		= {A Re-evaluation of the Statistical Model in {Pollet and
		  Nettle 2009}},
  journal	= {Evolution and Human Behavior},
  year		= 2010,
  volume	= {31},
  number	= 2,
  pages		= {150--151},
  code		= {http://cran.r-project.org/web/packages/multcomp/vignettes/chfls1.pdf}
}

@Article{	  backer_vroey_1998,
  author	= {M. D. Backer and C. D. Vroey and E. Lesaffre and I. Scheys
		  and P. D. Keyser},
  title		= {Twelve Weeks of Continuous Oral Therapy for Toenail
		  Onychomycosis Caused by Dermatophytes: A Double-blind
		  Comparative Trial of Terbinafine 250 mg/day versus
		  Itraconazole 200 mg/day},
  journal	= {Journal of the American Academy of Dermatology},
  year		= 1998,
  volume	= 38,
  number	= {5(2)},
  pages		= {S57--S63},
  doi		= {10.1016/S0190-9622(98)70486-4}
}

@Article{	  chow_heller_2006,
  author	= {Roberta T. Chow and Gillian Z. Heller and Les Barnsley},
  title		= {The Effect of 300 {mW}, 830 nm Laser on Chronic Neck Pain:
		  A Double-blind, Randomized, Placebo-controlled Study},
  journal	= {Pain},
  year		= 2006,
  volume	= 124,
  number	= {1--2},
  pages		= {201--210},
  doi		= {10.1016/j.pain.2006.05.018}
}

@Article{	  ogden_2015,
  author	= {Helen E. Ogden},
  title		= {A Sequential Reduction Method for Inference in Generalized
		  Linear Mixed Models},
  journal	= {Electronic Journal of Statistics},
  year		= 2015,
  volume	= 9,
  pages		= {135--152},
  doi		= {10.1214/15-EJS991}
}

@Article{	  belenky_wesensten_thorne_2003,
  author	= {Gregory Belenky and Nancy J. Wesensten and David R. Thorne
		  and Maria L. Thomas and Helen C. Sing and Daniel P. Redmond
		  and Michael B. Russo and Thomas J. Balkin},
  year		= 2003,
  title		= {Patterns of Performance Degradation and Restoration During
		  Sleep Restriction and Subsequent Recovery: {A} Sleep
		  Dose-response Study},
  journal	= {Journal of Sleep Research},
  volume	= 12,
  pages		= {1--12},
  doi		= {10.1046/j.1365-2869.2003.00337.x}
}

@Article{	  Manuguerra_Heller_2010,
  author	= {Maurizio Manuguerra and Gillian Z. Heller},
  title		= {Ordinal Regression Models for Continuous Scales},
  journal	= {International Journal of Biostatistics},
  year		= 2010,
  volume	= 6,
  number	= 1,
  pages		= 14,
  doi		= {10.2202/1557-4679.1230}
}

@Article{	  Box_Cox_1964,
  author	= {G. E. P. Box and D. R. Cox},
  title		= {An Analysis of Transformations},
  volume	= {26},
  number	= {2},
  pages		= {211--252},
  year		= {1964},
  journal	= {Journal of the Royal Statistical Society Series~B: Statistical Methodology},
  doi = {10.1111/j.2517-6161.1964.tb00553.x}
}

@article{Tukey_1957,
author = {John W. Tukey},
title = {On the Comparative Anatomy of Transformations},
volume = {28},
journal = {The Annals of Mathematical Statistics},
number = {3},
publisher = {Institute of Mathematical Statistics},
pages = {602--632},
year = {1957},
doi = {10.1214/aoms/1177706875},
}


@Article{Hothorn_Zeileis_2017,
author = {Torsten Hothorn and Achim Zeileis},
title = {Predictive Distribution Modeling Using Transformation Forests},
journal = {Journal of Computational and Graphical Statistics},
volume = {30},
number = {4},
pages = {1181--1196},
year  = {2021},
publisher = {Taylor & Francis},
doi = {10.1080/10618600.2021.1872581},
}

@article{Lohse_Rohrmann_Faeh_2017,
  author = {Tina Lohse and Sabine Rohrmann and David Faeh and Torsten Hothorn},
  title = {Continuous Outcome Logistic Regression for Analyzing 
           Body Mass Index Distributions},
  journal = {F1000Research},
  year = 2017, 
  volume = 6,
  pages = {1933},
  doi = {10.12688/f1000research.12934.1}
}

@article{Korepanova_Seibold_Steffen_2019,
  author = {Natalia Korepanova and  Heidi Seibold and 
            Verena Steffen and Torsten Hothorn},
  title = {Survival Forests under Test: Impact of the 
           Proportional Hazards Assumption on
           Prognostic and Predictive Forests for {ALS} Survival},
  journal = {Statistical Methods in Medical Research},
  volume = {29},
  number = {5},
  pages = {1403--1419},
  year = {2020},
  doi = {10.1177/0962280219862586},
}


@article{Hothorn_2020,
  author = {Torsten Hothorn},
  title = {Transformation Boosting Machines},
  year = 2020,
  journal = {Statistics and Computing},
  volume = {30},
  pages = {141--152},
  doi = {10.1007/s11222-019-09870-4}
}

@article{Hothorn_2018_SM,
  author = {Torsten Hothorn},
  title = {Top-Down Transformation Choice},
  year = 2018,
  journal = {Statistical Modelling},
  volume = 18,
  number = {3--4},
  pages = {274--298},
  doi = {10.1177/1471082X17748081}
}

@article{Hothorn_2018,
  author = {Torsten Hothorn},
  title = {Most Likely Transformations: The \pkg{mlt} Package},
  journal = {Journal of Statistical Software},
  year = {2018},
  volume = {92},
  number = {1},
  pages = {1--68},
  doi = {10.18637/jss.v092.i01},
}

@article{Seibold_Zeileis_Hothorn_2017,
  author = {Heidi Seibold and Achim Zeileis and Torsten Hothorn},
  title = {Individual Treatment Effect Prediction for {A}myotrophic {L}ateral
           {S}clerosis Patients},
  journal = {Statistical Methods in Medical Research},
  year = {2018},
  volume = 27,
  number = 10, 
  pages = {3104--3125},
  doi = {10.1177/0962280217693034}
}

@article{Seibold_Zeileis_Hothorn_2015,
  author = {Heidi Seibold and Achim Zeileis and Torsten Hothorn},
  title = {Model-Based Recursive Partitioning for Subgroup Analyses},
  journal = {International Journal of Biostatistics},
  year = 2016,
  doi = {10.1515/ijb-2015-0032},
  volume = 12,
  number = 1,
  pages = {45--63}
}

@Article{         Currie_Durban_Eilers_2006,
  author        = {I. D. Currie and M. Durban and P. H. C. Eilers},
  title         = {Generalized Linear Array Models With Applications to
                  Multidimensional Smoothing},
  year          = {2006},
  journal       = {Journal of the Royal Statistical Society B},
  volume        = {68},
  number        = {2}, 
  pages         = {259--280},
  doi           = {10.1111/j.1467-9868.2006.00543.x}
}

@book{vdGeer_2000,
  title = {Empirical Processes in M-Estimation},
  author = {Sarah van de Geer},
  year = 2000,
  publisher = {Cambridge University Press},
  address = {Cambridge, UK}
}

@book{vdVaart_1998,
  title = {Asymptotic Statistics},
  author = {Aart W. van der Vaart},
  year = 1998,
  publisher = {Cambridge University Press},
  address = {Cambridge, UK}
}

@book{Fraser_1968,
  title = {The Structure of Inference},
  author = {Donald A. S. Fraser},
  year = {1968},
  publisher = {John Wiley \& Sons},
  address = {New York, U.S.A.}
}

@article{Pitman_1939,
  title = {The Estimation of the Location and Scale Parameters
           of a Continuous Population of Any Given Form},
  author = {Edwin James George Pitman},
  journal = {Biometrika},
  volume = 30,
  number = {3/4},
  year = 1939,
  pages = {391--421}
}

@article{Fisher_1934,
  title = {Two New Properties of Mathematical Likelihood},
  author = {Ronald Aylmer Fisher},
  year = 1934,
  journal = {Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character},
  volume = 53,
  pages = {285--306}
}

@book{Lindsey_1996,
  title = {Parametric Statistical Inference},
  author = {Jim K. Lindsey},
  year = 1996,
  publisher = {Clarendon Press},
  address = {Oxford, UK}
}

@book{Tutz_2012,
  author = {Gerhard Tutz},
  year = 2012,
  title = {Regression for Categorical Data},
  publisher = {Cambridge University Press},
  address = {New York, U.S.A.},
}

@article{Hothorn_Kneib_Buehlmann_2014,
  author = {Torsten Hothorn and Thomas Kneib and Peter B{\"u}hlmann},
  title = {Conditional Transformation Models},
  journal = {Journal of the Royal Statistical Society Series~B: Statistical Methodology},
  year = {2014},
  volume = 76,
  number = 1,   
  doi = {10.1111/rssb.12017},
  pages = {3--27},
  code = {http://R-forge.R-project.org/projects/ctm},
  data = {http://R-forge.R-project.org/projects/ctm}
}

@Article{         Hayfield_Racine_2008,
  author        = {Tristen Hayfield and Jeffrey S. Racine},
  title         = {Nonparametric Econometrics: The np Package},
  journal       = {Journal of Statistical Software},
  volume        = {27},
  number        = {5},
  pages         = {1--32},
  day           = {29},
  month         = {7},
  year          = {2008},
  url           = {http://www.jstatsoft.org/v27/i05}
}

 
@Article{         Mayr_Fenske_Hofner_2012,  
  author        = {Andreas Mayr and Nora Fenske and Benjamin Hofner and
                  Thomas Kneib and Matthias Schmid},
  year          = 2012,
  title         = {{GAMLSS} for High-dimensional Data--{A} Flexible Approach
                  Based on Boosting},
  journal       = {Journal of the Royal Statistical Society: Series C
                  (Applied Statistics)},
  volume        = 61,
  number        = 3,
  pages         = {403--427},
  doi           = {10.1111/j.1467-9876.2011.01033.x}
}

@article{gbsg2:1994,
   author    = {M. Schumacher and G. Basert and H. Bojar and K. H\"ubner and
M. Olschewski and W. Sauerbrei and C. Schmoor and C. Beyerle and R. L. A.
Neumann and {Rauschecker, H. F., for the German Breast Cancer Study Group}},
   title     = {Randomized $2\times2$ Trial Evaluating Hormonal Treatment
and the Duration of Chemotherapy in Node-positive Breast Cancer Patients},
   journal   = {Journal of Clinical Oncology},
   year      = {1994},
   volume    = {12},
   pages     = {2086-2093}
}


@article{Hyndman_Yao_2002,
  author = {Rob J. Hyndman and Qiwei Yao},
  title = {Nonparametric Estimation and Symmetry Tests for Conditional Density Functions},
  year = {2002},
  journal = {Journal of Nonparametric Statistics},
  volume = {14},
  number = {3},
  DOI = {10.1080/10485250212374},
  pages = {259--278}
}

@article{Azzalini_Bowman_1990,
  author = {A. Azzalini and A. W. Bowman},
  title = {A Look at Some Data on the Old Faithful Geyser},
  year = {1990},
  journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  volume = {39},
  number = {3},
  DOI = {10.2307/2347385},
  pages = {357--365}
}

@Article{Fredriks_Buuren_Burgmeijer_2000,
  author        = {A. M. Fredriks and S. van Buuren and R. J. F. Burgmeijer
                  and J. F. Meulmeester and R. J. Beuker and E. Brugman and
                  M. J. Roede and S. P. Verloove-Vanhorick and J. Wit},
  title         = {Continuing Positive Secular Growth Change in {The}
                  {Netherlands} 1955--1997},
  year          = {2000},
  journal       = {Pediatric Research},
  volume        = {47},
  number        = {3},
  pages         = {316--323}
}

@Article{         Stasinopoulos_Rigby_2007,
  author        = {D. Mikis Stasinopoulos and Robert A. Rigby},
  title         = {Generalized Additive Models for Location Scale and Shape
                  {(GAMLSS)} in {R}},
  year          = {2007},
  journal       = {Journal of Statistical Software},
  volume        = {23},
  number        = {7},
  pages         = {1--46},
  url           = {http://www.jstatsoft.org/v23/i07}
}

@Article{Mueller_Hothorn_2004,
   author    = {J{\"o}rg M{\"u}ller and Torsten Hothorn},
   title     = {Maximally Selected Two-Sample Statistics as a New Tool for
                the Identification and Assessment of Habitat Factors with
                an Application to Breeding Bird Communities in Oak Forests},
   year      = {2004}, 
   volume = 123,
   journal   = {European Journal of Forest Research},
   pages = {218--228},
   DOI = {10.1007/s10342-004-0035-5},
}

@book{Klein_Moeschberger_2003,
  author = {John P. Klein and Melvin K. Moeschberger},
  title = {Survival Analysis. Techniques for Censored and Truncated Data.},
  year = {2003},
  edition = {2nd},
  publisher = {Springer-Verlag},
  address = {New York, U.S.A.}
}

%VIP %LTM %spezi %splines %pen_lik
% NEW iterative optimisation algorithm: combination of Newton's method and an
% iterative multiplicative algorithm
@article{Maetal_2014,
  title = {On the Maximum Penalized Likelihood Approach for 
           Proportional Hazard Models with Right Censored Survival Data},
  journal = {Computational Statistics \& Data Analysis},
  volume = {74},
  pages = {142--156},
  year = {2014},
  doi = {10.1016/j.csda.2014.01.005},
  author = {J. Ma and S. Heritier and S. N. L\^{o}}
}



%VIP %LTM %flex_int_y %spezi %full_lik %splines
% note: right-censored log-likelihood is parametrised in terms of the hazard function
% => hazard function needs to be (numerically) integrated / computational disadvantage 
@article {CrowtherLambert_2014,
  author = {M. J. Crowther and P. C. Lambert},
  title = {A General Framework for Parametric Survival Analysis},
  journal = {Statistics in Medicine},
  volume = 33,
  number = 30,
  pages = {5280--5297},
  doi = {10.1002/sim.6300},
  year = {2014}
}


%VIP %flex_int %spezi %full_lik %splines
% Note: Parametrisations for conditional and unconditional log-hazard functions.
% PH models, PH models with time-varying effects, nonparametric PH models are included.
@article{Kooperbergetal_1995,
  title = {Hazard Regression},
  author = {Kooperberg, Charles and Stone, Charles J. and Truong, Young K.},
  journal = {Journal of the American Statistical Association},
  volume = {90},
  number = {429},
  pages = {78--94},
  year = {1995}
}

%optional %flex_int %spezi %full_lik %splines
% Note: Extension of Kooperberg et al. (1995) to interval-censored data and 
%       time-dependent covariates.
%       Modified Newton-Raphson algorithm because the log-likelihood is not 
%       necessarily concave for interval-censored data.
@article{KooperbergClarkson_1997,
  title = {Hazard Regression with Interval-Censored Data},
  author = {Kooperberg, Charles and Clarkson, Douglas B.},
  journal = {Biometrics},
  volume = {53},
  number = {4},
  pages = {1485--1494},
  year = {1997}
}


%LTM %spezi %full_lik %splines
% Note: Baseline-hazard function is approximated with quadratic splines.
@article{Etezadi-Amoli_Ciampi_1987,
  title = {Extended Hazard Regression for Censored Survival Data with 
           Covariates: A Spline Approximation for the Baseline Hazard Function},
  author = {Etezadi-Amoli, Jamshid and Ciampi, Antonio},
  journal = {Biometrics},
  volume = {43},
  number = {1},
  pages = {181--192},
  year = {1987}
}


%hazard_est %spezi %pen_lik %splines
% Note: Hazard function is parametrised in M-splines; I-splines are corresponding
%       splines for the cumulative hazard function; identical basis coefficients.
%       Approach can be extended to include covariate information.
%       Interval censored and interval truncated observations are considered.
@article{Jolyetal_1998,
  title = {A Penalized Likelihood Approach for Arbitrarily Censored 
           and Truncated Data: Application to Age-Specific Incidence of Dementia},
  author = {Joly, Pierre and Commenges, Daniel and Letenneur, Luc},
  journal = {Biometrics},
  volume = {54},
  number = {1},
  pages = {185--194},
  year = {1998}
}


%hazard_est %spezi %pen_lik %splines %optional
% Note: sqrt(lambda(y)) is parametrised; roughness penalty is considered.
%       General spline function that minimises the penalised log-likelihood
%       can be determined (similar principal as for natural cubic splines???)
@article{Senthil_1992,
  title = {Nonparametric Estimation of Hazard Function from Left 
           Truncated and Right Censored Data},
  author = {Selvan A. Senthil},
  journal = {Journal of Nonparametric Statistics},
  volume = {2},
  number = {1},
  pages = {29--35},
  year = {1992},
  doi = {10.1080/10485259208832540}
}


%hazard_est %spezi %pen_lik %splines %optional
% Note: estimation of an unconditional log-hazard function or log-density.
@article{Osullivan_1988,
  title = {Fast Computation of Fully Automated Log-Density and Log-Hazard Estimators},
  author = {Finbarr O'Sullivan},
  journal = {SIAM Journal on Scientific and Statistical Computing},
  volume = {9},
  number = {2},
  pages = {363--379},
  year = {1988}
}

%LTM %spezi %full_lik %splines 
% Note: baseline function has density with mild smoothness conditions; 
%       density is parametrised by a truncated series expantion with fixed degree of
%       truncation; adaptive choice of degree of truncation;
%       Given examples only include LTMs, but AFT-extensions to heteroscedastic errors
%       and time-dependent covariates are given in the appendix.
@article{ZhangDavidian_2008,
  author = {Zhang, Min and Davidian, Marie},
  title = {''Smooth'' Semiparametric Regression Analysis for 
           Arbitrarily Censored Time-to-Event Data},
  journal = {Biometrics},
  volume = {64},
  number = {2},
  doi = {10.1111/j.1541-0420.2007.00928.x},
  pages = {567--576},
  year = {2008}
}


%optional %LTM $spezi %full_lik %splines (= parametric transformation) %bayes
% Note: Transform both sides model is more restrictive than LTMs because both sides of
%       the model equation are transformed in terms of the same function g_lambda!
%       Extension of Box-Cox power family.
@article{Polpoetal_2014,
  title = {Transform Both Sides Model: A Parametric Approach},
  journal = {Computational Statistics \& Data Analysis},
  volume = {71},
  pages = {903--913},
  year = {2014},
  doi = {10.1016/j.csda.2013.07.023},
  author = {A. Polpo and C. P. {de Campos} and D. Sinha and S. Lipsitz and J. Lin}
}


%optional %LTM %spezi %full_lik %splines (= parametric transformation)
% Note: Generalisation of Box-Cox, e.g. to arbitrary but fixed error distribution F.
@article{BickelDoksum_1981,
  author = {P. J. Bickel and K. A. Doksum},
  title = {An Analysis of Transformations Revisited},
  journal = {Journal of the American Statistical Association},
  volume = {76},
  number = {374},
  pages = {296--311},
  year = {1981},
  doi = {10.1080/01621459.1981.10477649}
}

%optional
% Note: Reference for Exponential PH and Weibull PH model.
@article{Prentice_1973,
  author = {R. L. Prentice}, 
  title = {Exponential Survivals with Censoring and Explanatory Variables},
  volume = {60}, 
  number = {2}, 
  pages = {279--288}, 
  year = {1973}, 
  doi = {10.1093/biomet/60.2.279}, 
  journal = {Biometrika} 
}


%VIP %LTM %random %spezi %NPMLE %profile_lik or %full_lik
% Note: relationship of LTMs and frailty models;
%       time-dependent covariates are considered;
%       log-likelihood is formulated based on a counting process.
%       Model estimation: direct maximisation of full-lik or profile likelihood 
%       (both NPMLE).
@article {ChoiHuang_2012,
  author = {S. Choi and X. Huang},
  title = {A General Class of Semiparametric Transformation Frailty 
           Models for Nonproportional Hazards Survival Data},
  journal = {Biometrics},
  volume = {68},
  number = {4},
  doi = {10.1111/j.1541-0420.2012.01784.x},
  pages = {1126--1135},
  year = {2012}
}


%optional %LTM %profile_lik %spezi %NPMLE
% Note: log-likelihood based on counting processes is used;
%       time-dependent covariates are considered.
%       Estimation: weighted Breslow-type estimator for jump sizes of the cumulative
%       baseline function; profile score equation for regression coefficients.
%       Extension of Chen et al. (2002) (unweighted Breslow-type estimator)!
@article{Chen_2009,
  author = {Chen, Yi-Hau}, 
  title = {Weighted Breslow-type and Maximum Likelihood Estimation in 
           Semiparametric Transformation Models},
  year = {2009}, 
  volume = 96,
  number = 3,
  pages = {591--600},
  doi = {10.1093/biomet/asp032}, 
  journal = {Biometrika} 
}


%optional %spezi %NPMLE
% Note: proportional intensity model (for counting processes) with time-dependent
%       covariates;
%       nonparametric log-likelihood for counting processes;
%       LTM and PH model are included as special cases;
%       in contrast to Chen et al. (2002) the estimators are asympt. efficient;
%       quasi-Newton method for model estimation.
@article{ZengLin_2006,
  author = {D. Zeng and D. Y. Lin}, 
  title = {Efficient Estimation of Semiparametric Transformation 
           Models for Counting Processes},
  volume = {93}, 
  number = {3}, 
  pages = {627--640}, 
  year = {2006}, 
  doi = {10.1093/biomet/93.3.627}, 
  journal = {Biometrika} 
}


%VIP %flex_int %random %spezi %NPMLE
% Note: General class of transformation models for counting processes that is able to
%       handle time-dependent covariates, heteroscedasticity, multiple types of events,
%       random effects;
%       unified and general asymptotic theory is provided.
@article {ZengLin_2007,
  author = {D. Zeng and D. Y. Lin},
  title = {Maximum Likelihood Estimation in Semiparametric 
           Regression Models with Censored Data},
  journal = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
  volume = {69},
  number = {4},
  doi = {10.1111/j.1369-7412.2007.00606.x},
  pages = {507--564},
  year = {2007}
}


%optional %LTM %random %spezi %NPMLE
% Note: Aim: Prove large sample existence and consistency of the NPMLE.  
@article {SludVonta_2004,
  author = {E. V. Slud and F. Vonta},
  title = {Consistency of the {NPML} Estimator in the Right-Censored Transformation Model},
  journal = {Scandinavian Journal of Statistics},
  volume = {31},
  number = {1},
  doi = {10.1111/j.1467-9469.2004.00370.x},
  pages = {21--41},
  year = {2004}
}

%VIP %LTM_flex %spezi %NPMLE
% Note: Varying coefficients for covariates not for the response! 
%       Partial linear transformation model is included as a special case;
%       Varying coefficients are parametrised using B-splines;
%       Iterative procedure is suggested for model estimation because direct maximisation
%       of the log-likelihood is problematic because of the high number of parameters.
@article{ChenTong_2010,
  author = {K. Chen and X. Tong}, 
  title = {Varying Coefficient Transformation Models with Censored Data},
  volume = {97}, 
  number = {4}, 
  pages = {969--976}, 
  year = {2010}, 
  doi = {10.1093/biomet/asq032}, 
  journal = {Biometrika} 
}


%VIP %LTM (PO model) %spezi %NPMLE 
% Note: NPMLE approach for the PO model;
%       important reference for the PO model for survival data.
@article {Bennett_1983a,
  author = {Bennett, Steve},
  title = {Analysis of Survival Data by the Proportional Odds Model},
  journal = {Statistics in Medicine},
  volume = {2},
  number = {2},
  doi = {10.1002/sim.4780020223},
  pages = {273--277},
  year = {1983}
}


%LTM (PO model) %spezi %NPMLE
% Note: authors show that Bennett (1983)'s estimates are efficient;
%       large sample porperties of the estimators are established;
%       Newton-Raphson algorithm.
@article {Murphyetal_1997,
  author = {S. A. Murphy and A. J. Rossini and A. W. van der Vaart},
  title = {Maximum Likelihood Estimation in the Proportional Odds Model},
  journal = {Journal of the American Statistical Association},
  volume = {92},
  number = {439},
  doi = {10.1080/01621459.1997.10474051},
  pages = {968--976},
  year = {1997}
}

%optional %LTM (PO model) %spezi %NPMLE
% Note: identical approach to Murphy et al. (1997) but different estimation algorithm;
%       minorisation-maximisation algorithm;
%       Newton-Raphson might be problematic for large data sets where number of
%       parameters exceeds the number of uncensored observations. 
@article{HunterLange_2002,
  year={2002},
  journal={Annals of the Institute of Statistical Mathematics},
  volume={54},
  number={1},
  doi={10.1023/A:1016126007531},
  title={Computing Estimates in the Proportional Odds Model},
  author={D. R. Hunter and K. Lange},
  pages={155--168}
}


%flex_int_y (PO model with time-varying effects) %spezi %NPMLE %estequ
% Note: Extended PO model with time-varying coefficients or time-dependent covariates;
%       Estimation techniques:
%       1) Moment-based estimating equations (Chen et al. (2002))
%       2) NPMLE (Zeng and Lin (2006, 2007))
@article {Chenetal_2012,
  author = {Y. Q. Chen and N. Hu and S.-C. Cheng and P. Musoke and L. P. Zhao},
  title = {Estimating Regression Parameters in an Extended Proportional Odds Model},
  journal = {Journal of the American Statistical Association},
  volume = {107},
  number = {497},
  year = {2012},
  pages = {318--330},
  doi = {10.1080/01621459.2012.656021}
}

%optional %LTM %spezi %NPMLE
% Note: authors propose an efficient algorithm for calculating MLEs;
%       dimensionality of the parameter space is dramatically reduced.
@article{YinZeng_2006,
  title = {Efficient Algorithm for Computing Maximum Likelihood 
           Estimates in Linear Transformation Models},
  author = {G. Yin and D. Zeng},
  journal = {Journal of Computational and Graphical Statistics},
  volume = {15},
  number = {1},
  pages = {228--245},
  doi = {10.1198/106186006X100542},
  year = {2006}
}

%LTM (PO model) %random %spezi %NPMLE
% Note: right-censored log-likelihood is integrated over the random effects;
%       random effects follow a normal distribution.
@article {Zengetal_2005,
  author = {D. Zeng and D. Y. Lin and G. Yin},
  title = {Maximum Likelihood Estimation for the Proportional Odds Model with Random Effects},
  journal = {Journal of the American Statistical Association},
  volume = {100},
  number = {470},
  doi = {10.1198/016214504000001420},
  pages = {470--483},
  year = {2005}
}

%LTM_flex %random %spezi %NPMLE
% Note: NPMLE approach for linear transformation models with time-varying covariates
%       and random effects for clustered or correlated failure times.
@article{Zengetal_2008,
  author = {D. Zeng and D. Y. Lin and X. Lin},
  title = {Semiparametric Transformation Models with Random Effects 
           for Clustered Failure Time Data},
  journal = {Statistica Sinica},
  volume = {18},
  number = {1},
  pages = {355--377},
  year = {2008}
}


%LTM_flex %random (= frailty PH model) %spezi %NPMLE
% Note: NPMLE approach for semiparametric frailty Cox models;
%       frailty parameter is from a known one-parameter family of distributions with 
%       mean 1;
%       linear predictor with time-varying covariates.
@article{Kosoroketal_2004,
  title = {Robust Inference for Univariate Proportional Hazards Frailty Regression Models},
  author = {M. R. Kosorok and B. L. Lee and J. P. Fine},
  journal = {The Annals of Statistics},
  volume = {32},
  number = {4},
  pages = {1448--1491},
  doi = {10.1214/009053604000000535},
  year = {2004}
}


%VIP %LTM %random %spezi %NPMLE
% Note: NPMLE approach for the frailty PH model with arbitrarily truncated and 
%       censored response;
%       approach can be generalised to frailty LTMs by adapting link G.
@article{HuberCarolVonta_2004,
  year = {2004},
  journal = {Lifetime Data Analysis},
  volume = {10},
  number = {4},
  doi = {10.1007/s10985-004-4773-y},
  title = {Frailty Models for Arbitrarily Censored and Truncated Data},
  author = {C. Huber-Carol and I. Vonta},
  pages = {369--388}
}

%LTM_flex %spezi %NPMLE
% Note: LTM with nonparametric covariate effects (additive transformation model); 
%       nonparametric covariate effects are estimated using local linear regression.
@article{Zhaoetal_2007,
  author = {X. Zhao and X. Zhou and X. Wu},
  title = {Local Linear Regression in Proportional Hazards Model with Censored Data},
  journal = {Communications in Statistics--Theory and Methods},
  volume = {36},
  number = {15},
  pages = {2761--2776},
  year = {2007},
  doi = {10.1080/03610920701386828}
}


%VIP %LTM %random %pen_lik %mixedmod
% Note: log-hazard function is parametrised using a piecewise-linear spline;
%       penalised likelihood is maximised by a mixed model - based approach
%       => smooth estimate of the hazard function, where amount of smoothing is
%          estimated from the data;
%       integrated log-likelihood is approximated by a PQL approach; 
%       variance parameter of the spline coefficients / random effects is estimated
%       using REML.
@article{CaiBetensky_2003,
  author = {T. Cai and R. A. Betensky},
  title = {Hazard Regression for Interval-Censored Data with Penalized Spline},
  journal = {Biometrics},
  volume = {59},
  number = {3},
  doi = {10.1111/1541-0420.00067},
  pages = {570--579},
  year = {2003}
}



%LTM_flex (AFT model) %spezi %NPMLE %profile_lik
% Note: nonparametric ML method for AFT models with possibly time-dependent covariates;
%       regression parameters are estimated by maximising a kernel-smoothed profile
%       likelihood function;
%       cumulative hazard function has to be smoothed in AFT models because otherwise
%       there exists no maximum of the log-likelihood!
@article{ZengLin_2007a,
  author = {D. Zeng and D. Y. Lin}, 
  title = {Efficient Estimation for the Accelerated Failure Time Model},
  volume = {102}, 
  number = {480}, 
  pages = {1387--1396}, 
  year = {2007}, 
  doi = {10.1198/016214507000001085},
  journal = {Journal of the American Statistical Association} 
}

%VIP %LTM %not_spezi %estequ
% Note: dichotomous comparisons {I(Y_i > Y_j)} are used => h can be ignored because
%       rank configurations of Y_i > Y_j and h(Y_i) > h(Y_j) are identical;
%       estimating equation for beta which can be solved using Newton-Raphson algorithm;
%       right-censored observations: reweight estimating equation by the inverse
%       squared marginal Kaplan-Meier estimator (IPCW approach).
@article{Chengetal_1995,
  author = 	{S. C. Cheng and L. J. Wei and Z. Ying}, 
  title = 	{Analysis of Transformation Models with Censored Data},
  volume = 	{82}, 
  number = 	{4}, 
  pages = 	{835--845}, 
  year = 	{1995}, 
  doi = 	{10.1093/biomet/82.4.835}, 
  journal = 	{Biometrika} 
}

%VIP %LTM %spezi %estequ
% Note: authors define an additional estimating equation for the response transformation
%       h; this is necessary for the prediction of survival probabilities;
%       beta and h are estimated separately based on two estimating equations
%       => no simultaneous estimation of h and beta!
@article{Chengetal_1997,
  title = {Predicting Survival Probabilities with Semiparametric Transformation Models},
  author = {S. C. Cheng and L. J. Wei and Z. Ying},
  journal = {Journal of the American Statistical Association},
  volume = {92},
  number = {437},
  pages = {227--235},
  doi = {10.1080/01621459.1997.10473620},
  year = {1997}
}

%optional %LTM %spezi %estequ
% Note: Estimating equations of Cheng et al. (1995,1997) are simply modified because the 
%       estimators are asymptotically biased when the support of the censoring variable
%       is shorter than the support of the failure time;
%       root-finding equations are replaced by a least-squares criterion;
%       no simultaneous estimation of beta and h; 
%       => unique and consistent estimator
@article{Fineetal_1998,
  author = {J. P. Fine and Z. Ying and L. G. Wei},
  journal = {Biometrika}, 
  number = {4},
  pages = {980--986},
  title = {On the Linear Transformation Model for Censored Data},
  volume = {85},
  doi = {10.1093/biomet/85.4.980},
  year = {1998}
}

%optional %LTM_flex %spezi %estequ
% Note: linear transformation model is extended to parametric covariate transformations;
%       extension seems simple at first sight, but inference is challenging due to 
%       loss of identifiability under the hypotheses of no effects of transformed 
%       covariates.    
@article{FanFine_2013,
  author = {C. Fan and J. P. Fine},
  title = {Linear Transformation Model with Parametric Covariate Transformations},
  journal = {Journal of the American Statistical Association},
  volume = {108},
  number = {502},
  pages = {701--712},
  year = {2013},
  doi = {10.1080/01621459.2013.770707}
}


%optional %LTM_flex %spezi %estequ
% Note: LTMs are extended to correlated observations;
%       introduction of subject- and cluster-specific time-dependent covariates:
%       h(T_ik) = - beta^T %*% Z_ik(t) + eps;
%       estimating equations for beta and h (GEE with indpendence working assumption);
%       approach is more similar to NPMLE than to alternative estimating equations.
@article{Caietal_2000,
  author = {T. Cai and L. J. Wei and M. Wilcox},
  journal = {Biometrika},
  number = {4},
  pages = {867--878},
  title = {Semiparametric Regression Analysis for Clustered Failure Time Data},
  volume = {87},
  doi = {10.1093/biomet/87.4.867},
  year = {2000}
}

%VIP %LTM %random %spezi %estequ
% Note: Linear transformation model with random effects; 
%       frailty Cox model is included as a special case;
%       distribution of the random effects is specified up to a parameter;
%       h and beta are not estimated simultaneously but using separate estimating
%       equations.
@article{Caietal_2002,
  author = {T. Cai and S. C. Cheng and L. J. Wei},
  title = {Semiparametric Mixed-Effects Models for Clustered Failure Time Data},
  journal = {Journal of the American Statistical Association},
  volume = {97},
  number = {458},
  pages = {514--522},
  year = {2002},
  doi = {10.1198/016214502760047041}
}


%optional %LTM %not_spezi %estequ
% Note: LTMs for interval-censored observations;
%       rank-based estimating equation for the regression coefficients is provided
%       => baseline-free approach; 
%       approach is restricted to discrete covariates!
%% no DOI (checked)
@article{Zhangetal_2005,
  title = {Regression Analysis of Interval-Censored Failure Time Data 
           with Linear Transformation Models},
  author = {Z. Zhang and L. Sun and X. Zhao and J. Sun},
  journal = {The Canadian Journal of Statistics},
  volume = {33},
  number = {1},
  pages = {61--70},
  year = {2005}
}

%optional %LTM %spezi %estequ
% Note: approach of Zhang et al. (2005) is extended to survival probability prediction
%       by defining a separate estimating equation for h;
%       beta and h are not estimated simultaneously in the presence of interval
%       censoring;
%       tools for model checking and model selection are additionally considered.
@article{Zhang_2009,
  author = {Z. Zhang}, 
  title = {Linear Transformation Models for Interval-Censored Data: 
           Prediction of Survival Probability and Model Checking},
  volume = {9}, 
  number = {4}, 
  pages = {321--343}, 
  year = {2009}, 
  doi = {10.1177/1471082X0900900404},  
  journal = {Statistical Modelling} 
}


%LTM %random %not_spezi %estequ
% Note: consideration of a panel data version of the LTM with random effects in 
%       ECONOMETRICS!
%       estimating equation only for the regression coefficients beta
%       => baseline-free approach
@article{Lee_2008,
  author = {S. Lee},
  title = {Estimating Panel Data Duration Models with Censored Data},
  journal = {Econometric Theory},
  volume = {24},
  number = {05},
  year = {2008},
  pages = {1254--1276},
  doi = {10.1017/S0266466608080493}
}


%VIP %LTM %spezi %estequ
% Note: most estimating equations (e.g. Cheng et al. (1995)) assume independence of 
%       the censoring time C and the covariates X because the marginal Kaplan-Meier
%       estimator of the censoring distribution is used in the IPCWs;
%       assumption is relaxed here + e.g. Cox model does not make this assumption
%       => Cox partial likelihood estimator results as a special case;
%       maringale-based estimating equations for beta and h => beta and h are 
%       estimated iteratively;
%       h is assumed to be a nondecreasing step function with jumps at the failure 
%       times. 
@article{Chenetal_2002,
  author = {K. Chen and Z. Jin and Z. Ying}, 
  title = {Semiparametric Analysis of Transformation Models with Censored Data},
  volume = {89}, 
  number = {3}, 
  pages = {659--668}, 
  year = {2002}, 
  doi = {10.1093/biomet/89.3.659}, 
  journal = {Biometrika} 
}


%LTM_flex %spezi %estequ
% Note: non-linear covariate effects are incorporated into the LTM
%       => partially linear transformation model;
%       global and kernel-weighted local estimating equations based on martingale theory
%       => extension of Chen et al. (2002)'s EEs to non-linear covariate effects.
%       Global EEs for beta and h (step function) similar to Chen et al. (2002);
%       Local kernel-weighted EE for nonlinear covariate effects given beta and h.
@article{LuZhang_2010,
  author = {W. Lu and H. H. Zhang},
  title = {On Estimation of Partially Linear Transformation Models},
  journal = {Journal of the American Statistical Association},
  volume = {105},
  number = {490},
  pages = {683--691},
  year = {2010},
  doi = {10.1198/jasa.2010.tm09302}
}

%VIP %flex_int_y %spezi %estequ
% Note: LTMs are extended to time-varying structure for the transformation function
%       => time-varying structure in the data is allowed, baseline function may 
%          depend on the covariates;
%       stratified LTM is included as a special case;
%       martingale estimating equations are defined for model estimation.
@article{Scheike_2006,
  year = {2006},
  journal = {Lifetime Data Analysis},
  volume = {12},
  number = {4},
  doi = {10.1007/s10985-006-9021-1},
  title = {A Flexible Semiparametric Transformation Model for Survival Data},
  author = {T. H. Scheike},
  pages = {461--480}
}



%LTM %not_spezi %partial_lik
@article{Cox_1972,
  author = {D. R. Cox},
  title = {Regression Models and Life-Tables},
  journal = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
  volume = {34},
  number = {2},
  pages = {187--220},
  year = {1972}, 
  url = {https://www.jstor.org/stable/2985181},
}

%LTM %not_spezi %partial_lik
@article{Cox_1975,
  author = {D. R. Cox},
  title = {Partial Likelihood},
  journal = {Biometrika},
  volume = {62},
  number = {2},
  pages = {269--276},
  year = {1975},
  doi = {10.2307/2335362},
}

%VIP %flex_int_y %not_spezi %partial_lik
% Note: Cox model with time-dependent coefficients;
%       estimation via local partial likelihood techniques;
%       local linear fitting techniques known from scatterplot smoothing are used;
%       coefficients are estimated locally based on the partial likelihood in a 
%       window around each time point;
%       approach can be used to check the validity of the PH assumption.
@article {CaiSun_2003,
  author = {Z. Cai and Y. Sun},
  title = {Local Linear Estimation for Time-Dependent 
           Coefficients in {C}ox's Regression Models},
  journal = {Scandinavian Journal of Statistics},
  volume = {30},
  number = {1},
  doi = {10.1111/1467-9469.00320},
  pages = {93--111},
  year = {2003}
}


%LTM_flex %not_spezi %partial_lik
@article{SlepperHarrington_1990,
  author = {Sleeper, Lynn A. and Harrington, David P.},
  title = {Regression Splines in the {C}ox Model with Application 
           to Covariate Effects in Liver Disease},
  journal = {Journal of the American Statistical Association},
  volume = {85},
  number = {412},
  pages = {941--949},
  year = {1990},
  doi = {10.1080/01621459.1990.10474965}
}


%flex_int %not_spezi %marg_lik
% Note: baseline-free approach for a general class of semiparametric transformation
%       models under interval censoring;
%       model estimation via maximising the marginal log-likelihood;
%       marginal log-likelihood has no closed analytic form => three-stage MCMC
%       stochastic approximation algorithm;
%       frailty models and heteroscedastic hazard/rank regression models are included
%       as special cases.
@article{Guetal_2005,
  year = {2005},
  journal = {Lifetime Data Analysis},
  volume = {11},
  number = {4},
  doi = {10.1007/s10985-005-5235-x},
  title = {A Baseline-free Procedure for Transformation Models Under Interval Censorship},
  author={M. Gu and L. Sun and G. Zuo},
  pages = {473--488}
}

%LTM (= PO model) %not_spezi %marg_lik
% Note: survival times are replaced by their ranks => marginal likelihood is maximised
%       w.r.t. the regression coefficients.
@article {Pettitt_1984,
  author = {A. N. Pettitt},
  title = {Proportional Odds Models for Survival Data and Estimates Using Ranks},
  journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  volume = {33},
  number = 2,
  pages = {169--175},
  year = {1984}
}


%LTM (= PO model) %not_spezi %marg_lik
% Note: baseline-free approach because only rank order information among patients is
%       used; rank order preserves information about the regression parameters;
%       marginal likelihood is approximated using a Monte Carlo method.
@article{LamLeung_2001,
  year = {2001},
  journal = {Lifetime Data Analysis},
  volume = {7},
  number = {1}, 
  doi = {10.1023/A:1009673026121},
  title = {Marginal Likelihood Estimation for Proportional Odds Models 
           with Right Censored Data},
  author = {K. F. Lam and T. L. Leung},
  pages = {39--54}
}


%LTM (= PO model) %random %not_spezi %marg_lik
% Note: Semiparametric random effects PO model for multivariate survival times with 
%       various types of dependence structures;
%       cluster data and repeated measurements are covered;
%       assumption of multivariate normal effects;
%       regression and variance parameters are estimated by maximising the 
%       marginal rank likelihood;
%       marginal likelihood is approximated by a Monte Carlo method.
@article{Lametal_2002,
  author = {K. F. Lam and Y. W. Lee and T. L. Leung},
  title = {Modeling Multivariate Survival Data by a Semiparametric 
           Random Effects Proportional Odds Model},
  journal = {Biometrics},
  volume = {58},
  number = {2},
  doi = {10.1111/j.0006-341X.2002.00316.x},
  pages = {316--323},
  year = {2002}
}


%LTM_flex %not_spezi %marg_lik
% Note: special case of Gu et al. (2005);
%       varying coefficient component is included in linear transformation models;
%       coefficient functions are parametrised using B-splines;
%       estimation is based on maximising the marginal rank log-likelihood;
%       three-stage MCMC stochastic approximation algorithm.
@article{Lietal_2012,
  author = {J. Li and M. Gu and T. Hu},
  title = {General Partially Linear Varying-Coefficient 
           Transformation Models for Ranking Data},
  journal = {Journal of Applied Statistics},
  volume = {39},
  number = {7},
  pages = {1475--1488},
  year = {2012},
  doi = {10.1080/02664763.2012.658357}
}

%VIP %LTM %spezi %bayes
% Note: Bayesian semiparametric transformation model;
%       PH, PH and AFT are included as special cases;
%       can be generalised to multivariate survival data using frailty models;
%       Priors: 
%       beta: multivariate normal
%       h: mixture of incomplete beta functions
%       F: Polya tree prior;
%       MCMC algorithm for model estimation.
@article{MallickWalker_2003,
  title = {A {B}ayesian Semiparametric Transformation Model Incorporating Frailties},
  journal = {Journal of Statistical Planning and Inference},
  volume = {112},
  number = {1--2},
  pages = {159--174},
  year = {2003},
  doi = {10.1016/S0378-3758(02)00330-0},
  author = {B. K. Mallick and S. Walker}
}


%LTM (= PO model) %spezi %bayes
% Note: Bayesian semiparametric PO model;
%       prior for the baseline survival function: mixture of finite Polya trees.
@article{HansonYang_2007,
  author = {T. Hanson and M. Yang},
  title = {Bayesian Semiparametric Proportional Odds Models},
  journal = {Biometrics},
  volume = {63},
  number = {1},
  doi = {10.1111/j.1541-0420.2006.00671.x},
  pages = {88--95},
  year = {2007}
}

%flex_int %spezi %bayes
% Note: Bayesian analysis of a class of generalised odds-rate hazards (GORH) models;
%       non-PH, PH, PO, AFT are included as special cases.
@article{Banerjeeetal_2007, 
  year = {2007},
  journal = {Lifetime Data Analysis},
  volume = {13},
  number = {2},
  doi = {10.1007/s10985-007-9035-3},
  title = {Bayesian Analysis of Generalized Odds-Rate Hazards Models for Survival Data},
  author = {T. Banerjee and M.-H Chen and D. K. Dey and S. Kim},
  pages = {241--260}
}


%further_extension %LTM %spezi %estequ
% Note: authors suggest a Box-Cox transformation of the survivor function;
%       model class is related to frailty models.
@article {ZuckerYang_2006,
  author = {D. M. Zucker and S. Yang},
  title = {Inference for a Family of Survival Models Encompassing 
           the Proportional Hazards and Proportional Odds Models},
  journal = {Statistics in Medicine},
  volume = {25},
  number = {6},
  doi = {10.1002/sim.2255},
  pages = {995--1014},
  year = {2006}
}

%further_extension %LTM %spezi %profile_lik
% Note: response transformation h is parametric, but F and covariate effects are 
%       nonparametric;
%       constraints: h, F and covariate effects are smooth; h and F monotone increasing.
@article{lintonetal_2008,
  author = {O. Linton and S. Sperlich and I. {van Keilegom}},
  doi = {10.1214/009053607000000848},
  journal = {The Annals of Statistics},
  number = {2},
  pages = {686--718},
  title = {Estimation of a Semiparametric Transformation Model},
  volume = {36},
  year = {2008}
}


%further_extension %LTM %spezi %marg_lik
% Note: h and F are unspecified; 
%       smoothed partial rank estimator is suggested;
@article{Songetal_2007,
  author = 	{X. Song and S. Ma and J. Huang and X.-H. Zhou}, 
  title = 	{A Semiparametric Approach for the Nonparametric 
                 Transformation Survival Model with Multiple Covariates},
  volume = 	{8}, 
  number = 	{2}, 
  pages = 	{197--211}, 
  year = 	{2007}, 
  doi = 	{10.1093/biostatistics/kxl001}, 
  journal = 	{Biostatistics} 
}


%VIP %furhter_extension
% Note: Transformation models in econometrics;
%       - h and F are parametric => maximum likelihood methods;
%       - h is parametric, F is nonparmetric => F is estimated based on the empirical 
%         distribution of the residuals; beta with the generalised method of moments
%       - h and F are nonparametric => estimation techniques for single index models
@book{Horowitz_2009,
  author = {J. L. Horowitz},
  title = {Semiparametric and Nonparametric Methods in Econometrics},
  publisher = {Springer-Verlag},
  year = {2009},
  address = {New York, U.S.A.}
}


% Semiparametric AFT models (i.e. F is nonparametric):
@article{Jinetal_2003,
  author = {Z. Jin and D. Y. Lin and L. J. Wei and Z. Ying}, 
  title = {Rank--based Inference for the Accelerated Failure Time Model},
  volume = {90}, 
  number = {2}, 
  pages = {341--353}, 
  year = {2003}, 
  doi = {10.1093/biomet/90.2.341}, 
  journal = {Biometrika} 
}

@article{Horowitz_1996,
  author = {Joel L. Horowitz},
  title = {Semiparametric Estimation of a Regression Model with an 
           Unknown Transformation of the Dependent Variable},
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  volume = 64,
  number = 1,
  year = 1996,
  pages = {103--137}
}

@article{Jones_Pewsey_2009,
  author = {M. C. Jones and A. Pewsey},
  title = {Sinh-arcsinh Distributions},
  year = {2009},
  journal = {Biometrika},
  volume = {96},
  number = {4},
  DOI = {10.1093/biomet/asp053},
  pages = {761--780}
}

@article{Bove_Held_2013,
  author = {Daniel {Saban{\'e}s Bov{\'e}} and Leonhard Held},
  title = {Comment on {Cai} and {Betensky} (2003), {On} the {Poisson} Approximation 
           for Hazard Regression},
  year = {2013},
  journal = {Biometrics},
  volume = {69},
  number = {3},
  DOI = {10.1111/biom.12088},
  pages = {795--795}
}

@article{Chang_Hsiung_Wu_2005,
  author = {I. Chang and Chao A. Hsiung and Yuh-Jenn Wu and Che-Chi Yany},
  title = {Bayesian Survival Analysis Using {Bernstein} Polynomials},
  year = {2005},
  journal = {Scandinavian Journal of Statistics},
  volume = {32},
  number = {3},
  pages = {447--466},
  doi = {10.1111/j.1467-9469.2005.00451.x}
}

@article{Curtis_Ghosh_2011,
  author = {S. McKay Curtis and Sujit K. Ghosh},
  title = {A Variable Selection Approach to Monotonic Regression 
           with {Bernstein} Polynomials},
  year = {2011},
  journal = {Journal of Applied Statistics},
  volume = {38},
  number = {5},
  DOI = {10.1080/02664761003692423},
  pages = {961--976}
}

@article{Farouki_2012,
  author = {Rida T. Farouki},
  title = {The {Bernstein} Polynomial Basis: A Centennial Retrospective},
  year = {2012},
  journal = {Computer Aided Geometric Design},
  volume = {29},
  number = {6},
  DOI = {10.1016/j.cagd.2012.03.001},
  pages = {379--419}
}

@article{Sun_Sundaram_Zhao_2009,
  author = {Yanqing Sun and Rajeshwari Sundaram and Yichuan Zhao},
  title = {Empirical Likelihood Inference for the {Cox} Model with Time-dependent
           Coefficients via Local Partial Likelihood},
  year = {2009},
  journal = {Scandinavian Journal of Statistics},
  volume = {36},
  number = {3},
  DOI = {10.1111/j.1467-9469.2008.00634.x},
  pages = {444--462}
}

@Article{Hothorn_Bretz_Westfall_2008,
  author = {Torsten Hothorn and Frank Bretz and Peter Westfall},  
  year = 2008,
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  volume = 50,
  number = 3,
  pages = {346--363},
  doi = {10.1002/bimj.200810425},
}

@Book{            Koenker_2005,
  title         = {Quantile Regression},
  publisher     = {Cambridge University Press},
  year          = {2005},
  author        = {Roger Koenker},
  series        = {Economic Society Monographs},
  language      = {english},
  address       = {New York, U.S.A.}
}

@Article{Varadhan_Gilbert_2009,
    title = {{BB}: An {R} Package for Solving a Large System of 
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}

@article{Chernozhukov_2013,
        author = {Victor Chernozhukov and Iv{\'a}n Fern{\'a}ndez-Val and Blaise Melly},        
	title = {Inference on Counterfactual Distributions},
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	doi = {10.3982/ECTA10582},
	number = {6},
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}

@article{Foresi_Peracchi_1995,
  author = {Silverio Foresi and Franco Peracchi},
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@techreport{Koenker_Leorato_Peracchi_2013,
  author = {Roger Koenker and Samantha Leorato and Franco Peracchi},
  title = {Distributional vs.~Quantile Regression},
  year = {2013},
  doi = {10.2139/ssrn.2368737},
  institution = {Centre for Economic and International Studies, University of Rome Tor Vergata},
  address = {Rome, Italy},
  volume = 11,
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}

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  author = {Christoph Rothe and Dominik Wied},
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  pages = {314--324}
}

@article{Thas_Neve_Clement_2012,
  author = {Olivier Thas and Jan De Neve and Lieven Clement and Jean-Pierre Ottoy},
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  journal = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
  volume = {74},
  number = {4},
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  pages = {623--671}
}

@article{Rigby_Stasinopoulos_2004,
  author = {Robert A. Rigby and D. Mikis Stasinopoulos},
  title = {Smooth Centile Curves for Skew and Kurtotic Data Modelled Using the {Box-Cox} Power Exponential Distribution},
  year = {2004},
  journal = {Statistics in Medicine},
  volume = {23},
  number = {19},
  DOI = {10.1002/sim.1861},
  pages = {3053--3076}
}


@Article{         Rigby_Stasinopoulos_2005,
  author        = {R. A. Rigby and D. M. Stasinopoulos},
  title         = {Generalized Additive Models for Location, Scale and
                  Shape},
  year          = {2005},
  journal       = {Journal of the Royal Statistical Society: Series C
                  (Applied Statistics)},
  volume        = {54},
  number        = {3},
  pages         = {507--554},
  doi           = {10.1111/j.1467-9876.2005.00510.x}
}

@Article{         Doksum_Gasko_1990,
  author        = {Kjell A. Doksum and Miriam Gasko},   
  title         = {On a Correspondence Between Models in Binary Regression
                  Analysis and in Survival Analysis},
  year          = {1990},
  journal       = {International Statistical Review},
  volume        = {58},
  number        = {3},
  pages         = {243--252}
}

@article{Gneiting_Katzfuss_2014,
  author = {Tilmann Gneiting and Matthias Katzfuss},
  title = {Probabilistic Forecasting},
  year = {2014},
  journal = {Annual Review of Statistics and Its Application},
  volume = {1},
  number = {1},
  DOI = {10.1146/annurev-statistics-062713-085831},
  pages = {125--151}
}

### constant effects of time-varying covariates
@article{Ding_Tian_Yu_2012,
  author = {A. Adam Ding and Shaonan Tian and Yan Yu and Hui Guo},
  title = {A Class of Discrete Transformation Survival Models With Application
           to Default Probability Prediction},
  year = {2012},
  journal = {Journal of the American Statistical Association},
  volume = {107},
  number = {499},
  DOI = {10.1080/01621459.2012.682806},
  pages = {990--1003}
}

@article{Feng_Sun_2014,
  author = {Yanqin Feng and Jianguo Sun},
  title = {Hazard Ratio Estimation for Two-sample Case Under Interval-censored Failure Time Data},
  year = {2014},
  journal = {Biometrical Journal},
  volume = {56},
  number = {2},
  DOI = {10.1002/bimj.201200273},
  pages = {219--229}
}

@article{Huang_2014,
  author = {Alan Huang},
  title = {Joint Estimation of the Mean and Error Distribution in 
           Generalized Linear Models},
  year = {2014},
  journal = {Journal of the American Statistical Association},
  volume = {109},
  number = {505},
  DOI = {10.1080/01621459.2013.824892},
  pages = {186--196}
}

@article{Lindsey_1999,
  author = {Jim K. Lindsey},
  title = {Some Statistical Heresies},
  year = 1999,
  journal = {Journal of the Royal Statistical Society: Series D (The Statistician)},
  volume = 48,
  number = 1,
  pages = {1--40}
}

@article{Moest_Hothorn_2015,
  title = {Conditional Transformation Models for Survivor
           Function Estimation},
  author = {Lisa M\"ost and Torsten Hothorn},
  journal = {International Journal of Biostatistics},
  year = {2015},
  volume = 11,
  number = 1,
  pages = {23--50},
  doi = {10.1515/ijb-2014-0006}
}

@article{Moest_Schmid_Faschingbauer_2014,
  author = {Lisa M\"ost and Matthias Schmid and
            Florian Faschingbauer and Torsten Hothorn},
  title = {Predicting Birth Weight with Conditionally Linear
           Transformation Models},
  journal = {Statistical Methods in Medical Research},
  year = {2016},
  volume = 25,
  number = 6,
  pages = {2781--2810},
  DOI = {10.1177/0962280214532745}
}
 
@article{Yang_Prentice_2015,
  author = {Song Yang and Ross L. Prentice},
  title = {Assessing Potentially Time-dependent Treatment Effect From 
           Clinical Trials and Observational Studies for Survival Data, 
           With Applications to the {Women's} {Health} {Initiative} Combined Hormone Therapy Trial},
  year = {2015},
  journal = {Statistics in Medicine},
  volume = {34},
  number = {11},
  DOI = {10.1002/sim.6453},
  pages = {1801--1817}
}

@article{Yu_2004,
  author = {Jun Yu},
  title = {Empirical Characteristic Function Estimation and Its Applications},
  year = {2004},
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  pages = {93--123}
}

@techreport{Hothorn_Moest_Buehlmann_2016,
  author = {Torsten Hothorn and Lisa M\"ost and Peter B\"uhlmann},
  title = {Most Likely Transformations (Extended Version)},
  year = {2017},
  institution = {arXiv 1508.06749},
  url = {http://arxiv.org/abs/1508.06749}
}

@article{Hothorn_Moest_Buehlmann_2017,
  author = {Torsten Hothorn and Lisa M\"ost and Peter B\"uhlmann},
  title = {Most Likely Transformations},
  year = {2018},
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  volume = 45,
  number = 1,
  pages = {110--134}
}
 
@Article{         Parish,
  author        = {W. L. Parish and E. O. Laumann},
  title         = {Chinese Health and Family Life Survey},
  year          = {2009},
  note          = {Accecibilty verified on May 18, 2009},
  url           = {http://www.spc.uchicago.edu/prc/chfls.php}
}

@article{Hothorn_Mueller_Held_2015,
  author = {Torsten Hothorn and J\"org M\"uller and Leonhard Held
            and Lisa M\"ost and Atle Mysterud},
  title = {Temporal Patterns of Deer-vehicle Collisions Consistent with Deer
           Activity Pattern and Density Increase but not General Accident Risk},
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  year = {2015},
  volume = 81,
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}

@article{Mroz_1987,
  author = {T. A. Mroz},
  year = 1987,
  title = {The Sensitivity of an Empirical Model of
     Married Women's Hours of Work to Economic and Statistical
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  journal = {Econometrica}, 
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}

@article{Tobin_1958,
  author = {James Tobin},
  title = {Estimation of Relationships for Limited Dependent Variables},
  year = 1958,
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@Book{Venables_Ripley_2002,
    title = {Modern Applied Statistics with S},
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    publisher = {Springer-Verlag},
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@book{Scheike_Martinussen_2006,
  author = {Thomas H. Scheike and Torben Martinussen},
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@Article{Gu_2014,
    title = {Smoothing Spline ANOVA Models: {R} Package {gss}},
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@book{Wood_2006,
  author = {Simon N. Wood},
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}

@article{Yee_2010,
  author = {Thomas W. Yee},
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@book{Fahrmeir_Kneib_Lang_2013,
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@article{Gurka_Edwards_2006,
  author = {Matthew J. Gurka and Lloyd J. Edwards and Keith E. Muller and
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  title = {Extending the {Box-Cox} Transformation to the Linear Mixed Model},
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@article{Hutmacher_French_2011,
  author = {Matthew M. Hutmacher and Jonathan L. French and Sriram Krishnaswami
            and Sujatha Menon},
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@article{Maruo_Yamaguchi_2017,
  author = {K. Maruo and Y. Yamaguchi and H. Noma and M. Gosho},
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@article{Tang_Wu_Chen_2018,
  title = {Semiparametric {B}ayesian Analysis of Transformation Linear
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@article{Wu_Wang_2019,
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@article{Sauter_Held_2016,
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@article{McLain_Ghosh_2013,
  author = {Alexander C. McLain and Sujit K. Ghosh},
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@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 = {2025},
  url = {https://www.R-project.org/},
}
@Manual{pkg:mlt,
  title = {\pkg{mlt}: Most Likely Transformations},
  author = {Torsten Hothorn},
  year = {2025},
  note = {\proglang{R}~package version~1.6-7},
  url = {https://CRAN.R-project.org/package=mlt},
}
@Manual{pkg:tram,
  title = {\pkg{tram}: Transformation Models},
  author = {Torsten Hothorn and Sandra Siegfried and Lucas Kook},
  year = {2025},
  note = {\proglang{R}~package version~1.2-4},
  url = {https://CRAN.R-project.org/package=tram},
}
@Manual{pkg:trtf,
  title = {\pkg{trtf}: Transformation Trees and Forests},
  author = {Torsten Hothorn},
  year = {2025},
  note = {\proglang{R}~package version~0.4-3},
  url = {https://CRAN.R-project.org/package=trtf},
  doi = {10.32614/CRAN.package.trtf},
}
@Manual{pkg:tramME,
  title = {\pkg{tramME}: Transformation Models with Mixed Effects},
  author = {Balint Tam{\'a}si},
  year = {2024},
  note = {\proglang{R}~package version~1.0.7},
  url = {https://CRAN.R-project.org/package=tramME},
  doi = {10.32614/CRAN.package.tramME},
}
@Manual{pkg:tbm,
  title = {\pkg{tbm}: Transformation Boosting Machines},
  author = {Torsten Hothorn},
  year = {2025},
  note = {\proglang{R}~package version~0.3-7},
  url = {https://CRAN.R-project.org/package=tbm},
  doi = {10.32614/CRAN.package.tbm},
}
@Manual{pkg:tramnet,
  title = {\pkg{tramnet}: Penalized Transformation Models},
  author = {Lucas Kook},
  year = {2023},
  note = {\proglang{R}~package version~0.0-8},
  url = {https://CRAN.R-project.org/package=tramnet},
  doi = {10.32614/CRAN.package.tramnet},
}
@Manual{pkg:survival,
  title = {\pkg{survival}: Survival Analysis},
  author = {Terry M Therneau},
  year = {2024},
  note = {\proglang{R}~package version~3.8-3},
  url = {https://CRAN.R-project.org/package=survival},
  doi = {10.32614/CRAN.package.survival},
}
@Manual{pkg:icenReg,
  title = {\pkg{icenReg}: Regression Models for Interval Censored Data},
  author = {Clifford Anderson-Bergman},
  year = {2024},
  note = {\proglang{R}~package version~2.0.16},
  url = {https://CRAN.R-project.org/package=icenReg},
  doi = {10.32614/CRAN.package.icenReg},
}
@Manual{pkg:TransModel,
  title = {\pkg{TransModel}: Fit Linear Transformation Models for Right Censored Data},
  author = {Jie Zhou and Jiajia Zhang and Wenbin Lu},
  year = {2022},
  note = {\proglang{R}~package version~2.3},
  url = {https://CRAN.R-project.org/package=TransModel},
  doi = {10.32614/CRAN.package.TransModel},
}
@Manual{pkg:rms,
  title = {\pkg{rms}: Regression Modeling Strategies},
  author = {Frank E {Harrell Jr}},
  year = {2025},
  note = {\proglang{R}~package version~8.0-0},
  url = {https://CRAN.R-project.org/package=rms},
  doi = {10.32614/CRAN.package.rms},
}
@Manual{pkg:ICsurv,
  title = {\pkg{ICsurv}: Semiparametric Regression Analysis of Interval-Censored Data},
  author = {Christopher S. McMahan and Lianming Wang},
  year = {2022},
  note = {\proglang{R}~package version~1.0.1},
  url = {https://CRAN.R-project.org/package=ICsurv},
  doi = {10.32614/CRAN.package.ICsurv},
}
@Manual{pkg:eha,
  title = {\pkg{eha}: Event History Analysis},
  author = {Göran Broström},
  year = {2024},
  note = {\proglang{R}~package version~2.11.5},
  url = {https://CRAN.R-project.org/package=eha},
  doi = {10.32614/CRAN.package.eha},
}
@Manual{pkg:rstpm2,
  title = {\pkg{rstpm2}: Smooth Survival Models, Including Generalized Survival Models},
  author = {Mark Clements and Xing-Rong Liu and Benjamin Christoffersen},
  year = {2025},
  note = {\proglang{R}~package version~1.6.9},
  url = {https://CRAN.R-project.org/package=rstpm2},
  doi = {10.32614/CRAN.package.rstpm2},
}
@Manual{pkg:flexsurv,
  title = {\pkg{flexsurv}: Flexible Parametric Survival and Multi-State Models},
  author = {Christopher Jackson},
  year = {2024},
  note = {\proglang{R}~package version~2.3.2},
  url = {https://CRAN.R-project.org/package=flexsurv},
  doi = {10.32614/CRAN.package.flexsurv},
}
@Manual{pkg:mgcv,
  title = {\pkg{mgcv}: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation},
  author = {Simon Wood},
  year = {2025},
  note = {\proglang{R}~package version~1.9-3},
  url = {https://CRAN.R-project.org/package=mgcv},
  doi = {10.32614/CRAN.package.mgcv},
}
@Manual{pkg:mpr,
  title = {\pkg{mpr}: Multi-Parameter Regression (MPR)},
  author = {Kevin Burke},
  year = {2022},
  note = {\proglang{R}~package version~1.0.6},
  url = {https://CRAN.R-project.org/package=mpr},
  doi = {10.32614/CRAN.package.mpr},
}
@Manual{pkg:gamlss,
  title = {\pkg{gamlss}: Generalized Additive Models for Location Scale and Shape},
  author = {Mikis Stasinopoulos and Robert Rigby},
  year = {2024},
  note = {\proglang{R}~package version~5.4-22},
  url = {https://CRAN.R-project.org/package=gamlss},
  doi = {10.32614/CRAN.package.gamlss},
}
@Manual{pkg:gamlss.cens,
  title = {\pkg{gamlss.cens}: Fitting an Interval Response Variable Using \pkg{gamlss.family}
Distributions},
  author = {Mikis Stasinopoulos and Bob Rigby and Nicoleta Mortan and Alexander Seipp},
  year = {2023},
  note = {\proglang{R}~package version~5.0-7},
  url = {https://CRAN.R-project.org/package=gamlss.cens},
  doi = {10.32614/CRAN.package.gamlss.cens},
}
@Manual{pkg:coxme,
  title = {\pkg{coxme}: Mixed Effects Cox Models},
  author = {Terry M. Therneau},
  year = {2024},
  note = {\proglang{R}~package version~2.2-22},
  url = {https://CRAN.R-project.org/package=coxme},
  doi = {10.32614/CRAN.package.coxme},
}
@Manual{pkg:frailtyEM,
  title = {\pkg{frailtyEM}: Fitting Frailty Models with the EM Algorithm},
  author = {Theodor Adrian Balan and Hein Putter},
  year = {2019},
  note = {\proglang{R}~package version~1.0.1},
  url = {https://CRAN.R-project.org/package=frailtyEM},
  doi = {10.32614/CRAN.package.frailtyEM},
}
@Manual{pkg:frailtypack,
  title = {\pkg{frailtypack}: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints},
  author = {Virginie Rondeau and Juan R. Gonzalez and Yassin Mazroui and Audrey Mauguen and Amadou Diakite and Alexandre Laurent and Myriam Lopez and Agnieszka Krol and Casimir L. Sofeu and Julien Dumerc and Denis Rustand and Jocelyn Chauvet and Quentin {Le Coent} and Romain Pierlot and Lacey Etzkorn and Derek Dinart and Adrien Orué},
  year = {2025},
  note = {\proglang{R}~package version~3.7.0},
  url = {https://CRAN.R-project.org/package=frailtypack},
  doi = {10.32614/CRAN.package.frailtypack},
}
@Manual{pkg:timereg,
  title = {\pkg{timereg}: Flexible Regression Models for Survival Data},
  author = {Thomas Scheike and Torben Martinussen},
  year = {2025},
  note = {\proglang{R}~package version~2.0.7},
  url = {https://CRAN.R-project.org/package=timereg},
  doi = {10.32614/CRAN.package.timereg},
}
%% ---- CAO Example ----
@article{Hofheinz_Arnold_Fokas_2018,
  title = {Impact of Age on the Efficacy of Oxaliplatin in the Preoperative
  Chemoradiotherapy and Adjuvant Chemotherapy of Rectal Cancer: A Post Hoc
  Analysis of the {CAO/ARO/AIO-04} Phase {III} Trial},
  journal = {Annals of Oncology},
  volume = {29},
  number = {8},
  pages = {1793--1799},
  year = {2018},
  doi = {10.1093/annonc/mdy205},
  author = {R.-D. Hofheinz and D. Arnold and E. Fokas and M. Kaufmann and T. Hothorn and
  G. Folprecht and R. Fietkau and W. Hohenberger and M. Ghadimi and T. Liersch and
  G.G. Grabenbauer and R. Sauer and C. Rödel and U. Graeven},
  keywords = {elderly patients, oxaliplatin, efficacy, chemoradiotherapy, rectal cancer},
}

@article{Roedel_Graeven_Fietkau_2015,
  title = {Oxaliplatin Added to Fluorouracil-Based Preoperative Chemoradiotherapy And
  Postoperative Chemotherapy of Locally Advanced Rectal Cancer (The {German}
  {CAO/ARO/AIO-04} Study): Final Results of the Multicentre, Open-Label,
  Randomised, Phase 3 Trial},
  journal = {The Lancet Oncology},
  volume = {16},
  number = {8},
  pages = {979--989},
  year = {2015},
  doi = {10.1016/S1470-2045(15)00159-X},
  author = {Claus Rödel and Ullrich Graeven and Rainer Fietkau and Werner Hohenberger and
  Torsten Hothorn and Dirk Arnold and Ralf-Dieter Hofheinz and Michael Ghadimi and
  Hendrik A Wolff and Marga Lang-Welzenbach and Hans-Rudolf Raab and Christian Wittekind and
  Philipp Ströbel and Ludger Staib and Martin Wilhelm and Gerhard G Grabenbauer and
  Hans Hoffmanns and Fritz Lindemann and Anke Schlenska-Lange and Gunnar Folprecht and
  Rolf Sauer and Torsten Liersch},
}

@article{Kaplan_Meier_1958,
  title = {Nonparametric Estimation from Incomplete Observations},
  author = {Kaplan, Edward L and Meier, Paul},
  journal = {Journal of the American Statistical Association},
  volume = {53},
  number = {282},
  pages = {457--481},
  year = {1958},
  publisher = {Taylor \& Francis}
}

@article{Turnbull_1974,
  title = {Nonparametric Estimation of a Survivorship Function with Doubly Censored Data},
  author = {Turnbull, Bruce W},
  journal = {Journal of the American Statistical Association},
  volume = {69},
  number = {345},
  pages = {169--173},
  year = {1974},
  publisher = {Taylor \& Francis}
}

@article{Turnbull_1976,
  title = {The Empirical Distribution Function with Arbitrarily Grouped, Censored and Truncated Data},
  author = {Turnbull, Bruce W},
  journal = {Journal of the Royal Statistical Society Series~B: Statistical Methodology},
  volume = {38},
  number = {3},
  pages = {290--295},
  year = {1976},
  publisher = {Wiley Online Library}
}


%% ---- General ----
%% tutorialexample
@article{Cox_Chu_Schneider_2007,
  title = {Parametric Survival Analysis and Taxonomy of Hazard Functions for the Generalized Gamma Distribution},
  author = {Cox, Christopher and Chu, Haitao and Schneider, Michael F. and Mu\~{n}oz, Alvaro},
  journal = {Statistics in Medicine},
  volume = {26},
  number = {23},
  pages = {4352--4374},
  doi = {10.1002/sim.2836},
  year = {2007}
}

%% test, martingale residuals, variation over group
@article{Gray_1995,
  title = {Tests for Variation Over Groups in Survival Data},
  author = {Robert J. Gray},
  journal = {Journal of the American Statistical Association},
  volume = {90},
  number = {429},
  pages = {198--203},
  year  = {1995},
  doi = {10.1080/01621459.1995.10476502},
}

%% collapsibility, 
@Article{Hougaard_1999,
  title = {Fundamentals of Survival Data},
  author = {Philip Hougaard},
  journal = {Biometrics},
  volume = {55},
  number = {1},
  pages = {13--22},
  year = {1999},
  publisher = {John Wiley \& Sons},
  doi = {10.1111/j.0006-341x.1999.00013.x},
}

@Book{Lawless_2011,
  title = {Statistical Models and Methods for Lifetime Data},
  author = {Jerald F Lawless},
  year = {2011},
  publisher = {John Wiley \& Sons},
  edition = {2nd},
}

%% AFT models: first paper?
@article{Wei_1992,
  title = {The Accelerated Failure Time Model: A Useful Alternative to the
  {Cox} Regression Model in Survival Analysis},
  author = {Wei, Lee-Jen},
  journal = {Statistics in Medicine},
  volume = {11},
  number = {14-15},
  pages = {1871--1879},
  year = {1992},
  publisher = {Wiley Online Library},
  doi = {10.1002/sim.4780111409}
}

%% aalen model; "linear" model, drawbacks of coxph
@article{Aalen_1989,
  title = {A Linear Regression Model for the Analysis of Life Times},
  author = {Aalen, Odd O.},
  journal = {Statistics in Medicine},
  volume = {8},
  number = {8},
  pages = {907--925},
  doi = {10.1002/sim.4780080803},
  year = {1989}
}

%% Likelihoods for Aalen models
@article{Putter_2023,
  author = {Lu, Chengyuan and Goeman, Jelle and Putter, Hein},
  title = {Maximum likelihood estimation in the additive hazards model},
  journal = {Biometrics},
  volume = {},
  number = {},
  pages = {},
  keywords = {additive hazards, constrained optimization, maximum likelihood},
  doi = {10.1111/biom.13764},
  year = {2023},
}


%% relative mortality, 
@article{Ederer_1961,
  title = {The Relative Survival Rate: A Statistical Methodology},
  author = {F. Ederer and L. M. Axtell and S. J. Cutler},
  year = {1961},
  journal = {National Cancer Institute Monograph},
  volume = {6},
  pages = {101--121}
}

%% parameteric distributions in Ch. 2
@book{Kalbfleisch_Prentice_2002,
  title = {The Statistical Analysis of Failure Time Data},
  author = {Kalbfleisch, John D and Prentice, Ross L},
  volume = {360},
  year = {2002},
  publisher = {John Wiley \& Sons},
  doi = {10.1002/9781118032985},
}

%% ---- "causality ---
%% survival; no causality for Cox of RCT, collapsibility of AFT & additiv models 
@Article{Aalen_2015,
  title = {Does {Cox} Analysis of a Randomized Survival Study Yield a Causal Treatment Effect?},
  author = {Odd O Aalen and Richard J Cook and Kjetil Røysland},
  journal = {Lifetime Data Analysis},
  volume = {21},
  number = {4},
  pages = {579--593},
  year = {2015},
  publisher = {Springer-Verlag},
  doi = {10.1007/s10985-015-9335-y},
}

@Article{Martinez_MacKenzie_2022,
  title = {Estimating Population-Averaged Hazard Ratios in the Presence of Unmeasured Confounding},
  author = {Pablo Mart{\'\i}nez-Camblor and Todd A MacKenzie and A James O'Malley},
  journal = {The International Journal of Biostatistics},
  year = {2022},
  publisher = {De Gruyter},
  doi = {10.1515/ijb-2021-0096},
}

%% non-collapsible estimator
@article{Ford_Norrie_Ahmadi_1995,
  title = {Model Inconsistency, Illustrated by the {Cox} Proportional Hazards Model},
  author = {Ford, Ian and Norrie, John and Ahmadi, Susan},
  journal = {Statistics in Medicine},
  volume = {14},
  number = {8},
  pages = {735--746},
  doi = {10.1002/sim.4780140804},
  year = {1995}
}

@article{Ford_Norrie_2002,
  title = {The Role of Covariates in Estimating Treatment Effects and Risk in Long-term Clinical Trials},
  author = {Ford, Ian and Norrie, John},
  journal = {Statistics in Medicine},
  volume = {21},
  number = {19},
  pages = {2899--2908},
  doi = {10.1002/sim.1294},
  year = {2002}
}

@article{Struthers_Kalbfleisch_1986,
  author = {Struthers, C. A. and Kalbfleisch, J. D.},
  title = {Misspecified Proportional Hazard Models},
  journal = {Biometrika},
  volume = {73},
  number = {2},
  pages = {363--369},
  year = {1986},
  month = {08},
  doi = {10.1093/biomet/73.2.363},
}

%% Aalen model = collapsible
@article{Martinussen_2013,
  title = {On Collapsibility and Confounding Bias in {Cox} and {Aalen} Regression Models},
  author = {Martinussen, Torben and Vansteelandt, Stijn},
  journal = {Lifetime Data Analysis},
  volume = {19},
  number = {3},
  pages = {279--296},
  year = {2013},
  publisher = {Springer}
}


%% should be possible with tram; definitely have a look
@Article{Rhian_2021,
  title = {Making Apples From Oranges: Comparing Noncollapsible Effect Estimators And
  Their Standard Errors After Adjustment for Different Covariate Sets},
  author = {Daniel, Rhian and Zhang, Jingjing and Farewell, Daniel},
  journal = {Biometrical Journal},
  volume = {63},
  number = {3},
  pages = {528--557},
  doi = {10.1002/bimj.201900297},
  year = {2021}
}

%% ---- Cox ----
@Article{Royston_Parmar_2002,
  title = {Flexible Parametric Proportional-Hazards and Proportional-Odds Models
  for Censored Survival Data, with Application to Prognostic Modelling and Estimation of Treatment Effects},
  author = {Patrick Royston and Mahesh KB Parmar},
  journal = {Statistics in Medicine},
  volume = {21},
  number = {15},
  pages = {2175--2197},
  year = {2002},
  publisher = {John Wiley \& Sons},
  doi = {10.1002/sim.1203},
}

%% smooth AFT model
@article{Pang_2021,
  title = {Spline-Based Accelerated Failure Time Model},
  author = {Pang, Menglan and Platt, Robert W. and Schuster, Tibor and Abrahamowicz, Michal},
  journal = {Statistics in Medicine},
  volume = {40},
  number = {2},
  pages = {481-497},
  keywords = {accelerated failure time model, model misspecification, simulations, spline-based method, survival analysis},
  doi = {10.1002/sim.8786},
  year = {2021}
}


%% smooth AFT model = collapsible
@article{Crowther_Royston_Clements_2022,
  title = {A Flexible Parametric Accelerated Failure Time Model and the Extension to Time-Dependent Acceleration Factors},
  author = {Crowther, Michael J and Royston, Patrick and Clements, Mark},
  journal = {Biostatistics},
  year = {2023},
  volume = 24,
  number = 3, 
  pages = {811--831},
  doi = {10.1093/biostatistics/kxac009}
}


%% ---- nonPH / location-scale ----
@article{Zhang_Peng_2009,
  title = {Crossing Hazard Functions in Common Survival Models},
  author = {Jiajia Zhang and Yingwei Peng},
  journal = {Statistics \& Probability Letters},
  volume = {79},
  number = {20},
  pages = {2124--2130},
  year = {2009},
  doi = {10.1016/j.spl.2009.07.002},
}

%% nonPH; location-scale
%% outcome: right-censored
%% BL hazard: Weibull
%% Software: mpr pkg
%% Parameterisation: same as stram order = 1
@article{Burke_2017,
  title = {Multi-Parameter Regression Survival Modeling: An Alternative to Proportional Hazards},
  author = {Burke, K. and MacKenzie, G.},
  journal = {Biometrics},
  volume = {73},
  number = {2},
  pages = {678--686},
  doi = {10.1111/biom.12625},
  year = {2017}
}

%% nonPH; location-scale
%% outcome: interval-censored
%% BL hazard: Weibull
%% Software; none, but can be estimated with gamlss.cens pkg
%% Parameterisation: same as stram order = 1
@article{Burke_SiM_2020,
  title = {A Multiparameter Regression Model for Interval-Censored Survival Data},
  author = {Peng, Defen and MacKenzie, Gilbert and Burke, Kevin},
  journal = {Statistics in Medicine},
  volume = {39},
  number = {14},
  pages = {1903--1918},
  doi = {10.1002/sim.8508},
  year = {2020}
}

%% nonPH; location-scale
%% BL hazard: Weibull, power generalized Weibull distributions with 2 shape parameters 
%% containing log-logistic, Weibull and Gompertz family
%% software: none
@article{Burke_2020,
  title = {A Flexible Parametric Modelling Framework for Survival Analysis},
  author = {Burke, Kevin and Jones, M. C. and Noufaily, Angela},
  journal = {Journal of the Royal Statistical Society: Series~C (Applied Statistics)},
  volume = {69},
  number = {2},
  pages = {429--457},
  doi = {10.1111/rssc.12398},
  year = {2020}
}

%% nonPH; location-scale; unspecified BL transformation; no software
@article{Burke_SJoS_2020,
  title = {Semiparametric Multiparameter Regression Survival Modeling},
  author = {Burke, Kevin and Eriksson, Frank and Pipper, C. B.},
  journal = {Scandinavian Journal of Statistics},
  volume = {47},
  number = {2},
  pages = {555--571},
  doi = {10.1111/sjos.12416},
  year = {2020}
}

%% nonPH; probabilistic index
@article{Dunkler_2018,
  title = {Weighted {Cox} Regression Using the \proglang{R}~Package \pkg{coxphw}},
  author = {Dunkler, Daniela and Ploner, Meinhard and Schemper, Michael and Heinze, Georg},
  journal = {Journal of Statistical Software},
  volume = {84},
  pages = {1--26},
  number = {2},
  doi = {10.18637/jss.v084.i02},
  year = {2018},
}

%% nonPH; similar to stram
@article{Begun_2023,
  author = {Begun, Alexander and Kulinskaya, Elena and Ncube, Njabulo},
  title = {A double-Cox model for non-proportional hazards survival analysis with frailty},
  journal = {Statistics in Medicine},
  volume = {},
  number = {},
  pages = {},
  keywords = {Cox regression, marginal likelihood, parametric survival analysis, shape and scale modeling, shared frailty},
  doi = {10.1002/sim.9760},
}

%% ---- cure models ----
%% cure; eqn 1 implemented in pkg mlt
@article{Price_2001,
  author = {Price, Dionne L. and Manatunga, Amita K.},
  title = {Modelling Survival Data With a Cured Fraction Using Frailty Models},
  journal = {Statistics in Medicine},
  volume = {20},
  number = {9-10},
  pages = {1515--1527},
  doi = {10.1002/sim.687},
  year = {2001}
}

%% cure; unified: mixture + non-mixture
@article{Yin_Ibrahim_2005,
  title = {Cure Rate Models: A Unified Approach},
  author = {Yin, Guosheng and Ibrahim, Joseph G.},
  journal = {Canadian Journal of Statistics},
  volume = {33},
  number = {4},
  pages = {559--570},
  keywords = {Bayesian inference, Box-Cox transformation, cure fraction, Gibbs sampling, mixture cure model, promotion time cure model},
  doi = {10.1002/cjs.5550330407},
  year = {2005}
}

%% cure; unified: mixture + non-mixture
@article{Pal_Roy_2023,
   title = {On the Parameter Estimation of Box-Cox Transformation Cure Model},
  author = {Pal, Suvra and Roy, Souvik},
  journal = {Statistics in Medicine},
  volume = {42},
  number = {15},
  pages = {2600--2618},
  keywords = {line search, long-term survivors, melanoma, profile likelihood},
  doi = {10.1002/sim.9739},
  year = {2023}
}

@article{Wenbin_2004,
  title = {On Semiparametric Transformation Cure Models},
  author = {Wenbin Lu and Zhiliang Ying},
  journal = {Biometrika},
  number = {2},
  pages = {331--343},
  publisher = {Oxford University Press, Biometrika Trust},
  volume = {91},
  year = {2004},
  url = {https://www.jstor.org/stable/20441105},
}

%% cure; location-scale
%% BL hazard: non-parametric
@article{Chown_Heuchenne_Keilegom_2020,
  title = {The Nonparametric Location-Scale Mixture Cure Model},
  author = {Chown, Justin and Heuchenne, C{\'e}dric and Van Keilegom, Ingrid},
  journal = {Test},
  volume = {29},
  pages = {1008--1028},
  year = {2020},
  publisher = {Springer},
  doi = {10.1007/s11749-019-00698-8},
}

%% cure 
@article{Musta_Patilea_Keilegom_2022,
  title = {A Presmoothing Approach for Estimation in the Semiparametric {Cox} Mixture Cure Model},
  author = {Eni Musta and Valentin Patilea and Ingrid Van Keilegom},
  volume = {28},
  journal = {Bernoulli},
  number = {4},
  pages = {2689--2715},
  year = {2022},
  doi = {10.3150/21-BEJ1434},
}

%% cure
%% Software: cuRe and rstpm2 pkg
@article{Jensen_Clements_2022,
  title = {Fitting parametric cure models in \proglang{R} using the packages \pkg{cuRe} and \pkg{rstpm2}},
   author = {Rasmus Kuhr Jensen and Mark Clements and Lars Klingen Gj{\ae}rde and Lasse Hjort Jakobsen},
  journal = {Computer Methods and Programs in Biomedicine},
  volume = {226},
  pages = {107125},
  year = {2022},
  doi = {10.1016/j.cmpb.2022.107125},
  keywords = {Cure models, Parametric models, Splines, Relative survival, CuRe, Rstpm2},
}

%% cure; covariate dependent cure fraction; identifiability
%% Software: rely on smcure pkg
@article{Parsa_Keilegom_2022,
  title = {Accelerated Failure Time {vs} {Cox} Proportional Hazards Mixture Cure Models: {David vs Goliath}?},
  author = {Parsa, Motahareh and Van Keilegom, Ingrid},
  journal = {Statistical Papers},
  pages = {1--21},
  year = {2022},
  publisher = {Springer},
  doi = {10.1007/s00362-022-01345-5}
}

%% cure; nonPH (location-scale)
%% BL hazard: non-parametric
%% software: fhc pkg (GitHub)
%% Parameterisation: same as stram with cure fraction
@article{Xie_Huang_Li_2022,
  title = {A Flexible-Hazards Cure Model With Application to Patients With Soft Tissue Sarcoma},
  author = {Xie, Can and Huang, Xuelin and Li, Ruosha and Pisters, Peter W. T.},
  journal = {Statistics in Medicine},
  volume = {41},
  number = {29},
  pages = {5698--5714},
  keywords = {cure model, nonproportional hazards regression, profile likelihood estimation, promotion time cure model, proportional hazards, survival analysis},
  doi = {10.1002/sim.9588},
  year = {2022}
}

%% ---- frailty ----
@article{Hougaard_1986,
 title = {Survival Models for Heterogeneous Populations Derived from Stable Distributions},
 author = {Philip Hougaard},
 journal = {Biometrika},
 number = {2},
 pages = {387--396},
 publisher = {Oxford University Press, Biometrika Trust},
 volume = {73},
 year = {1986},
 doi = {10.2307/2336215},
}

%% frailty
@article{Hougaard_1995,
  title = {Frailty Models for Survival Data},
  author = {Hougaard, Philip},
  journal = {Lifetime Data Analysis},
  volume = {1},
  pages = {255--273},
  year = {1995},
  publisher = {Springer},
  doi = {10.1007/BF00985760},
}

%% frailty PO model
@article{Dabrowska_Doksum_1988,
  title = {Estimation and Testing in a Two-Sample Generalized Odds-Rate Model},
  author = {Dabrowska, Dorota M and Doksum, Kjell A},
  journal = {Journal of the American Statistical Association},
  volume = {83},
  number = {403},
  pages = {744--749},
  year = {1988},
  publisher = {Taylor \& Francis},
  doi = {10.1080/01621459.1988.10478657},
}

@article{Balan_Putter_2020,
  author = {Theodor A Balan and Hein Putter},
  title = {A Tutorial on Frailty Models},
  journal = {Statistical Methods in Medical Research},
  volume = {29},
  number = {11},
  pages = {3424--3454},
  year = {2020},
  doi = {10.1177/0962280220921889},
}

@article{Balan_Putter_2019,
  author = {Balan, Theodor Adrian and Putter, Hein},
  title = {Nonproportional hazards and unobserved heterogeneity in clustered survival data: When can we tell the difference?},
  journal = {Statistics in Medicine},
  volume = {38},
  number = {18},
  pages = {3405--3420},
  keywords = {frailty, proportional hazards, unobserved heterogeneity}, 
  doi = {10.1002/sim.8171},
  year = {2019}
}

@article{Chauvet_Rondea_2023,
  author = {Chauvet, Jocelyn and Rondeau, Virginie},
  title = {A flexible class of generalized joint frailty models for the analysis of survival endpoints},
  journal = {Statistics in Medicine},
  volume = {42},
  number = {8},
  pages = {1233--1262},
  keywords = {frailty models, generalized survival models, joint modeling, recurrent events, terminal event},
  doi = {10.1002/sim.9667},
  year = {2023}
}

@article{Choi_Huang_2012,
  author = {Choi, Sangbum and Huang, Xuelin},
  title = {A General Class of Semiparametric Transformation Frailty Models for Nonproportional Hazards Survival Data},
  journal = {Biometrics},
  volume = {68},
  number = {4},
  pages = {1126--1135},
  keywords = {Compound Poisson frailty, Counting process, Cure fraction, Discrete frailty, Nonparametric likelihood, Survival analysis, Transformation models},
  doi = {10.1111/j.1541-0420.2012.01784.x},
  year = {2012}
}

%%
@article{Commenges_Andersen_1995,
  title = {Score Test of Homogeneity for Survival Data},
  author = {Commenges, Daniel and Andersen, Per Kragh},
  journal = {Lifetime Data Analysis},
  volume = {1},
  number = {2},
  pages = {145--156},
  year = {1995},
  publisher = {Springer},
  doi = {10.1007/bf00985764},
}

%% ---- random effects ----
%% REs, flexible parameteric; package "rstpm2"
@article{Liu_Pawitan_Clements_2017,
  author = {Liu, Xing-Rong and Pawitan, Yudi and Clements, Mark},
  title = {Generalized Survival Models for Correlated Time-To-Event Data},
  journal = {Statistics in Medicine},
  volume = {36},
  number = {29},
  pages = {4743--4762},
  doi = {10.1002/sim.7451},
  year = {2017}
}

%% ---- dependent censoring ---
@article{Deresa_Keilegom_2023,
  author = {Negera Wakgari Deresa and Ingrid {Van Keilegom}},
  title = {Copula Based {Cox} Proportional Hazards Models for Dependent Censoring},
  journal = {Journal of the American Statistical Association},
  year  = {2024},
  volume = {119},
  number = {546},
  pages = {1044-1054},
  doi = {10.1080/01621459.2022.2161387},
}

@article{Cazado_Keilegom_2022,
  author = {Czado, C and {Van Keilegom}, I},
  title = {Dependent Censoring Based on Parametric Copulas},
  journal = {Biometrika},
  year = {2023},
  volume = 110, 
  number = 3,
  pages = {721--738},
  doi = {10.1093/biomet/asac067},
}

%% ---- competing risk ----
%% competing risk; direct modelling of subhazards
@article{Lambert_Wilkes_Crowther_2017,
  title = {Flexible Parametric Modelling of the Cause-Specific Cumulative Incidence Function},
  author = {Lambert, Paul C. and Wilkes, Sally R. and Crowther, Michael J.},
  journal = {Statistics in Medicine},
  volume = {36},
  number = {9},
  pages = {1429--1446},
  keywords = {competing risks, cumulative incidence function, flexible parametric models},
  doi = {10.1002/sim.7208},
  year = {2017}
}

%% competing risk; cause-specfic models
@article{Hinchliffe_Lambert_2013,
  title = {Flexible Parametric Modelling of Cause-Specific Hazards to Estimate Cumulative Incidence Functions},
  author = {Hinchliffe, Sally R and Lambert, Paul C},
  journal = {BMC Medical Research Methodology},
  volume = {13},
  pages = {1--14},
  year = {2013},
  publisher = {Springer},
  doi = {10.1186/1471-2288-13-13}
}

%% REs, multivariate
@Article{Zeng_2009,
  title = {Semiparametric Transformation Models with Random Effects for Joint Analysis of Recurrent and Terminal Events},
  author = {Donglin Zeng and DY Lin},
  journal = {Biometrics},
  volume = {65},
  number = {3},
  pages = {746--752},
  year = {2009},
  publisher = {John Wiley \& Sons},
  doi = {10.1111/j.1541-0420.2008.01126.x},
}

%% frailty; crisk
@Article{Jiang_Haneuse_2017,
  title = {A Semi-Parametric Transformation Frailty Model for Semi-Competing Risks Survival Data},
  author = {Fei Jiang and Sebastien Haneuse},
  journal = {Scandinavian Journal of Statistics},
  volume = {44},
  number = {1},
  pages = {112--129},
  year = {2017},
  publisher = {John Wiley \& Sons},
  doi = {10.1111/sjos.12244},
}

%% frailty; multivariate
@article{Zeng_2009,
  title = {Gamma Frailty Transformation Models for Multivariate Survival Times},
  author = {Zeng, Donglin and Chen, Qingxia and Ibrahim, Joseph G.},
  journal = {Biometrika},
  volume = {96},
  number = {2},
  pages = {277--291},
  year = {2009},
  doi = {10.1093/biomet/asp008},
}

%% crisk
@Article{Mao_Lin,
  title = {Efficient Estimation of Semiparametric Transformation Models for the Cumulative Incidence of Competing Risks},
  author = {Lu Mao and DY Lin},
  journal = {Journal of the Royal Statistical Society Series~B: Statistical Methodology},
  volume = {79},
  number = {2},
  pages = {573--587},
  year = {2017},
  publisher = {John Wiley \& Sons},
  doi = {10.1111/rssb.12177},
}

%% crisk; i-cens
@Article{Mao_Lin_Zeng_2017,
  title = {Semiparametric Regression Analysis of Interval-Censored Competing Risks Data},
  author = {Lu Mao and Dan-Yu Lin and Donglin Zeng},
  journal = {Biometrics},
  volume = {73},
  number = {3},
  pages = {857--865},
  year = {2017},
  publisher = {John Wiley \& Sons},
  doi = {10.1111/biom.12664},
}

%% crisk; copula
@misc{Wei_2023,
  title = {Bivariate Copula Regression Models for Semi-competing Risks}, 
  author = {Yinghui Wei and Malgorzata Wojtys and Lexy Sorrell and Peter Rowe},
  year = {2023},
  eprint = {2304.02954},
  archivePrefix = {arXiv},
  primaryClass = {stat.ME}
}

%% crisk; copula
@article{Lo_Wilke_2010,
 author = {Simon M. S. Lo and Ralf A. Wilke},
 journal = {Journal of the Royal Statistical Society. Series C (Applied Statistics)},
 number = {2},
 pages = {359--376},
 publisher = {Wiley, Royal Statistical Society},
 title = {A Copula Model for Dependent Competing Risks},
 volume = {59},
 year = {2010},
 url = {https://www.jstor.org/stable/40541690}
}

%% bivariate log-log
@TechReport{Vasudevan_Asha_2022,
  doi = {10.48550/ARXIV.2212.13383},
  author = {Vasudevan, Durga and Asha, G.},
  title = {On Modeling Bivariate Left Censored Data using Reversed Hazard Rates},
  institution = {arXiv.org E-Print Archive},
  year = {2022},
  type = {arXiv},
  number = {2212.13383},
}

%% competing risk
@article{He_2022,
  author = {He, Yizeng and Kim, Soyoung and Mao, Lu and Ahn, Kwang Woo},
  title = {Marginal Semiparametric Transformation Models for Clustered Multivariate Competing Risks Data},
  journal = {Statistics in Medicine},
  volume = {41},
  number = {26},
  pages = {5349--5364},
  doi = {10.1002/sim.9573},
  year = {2022}
}

@article{Lo_Wilke_2023,
  author = {Lo, Simon M S and Wilke, Ralf A},
  title = {A parametric competing risks regression model with unknown dependent censoring},
  journal = {Journal of the Royal Statistical Society Series~C (Applied Statistics)},
  pages = {qlad042},
  year = {2023},
  doi = {10.1093/jrsssc/qlad042},
}

@article{Eletti_2023,
  title = {A Spline-Based Framework for the Flexible Modelling of Continuously Observed Multistate Survival Processes},
  publisher = {SAGE Publications},
  year = {2023},
  journal = {Statistical Modelling: An International Journal},
  note = {This article has been accepted for publication in Statistical Modelling. Reuse is restricted to non-commercial and no derivative uses.},
  keywords = {additive predictor; multistate process; shape constrained P-splines; survival analysis; transition probabilities},
  url = {https://openaccess.city.ac.uk/id/eprint/30316/},
  author = {Eletti, A. and Marra, G. and Radice, R.}
}

%% "timereg" package
@Article{pkg:timereg:JSS,
  title = {Analyzing Competing Risk Data Using the \proglang{R} \pkg{timereg} Package},
  author = {Thomas H. Scheike and Mei-Jie Zhang},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {38},
  number = {2},
  pages = {1--15},
  doi = {10.18637/jss.v038.i02},
}

%% "timereg" package
@article{Scheike_2006,
  title = {A Flexible Semiparametric Transformation Model for Survival Data},
  author = {Scheike, Thomas H},
  journal = {Lifetime Data Analysis},
  volume = {12},
  pages = {461--480},
  year = {2006},
  publisher = {Springer}, 
  doi = {10.1007/s10985-006-9021-1},
}

%% "timereg" package
@book{Martinussen_2006,
  title = {Dynamic Regression Models for Survival Data},
  author = {Martinussen, Torben and Scheike, Thomas H},
  volume = {1},
  year = {2006},
  publisher = {Springer}
}

%% mgcv package: Smooth Cox model
@Article{Wood_2016,
  title = {Smoothing Parameter and Model Selection for General Smooth Models (with Discussion)},
  author = {S.N. Wood and N. Pya and B. S{\"a}fken},
  journal = {Journal of the American Statistical Association},
  year = {2016},
  pages = {1548--1575},
  volume = {111},
  doi = {10.1080/01621459.2016.1180986}
}

%% "rstpm2" package
@article{Liu_Pawitan_Clements_2016,
  doi = {10.1177/0962280216664760},
  year = {2016},
  publisher = {{SAGE} Publications},
  volume = {27},
  number = {5},
  pages = {1531--1546},
  author = {Xing-Rong Liu and Yudi Pawitan and Mark Clements},
  title = {Parametric and Penalized Generalized Survival Models},
  journal = {Statistical Methods in Medical Research}
}

%% "frailtyEM" package
@article{pkg:frailtyEM:JSS,
  doi = {10.18637/jss.v090.i07},
  year = {2019},
  publisher = {Foundation for Open Access Statistic},
  volume = {90},
  number = {7},
  author = {Theodor Adrian Balan and Hein Putter},
  title = {\pkg{frailtyEM}: An \proglang{R} Package for Estimating Semiparametric Shared Frailty Models},
  journal = {Journal of Statistical Software}
}

%% "survival" package
@book{Therneau_Grambsch_2000,
  author = {Terry M. Therneau and Patricia M. Grambsch},
  year = 2000,
  title = {Modeling Survival Data: Extending the Cox Model},
  publisher = {Springer-Verlag}, 
  address = {New York, U.S.A}
}
 
 %% "survival" package: Gamma frailty for coxph
 @article{Thernau_2003,
 URL = {http://www.jstor.org/stable/1391074},
 author = {Terry M. Therneau and Patricia M. Grambsch and V. Shane Pankratz},
 journal = {Journal of Computational and Graphical Statistics},
 number = {1},
 pages = {156--175},
 publisher = {[American Statistical Association, Taylor & Francis, Ltd., Institute of Mathematical Statistics, Interface Foundation of America]},
 title = {Penalized Survival Models and Frailty},
 volume = {12},
 year = {2003}
}

%% "ICsurv" package
@article{Wang_2015,
  doi = {10.1111/biom.12389},
  year = {2015},
  publisher = {Wiley},
  volume = {72},
  number = {1},
  pages = {222--231},
  author = {Lianming Wang and Christopher S. McMahan and Michael G. Hudgens and Zaina P. Qureshi},
  title = {A flexible,  computationally efficient method for fitting the proportional hazards model to interval-censored data},
  journal = {Biometrics}
}

 %% "survival" package: Gaussian frailty for coxph
@article{Ripatti_Palmgren_2000,
author = {Ripatti, Samuli and Palmgren, Juni},
title = {Estimation of Multivariate Frailty Models Using Penalized Partial Likelihood},
journal = {Biometrics},
volume = {56},
number = {4},
pages = {1016--1022},
keywords = {Dependent failure times, Frailty, Multivariate survival models, Penalized partial likelihood, Proportional hazards model, Random effects model, Variance components},
doi = {10.1111/j.0006-341X.2000.01016.x},
year = {2000}
}

%% "frailtypack" package: 
@article{pkg:frailtypack:JSS,
 title={\pkg{frailtypack}: An \proglang{R} Package for the Analysis of Correlated Survival Data with Frailty Models Using Penalized Likelihood Estimation or Parametrical Estimation},
 volume={47},
 doi={10.18637/jss.v047.i04},
 number={4},
 journal={Journal of Statistical Software},
 author={Rondeau, Virginie and Marzroui, Yassin and Gonzalez, Juan R.},
 year={2012},
 pages={1--28}
}

%% "TransModel" package
@article{pkg:TransModel:JSS,
 title={\pkg{TransModel}: An \proglang{R} Package for Linear Transformation Model with Censored Data},
 volume={101},
 doi={10.18637/jss.v101.i09},
 number={9},
 journal={Journal of Statistical Software},
 author={Zhou, Jie and Zhang, Jiajia and Lu, Wenbin},
 year={2022},
 pages={1--12}
}

%% "coxinterval" package: archived
@Manual{pkg:coxinterval,
  title = {\pkg{coxinterval}: Cox-Type Models for Interval-Censored Data},
  author = {Audrey Boruvka and Richard J. Cook},
  year = {2014},
  note = {\proglang{R}~package version~1.0},
  url = {https://CRAN.R-project.org/src/contrib/Archive/coxinterval/},
}

@article{pkg:icenReg:JSS,
 title={\pkg{icenReg}: Regression Models for Interval Censored Data in \proglang{R}},
 volume={81},
 doi={10.18637/jss.v081.i12},
 number={12},
 journal={Journal of Statistical Software},
 author={Anderson-Bergman, Clifford},
 year={2017},
 pages={1--23}
}

@article{pkg:gamlss:JSS,
 title={Generalized Additive Models for Location Scale and Shape ({GAMLSS}) in \proglang{R}},
 volume={23},
 doi={10.18637/jss.v023.i07},
 number={7},
 journal={Journal of Statistical Software},
 author={Stasinopoulos, D. Mikis and Rigby, Robert A.},
 year={2007},
 pages={1--46}
}

%% ---- ?? ----
@Article{Strohmaier_2015,
  title = {Dynamic Path Analysis -- A Useful Tool to Investigate Mediation Processes in Clinical Survival Trials},
  author = {Susanne Strohmaier and Kjetil R{\o}ysland and Rune Hoff and {\O}rnulf Borgan and Terje R Pedersen and Odd O Aalen},
  journal = {Statistics in Medicine},
  volume = {34},
  number = {29},
  pages = {3866--3887},
  year = {2015},
  publisher = {John Wiley \& Sons},
  doi = {10.1002/sim.6598},
}

@article{Bender_Augustin_Blettner_2005,
author = {Bender, Ralf and Augustin, Thomas and Blettner, Maria},
title = {Generating Survival Times to Simulate {Cox} Proportional Hazards Models},
journal = {Statistics in Medicine},
volume = {24},
number = {11},
pages = {1713--1723},
doi = {10.1002/sim.2059},
year = {2005},
}

