book.bib

@book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.name/knitr/},
}

@incollection{diaz2018stochastic,
  title={Stochastic Treatment Regimes},
  author={D{\'\i}az, Iv{\'a}n and {van der Laan}, Mark J},
  booktitle={Targeted Learning in Data Science: Causal Inference for Complex
    Longitudinal Studies},
  pages={167--180},
  year={2018},
  publisher={Springer Science \& Business Media}
}

@article{diaz2012population,
  title={Population intervention causal effects based on stochastic
    interventions},
  author={D{\'\i}az, Iv{\'a}n and {van der Laan}, Mark J},
  journal={Biometrics},
  volume={68},
  number={2},
  pages={541--549},
  year={2012},
  publisher={Wiley Online Library}
}

@book{vdl2018targeted,
  title={Targeted Learning in Data Science: Causal Inference for Complex
    Longitudinal Studies},
  author={{van der Laan}, Mark J and Rose, Sherri},
  year={2018},
  publisher={Springer Science \& Business Media}
}

@book{vdl2011targeted,
  title={Targeted learning: causal inference for observational and experimental
         data},
  author={{van der Laan}, Mark J and Rose, Sherri},
  year={2011},
  publisher={Springer Science \& Business Media}
}

@article{diaz2011super,
  title={Super learner based conditional density estimation with application to
    marginal structural models},
  author={D{\'\i}az, Iv{\'a}n and {van der Laan}, Mark J},
  journal={The International Journal of Biostatistics},
  volume={7},
  number={1},
  pages={1--20},
  year={2011},
  publisher={De Gruyter}
}

@article{vdl2006targeted,
  title={Targeted maximum likelihood learning},
  author={{van der Laan}, Mark J and Rubin, Daniel},
  journal={The International Journal of Biostatistics},
  volume={2},
  number={1},
  year={2006}
}

@article{vdl2004asymptotic,
  title={Asymptotic optimality of likelihood-based cross-validation},
  author={{van der Laan}, Mark J and Dudoit, Sandrine and Keles, Sunduz},
  journal={Statistical Applications in Genetics and Molecular Biology},
  volume={3},
  number={1},
  pages={1--23},
  year={2004}
}

@article{dudoit2005asymptotics,
  title={Asymptotics of cross-validated risk estimation in estimator selection
    and performance assessment},
  author={Dudoit, Sandrine and {van der Laan}, Mark J},
  journal={Statistical Methodology},
  volume={2},
  number={2},
  pages={131--154},
  year={2005},
  publisher={Elsevier}
}

@article{vdl2007super,
  title={{Super Learner}},
  author={{van der Laan}, Mark J and Polley, Eric C and Hubbard, Alan E},
  journal={Statistical Applications in Genetics and Molecular Biology},
  volume={6},
  number={1},
  year={2007}
}

@article{breiman1996stacked,
  title={Stacked regressions},
  author={Breiman, Leo},
  journal={Machine Learning},
  volume={24},
  number={1},
  pages={49--64},
  year={1996},
  publisher={Springer}
}

@book{pearl2009causality,
  title={Causality: Models, Reasoning, and Inference},
  author={Pearl, Judea},
  year={2009},
  publisher={Cambridge University Press}
}

@article{holland1986statistics,
  title={Statistics and causal inference},
  author={Holland, Paul W},
  journal={Journal of the American statistical Association},
  volume={81},
  number={396},
  pages={945--960},
  year={1986},
  publisher={Taylor \& Francis}
}

@article{rosenbaum1983central,
  title={The central role of the propensity score in observational studies for
    causal effects},
  author={Rosenbaum, Paul R and Rubin, Donald B},
  journal={Biometrika},
  volume={70},
  number={1},
  pages={41--55},
  year={1983},
  publisher={Biometrika Trust}
}

@article{haneuse2013estimation,
  title={Estimation of the effect of interventions that modify the received
    treatment},
  author={Haneuse, Sebastian and Rotnitzky, Andrea},
  journal={Statistics in medicine},
  volume={32},
  number={30},
  pages={5260--5277},
  year={2013},
  publisher={Wiley Online Library}
}

@article{young2014identification,
  title={Identification, estimation and approximation of risk under
    interventions that depend on the natural value of treatment using
    observational data},
  author={Young, Jessica G and Hern{\'a}n, Miguel A and Robins, James M},
  journal={Epidemiologic methods},
  volume={3},
  number={1},
  pages={1--19},
  year={2014},
  publisher={De Gruyter}
}

@article{rubin2005causal,
  title={Causal inference using potential outcomes: Design, modeling,
    decisions},
  author={Rubin, Donald B},
  journal={Journal of the American Statistical Association},
  volume={100},
  number={469},
  pages={322--331},
  year={2005},
  publisher={Taylor \& Francis}
}

@article{rubin1978bayesian,
  title={Bayesian inference for causal effects: The role of randomization},
  author={Rubin, Donald B},
  journal={The Annals of statistics},
  pages={34--58},
  year={1978},
  publisher={JSTOR}
}

@article{rubin1980randomization,
  title={Randomization analysis of experimental data: The Fisher randomization
    test comment},
  author={Rubin, Donald B},
  journal={Journal of the American Statistical Association},
  volume={75},
  number={371},
  pages={591--593},
  year={1980},
  publisher={JSTOR}
}

@article{kennedy2017non,
  title={Non-parametric methods for doubly robust estimation of continuous
    treatment effects},
  author={Kennedy, Edward H and Ma, Zongming and McHugh, Matthew D and Small,
    Dylan S},
  journal={Journal of the Royal Statistical Society: Series B (Statistical
    Methodology)},
  volume={79},
  number={4},
  pages={1229--1245},
  year={2017},
  publisher={Wiley Online Library}
}

@article{wolpert1992stacked,
  title={Stacked generalization},
  author={Wolpert, David H},
  journal={Neural networks},
  volume={5},
  number={2},
  pages={241--259},
  year={1992},
  publisher={Elsevier}
}

@article{kennedy2018nonparametric,
  title={Nonparametric causal effects based on incremental propensity score
    interventions},
  author={Kennedy, Edward H},
  journal={Journal of the American Statistical Association},
  number={just-accepted},
  year={2018},
  publisher={Taylor \& Francis}
}

@article{hejazi2019+generally,
  doi = {},
  url = {},
  year = {2019+},
  publisher = {},
  volume = {},
  number = {},
  pages = {},
  author = {Hejazi, Nima S and Benkeser, David C and Janes, Holly E and
    Gilbert, Peter B and {van der Laan}, Mark J},
  title = {Generally efficient nonparametric inference under two-phase
    sampling, with applications to stochastic interventions},
  journal = {}
}

@article{cvtmle2010,
  author = {Zheng, W. and {van der Laan}, M.~J},
  title = "{Asymptotic Theory for Cross-validated Targeted Maximum Likelihood
    Estimation}",
  journal = {U.C. Berkeley Division of Biostatistics Working Paper Series.},
  year = 2010,
  adsurl = {https://biostats.bepress.com/ucbbiostat/paper273},
}

@article{luedtke2016super,
  Author = {Luedtke, A. and {van der Laan}, M.~J},
  Journal = {International Journal of Biostatistics},
  Note = {PMID: 27227726},
  Number = {1},
  Pages = {305--332},
  Title = {Super-learning of an optimal dynamic treatment rule},
  Volume = {12},
  Year = {2016}
}

@article{vanderLaanLuedtke15,
  Author = {{van der Laan}, M.~J and Luedtke, A.},
  Journal = {Journal of Causal Inference},
  Note = {PMCID: PMC4517487},
  Number = {1},
  Pages = {61--95},
  Title = {Targeted learning of the mean outcome under an optimal dynamic
    treatment rule},
  Volume = {3},
  Year = {2015}
}

@book{Sutton1998,
  title={Introduction to reinforcement learning},
  author={Sutton, Richard S and Barto, Andrew G and others},
  volume={135},
  year={1998},
  publisher={MIT press Cambridge}
}

@article{murphy2003,
  title={Optimal dynamic treatment regimes},
  author={Murphy, Susan A},
  journal={Journal of the Royal Statistical Society: Series B (Statistical
    Methodology)},
  volume={65},
  number={2},
  pages={331--355},
  year={2003},
  publisher={Wiley Online Library}
}

@Inbook{robins2004,
  author="Robins, James M.",
  editor="Lin, D. Y. and Heagerty, P. J.",
  title="Optimal Structural Nested Models for Optimal Sequential Decisions",
  bookTitle="Proceedings of the Second Seattle Symposium in Biostatistics:
    Analysis of Correlated Data",
  year="2004",
  publisher="Springer New York",
  address="New York, NY",
  pages="189--326",
  doi="10.1007/978-1-4419-9076-1_11",
  url="https://doi.org/10.1007/978-1-4419-9076-1_11"
}

@article{vdl2014entering,
  title={Entering the era of data science: Targeted learning and the
    integration of statistics and computational data analysis},
  author={{van der Laan}, Mark J and Starmans, Richard JCM},
  journal={Advances in Statistics},
  volume={2014},
  year={2014},
  publisher={Hindawi}
}

@article{vdl2003unified,
  title={Unified cross-validation methodology for selection among estimators
    and a general cross-validated adaptive epsilon-net estimator: Finite sample
    oracle inequalities and examples},
  author={{van der Laan}, Mark J and Dudoit, Sandrine},
  year={2003},
  journal={bepress},
  publisher={bepress}
}

@article{wolpert1992stacked,
  title={Stacked generalization},
  author={Wolpert, David H},
  journal={Neural networks},
  volume={5},
  number={2},
  pages={241--259},
  year={1992},
  publisher={Elsevier}
}


@article{naturenews_2015,
  title={Let’s think about cognitive bias},
  author={{Nature Editorial}},
  journal={Nature},
  publisher={Springer Nature},
  year={2015},
  month={Oct},
  volume={526},
  number={7572}
}

@article{peng2015reproducibility,
  title={The reproducibility crisis in science: A statistical counterattack},
  author={Peng, Roger},
  journal={Significance},
  volume={12},
  number={3},
  pages={30--32},
  year={2015},
  publisher={Wiley Online Library}
}

@article{munafo2017manifesto,
  title={A manifesto for reproducible science},
  author={Munaf{\`o}, Marcus R and Nosek, Brian A and Bishop, Dorothy VM and
    Button, Katherine S and Chambers, Christopher D and Du Sert, Nathalie
    Percie and Simonsohn, Uri and Wagenmakers, Eric-Jan and Ware, Jennifer J
    and Ioannidis, John PA},
  journal={Nature Human Behaviour},
  volume={1},
  number={1},
  pages={0021},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{naturenews2_2015,
  author={{Nature Editorial}},
  title={How scientists fool themselves --- and how they can stop},
  journal={Nature},
  publisher={Springer Nature},
  year={2015},
  month={Oct},
  volume={526},
  number={7572}
}

@article{forstmeier2017detecting,
  title={Detecting and avoiding likely false-positive findings--a practical
    guide},
  author={Forstmeier, Wolfgang and Wagenmakers, Eric-Jan and Parker, Timothy
    H},
  journal={Biological Reviews},
  volume={92},
  number={4},
  pages={1941--1968},
  year={2017},
  publisher={Wiley Online Library}
}

@article{nosek2018preregistration,
  title={The preregistration revolution},
  author={Nosek, Brian A and Ebersole, Charles R and DeHaven, Alexander C and
    Mellor, David T},
  journal={Proceedings of the National Academy of Sciences},
  volume={115},
  number={11},
  pages={2600--2606},
  year={2018},
  publisher={National Acad Sciences}
}

@article{baker2016there,
  title={Is there a reproducibility crisis? A Nature survey lifts the lid on
    how researchers view the crisis rocking science and what they think will
    help},
  author={Baker, Monya},
  journal={Nature},
  volume={533},
  number={7604},
  pages={452--455},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{szucs2017null,
  title={When null hypothesis significance testing is unsuitable for research:
    a reassessment},
  author={Szucs, Denes and Ioannidis, John},
  journal={Frontiers in human neuroscience},
  volume={11},
  pages={390},
  year={2017},
  publisher={Frontiers}
}

@article{pullenayegum2016knowledge,
  title={Knowledge translation in biostatistics: a survey of current practices,
    preferences, and barriers to the dissemination and uptake of new
      statistical methods},
  author={Pullenayegum, Eleanor M and Platt, Robert W and Barwick, Melanie and
    Feldman, Brian M and Offringa, Martin and Thabane, Lehana},
  journal={Statistics in medicine},
  volume={35},
  number={6},
  pages={805--818},
  year={2016},
  publisher={Wiley Online Library}
}

@article{stromberg2004write,
  title={Why write statistical software? The case of robust statistical
    methods},
  author={Stromberg, Arnold and others},
  journal={Journal of Statistical Software},
  volume={10},
  number={5},
  pages={1--8},
  year={2004}
}

@article{stark2018cargo,
  title={Cargo-cult statistics and scientific crisis},
  author={Stark, Philip B and Saltelli, Andrea},
  journal={Significance},
  volume={15},
  number={4},
  pages={40--43},
  year={2018},
  publisher={Wiley Online Library}
}

@article{luby2018effects,
  title={Effects of water quality, sanitation, handwashing, and nutritional
    interventions on diarrhoea and child growth in rural Bangladesh: a cluster
    randomised controlled trial},
  author={Luby, Stephen P and Rahman, Mahbubur and Arnold, Benjamin F and
    Unicomb, Leanne and Ashraf, Sania and Winch, Peter J and Stewart, Christine
    P and Begum, Farzana and Hussain, Faruqe and Benjamin-Chung, Jade and
    others},
  journal={The Lancet Global Health},
  volume={6},
  number={3},
  pages={e302--e315},
  year={2018},
  publisher={Elsevier}
}

@book{moodie2013,
  Author = {Chakraborty, Bibhas and Moodie, Erica EM},
  Title = {Statistical Methods for Dynamic Treatment Regimes: Reinforcement
    Learning, Causal Inference, and Personalized Medicine (Statistics for
    Biology and Health)},
  Publisher = {Springer},
  Year = {2013},
  ISBN = {1461474272},
}

@article{robins2014,
author = "Robins, James and Rotnitzky, Andrea",
doi = "10.1214/14-EJS908",
fjournal = "Electronic Journal of Statistics",
journal = "Electron. J. Statist.",
number = "1",
pages = "1273--1289",
publisher = "The Institute of Mathematical Statistics and the Bernoulli
  Society",
title = "Discussion of “Dynamic treatment regimes: Technical challenges and
  applications”",
url = "https://doi.org/10.1214/14-EJS908",
volume = "8",
year = "2014"
}

@article{polley2010super,
  title={Super learner in prediction},
  author={Polley, Eric C and {van der Laan}, Mark J},
  year={2010},
  journal={bepress},
  publisher={bepress}
}

@article{van2006oracle,
  title={Oracle inequalities for multi-fold cross validation},
  author={{van der Vaart}, Aad W and Dudoit, Sandrine and {van der Laan}, Mark
    J},
  journal={Statistics \& Decisions},
  volume={24},
  number={3},
  pages={351--371},
  year={2006},
  publisher={Oldenbourg Wissenschaftsverlag}
}

@incollection{buckheit1995wavelab,
  title={Wavelab and reproducible research},
  author={Buckheit, Jonathan B and Donoho, David L},
  booktitle={Wavelets and statistics},
  pages={55--81},
  year={1995},
  publisher={Springer}
}

@software{hejazi2020haldensify,
  author = {Hejazi, Nima S and Benkeser, David C and {van der Laan}, Mark J},
  title = {{haldensify}: Highly adaptive lasso conditional density estimation},
  year  = {2020},
  howpublished = {\url{https://github.com/nhejazi/haldensify}},
  note = {{R} package version 0.0.5},
  url = {https://doi.org/10.5281/zenodo.3698329},
  doi = {10.5281/zenodo.3698329}
}

@software{coyle2020hal9001,
  author = {Coyle, Jeremy R and Hejazi, Nima S and {van der Laan}, Mark J},
  title = {{hal9001}: The scalable highly adaptive lasso},
  year  = {2020},
  url = {https://doi.org/10.5281/zenodo.3558313},
  doi = {10.5281/zenodo.3558313},
  note = {{R} package version 0.2.7}
}

@article{hejazi2020hal9001,
  author = {Hejazi, Nima S and Coyle, Jeremy R and {van der Laan}, Mark J},
  title = {{hal9001}: Scalable highly adaptive lasso regression in {R}},
  year  = {2020},
  url = {https://doi.org/10.21105/joss.02526},
  doi = {10.21105/joss.02526},
  journal = {Journal of Open Source Software},
  publisher = {The Open Journal}
}

@inproceedings{benkeser2016hal,
  doi = {10.1109/dsaa.2016.93},
  url = {https://doi.org/10.1109/dsaa.2016.93},
  year  = {2016},
  publisher = {{IEEE}},
  author = {Benkeser, David and {van der Laan}, Mark J},
  title = {The Highly Adaptive Lasso Estimator},
  booktitle = {2016 {IEEE} International Conference on Data Science and
    Advanced Analytics ({DSAA})}
}

@book{wickham2014advanced,
  title={Advanced r},
  author={Wickham, Hadley},
  year={2014},
  publisher={Chapman and Hall/CRC}
}

@article{vaart2006oracle,
  title={Oracle inequalities for multi-fold cross validation},
  author={Van der Vaart, Aad W and Dudoit, Sandrine and van der Laan, Mark J},
  journal={Statistics \& Decisions},
  volume={24},
  number={3},
  pages={351--371},
  year={2006},
  publisher={Oldenbourg Wissenschaftsverlag}
}

@article{rvp2022super,
  doi = {10.48550/ARXIV.2204.06139},
  url = {https://arxiv.org/abs/2204.06139},
  author = {Phillips, Rachael V and {van der Laan}, Mark J and Lee, Hana and
    Gruber, Susan},
  title = {Practical considerations for specifying a super learner},
  publisher = {arXiv},
  year = {2022}
}

@Manual{SuperLearner,
 title = {SuperLearner: Super Learner Prediction},
 author = {Eric Polley and Erin LeDell and Chris Kennedy and Mark
   {van der Laan}},
 year = {2021},
 note = {R package version 2.0-28},
 url = {https://CRAN.R-project.org/package=SuperLearner},
}

@article{naimi2018stacked,
  title={Stacked generalization: an introduction to super learning},
  author={Naimi, Ashley I and Balzer, Laura B},
  journal={European Journal of Epidemiology},
  volume={33},
  number={5},
  pages={459--464},
  year={2018},
  publisher={Springer}
}