References

Agresti, Alan. 2010. Analysis of Ordinal Categorical Data. Vol. 656. John Wiley & Sons.

———. 2012. Categorical Data Analysis. Vol. 792. John Wiley & Sons. https://www.wiley.com/en-us/Categorical+Data+Analysis%2C+3rd+Edition-p-9780470463635.

———. 2015. Foundations of Linear and Generalized Linear Models. John Wiley & Sons. https://www.wiley.com/en-us/Foundations+of+Linear+and+Generalized+Linear+Models-p-9781118730034.

———. 2018. An Introduction to Categorical Data Analysis. John Wiley & Sons. https://www.wiley.com/en-us/An+Introduction+to+Categorical+Data+Analysis%2C+3rd+Edition-p-9781119405283.

Anderson, Edgar. 1935. “The Irises of the Gaspe Peninsula.” Bulletin of American Iris Society 59: 2–5.

Andrews, David F, and Agnes M Herzberg. 2012. Data: A Collection of Problems from Many Fields for the Student and Research Worker. Springer Science & Business Media. https://link.springer.com/book/10.1007/978-1-4612-5098-2.

Aragon, Tomas J. 2018. “Population Health Thinking with Bayesian Networks.” https://escholarship.org/uc/item/8000r5m5.

Aragon, Tomas J. 2013. Applied Epidemiology Using R. Online. https://tbrieder.org/epidata/course_reading/e_aragon.pdf.

———. 2017. Population Health Data Science with R: Transforming Data into Actionable Knowledge. Online. https://bookdown.org/medepi/phds/.

Bache, Stefan Milton, and Hadley Wickham. 2022. Magrittr: A Forward-Pipe Operator for r. https://CRAN.R-project.org/package=magrittr.

Banerjee, Sudipto, and Anindya Roy. 2014. Linear Algebra and Matrix Analysis for Statistics. Vol. 181. Crc Press Boca Raton. https://www.routledge.com/Linear-Algebra-and-Matrix-Analysis-for-Statistics/Banerjee-Roy/p/book/9781420095388.

Banner, Adrian D. 2007. The Calculus Lifesaver : All the Tools You Need to Excel at Calculus. A Princeton Lifesaver Study Guide. Princeton, New Jersey: Princeton University Press. https://press.princeton.edu/books/paperback/9780691130880/the-calculus-lifesaver.

Batra, Neale, ed. 2024. The Epidemiologist R Handbook. Online. https://www.epirhandbook.com/.

Bliss, C. I. 1935. “The Calculation of the Dosage-Mortality Curve.” Annals of Applied Biology 22 (1): 134–67. https://doi.org/10.1111/j.1744-7348.1935.tb07713.x.

Box, George E. P., and Norman Richard. Draper. 1987. Empirical Model-Building and Response Surfaces. Wiley Series in Probability and Mathematical Statistics. Applied Probability and Statistics. New York: Wiley.

Canchola, Alison J, Susan L Stewart, Leslie Bernstein, Dee W West, Ronald K Ross, Dennis Deapen, Richard Pinder, et al. 2003. “Cox Regression Using Different Time-Scales.” Western Users of SAS Software. https://www.lexjansen.com/wuss/2003/DataAnalysis/i-cox_time_scales.pdf.

Cannell, Brad, and Melvin Livingston. 2024. R for Epidemiology. Online. https://www.r4epi.com/.

Casella, George, and Roger Berger. 2002. Statistical Inference. 2nd ed. Cengage Learning. https://www.cengage.com/c/statistical-inference-2e-casella-berger/9780534243128/.

Chang, Winston. 2024. R Graphics Cookbook: Practical Recipes for Visualizing Data. O’Reilly Media. https://r-graphics.org/.

Chatterjee, Samprit, and Ali S Hadi. 2015. Regression Analysis by Example. John Wiley & Sons. https://www.wiley.com/en-us/Regression+Analysis+by+Example%2C+4th+Edition-p-9780470055458.

Clayton, David, and Michael Hills. 2013. Statistical Models in Epidemiology. Oxford University Press. https://global.oup.com/academic/product/statistical-models-in-epidemiology-9780199671182.

Congdon, Peter D. 2020. Bayesian Hierarchical Models: With Applications Using R, Second Edition. 2nd edition. Milton: CRC Press.

Copelan, Edward A, James C Biggs, James M Thompson, Pamela Crilley, Jeff Szer, John P Klein, Neena Kapoor, Belinda R Avalos, Isabel Cunningham, and Kerry Atkinson. 1991. “Treatment for Acute Myelocytic Leukemia with Allogeneic Bone Marrow Transplantation Following Preparation with BuCy2.” https://doi.org/10.1182/blood.V78.3.838.838.

Dalgaard, Peter. 2008. Introductory Statistics with r. New York, NY: Springer New York. https://link.springer.com/book/10.1007/978-0-387-79054-1.

Diggle, Peter, Scott Zeger, Patrick Heagerty, and Kung-Yee Liang. 2013. Analysis of Longitudinal Data. Second edition. Vol. 25. Oxford Statistical Science Series. United Kingdom: Oxford University Press.

Dobson, Annette J, and Adrian G Barnett. 2018. An Introduction to Generalized Linear Models. 4th ed. CRC press. https://doi.org/10.1201/9781315182780.

Dunn, Peter K, and Gordon K Smyth. 2018. Generalized Linear Models with Examples in R. Vol. 53. Springer. https://link.springer.com/book/10.1007/978-1-4419-0118-7.

Edelmann, Dominic. 2019. “Generalized Linear Models with Examples in r. Peter k.dunnand Gordon k.smyth (2018). Berlin, Germany: Springer Science+business Media, Pp. 562 Pages, ISBN: 978‐1‐4419‐0118‐7.” Biometrical Journal 62 (1): 253–53. https://doi.org/10.1002/bimj.201900264.

Efron, Bradley, and David V Hinkley. 1978. “Assessing the Accuracy of the Maximum Likelihood Estimator: Observed Versus Expected Fisher Information.” Biometrika 65 (3): 457–83.

Faraway, Julian J. 2016. Extending the Linear Model with r: Generalized Linear, Mixed Effects and Nonparametric Regression Models. 2nd ed. Chapman; Hall/CRC. https://doi.org/10.1201/9781315382722.

———. 2025. Linear Models with R. https://www.routledge.com/Linear-Models-with-R/Faraway/p/book/9781032583983.

Fay, Colin, Sébastien Rochette, Vincent Guyader, and Cervan Girard. 2021. Engineering Production-Grade Shiny Apps. Chapman; Hall/CRC. https://engineering-shiny.org/.

Fieller, Nick. 2016. Basics of Matrix Algebra for Statistics with R. Chapman; Hall/CRC. https://doi.org/10.1201/9781315370200.

Fitzmaurice, Garrett M, Marie Davidian, Geert Verbeke, and Geert Molenberghs. 2009. Longitudinal Data Analysis. Chapman & Hall/CRC Handbooks of Modern Statistical Methods. Boca Raton: CRC Press. https://doi.org/10.1201/9781420011579.

Fitzmaurice, Garrett M, Nan M Laird, and James H Ware. 2012. Applied Longitudinal Analysis. 2nd ed. Vol. 998. Wiley Series in Probability and Statistics. Chicester: Wiley. https://doi.org/10.1002/9781119513469.

Fox, John. 2015. Applied Regression Analysis and Generalized Linear Models. Sage publications.

Gałecki, Andrzej T., and Tomasz. Burzykowski. 2013. Linear Mixed-Effects Models Using R : A Step-by-Step Approach. Springer Texts in Statistics. New York, NY: Springer. https://doi.org/10.1007/978-1-4614-3900-4.

Gelman, Andrew, and Jennifer Hill. 2007. Data Analysis Using Regression and Multilevel/Hierarchical Models. Analytical Methods for Social Research. Cambridge, MA: Cambridge University Press.

Grambsch, Patricia M, and Terry M Therneau. 1994. “Proportional Hazards Tests and Diagnostics Based on Weighted Residuals.” Biometrika 81 (3): 515–26. https://doi.org/10.1093/biomet/81.3.515.

Greenland, Sander. 2014. “Regression Methods for Epidemiological Analysis.” In Handbook of Epidemiology, edited by Wolfgang Ahrens and Iris Pigeot, 1087–1159. New York, NY: Springer New York. https://doi.org/10.1007/978-0-387-09834-0_17.

Grinberg, Raffi. 2017. The Real Analysis Lifesaver: All the Tools You Need to Understand Proofs. 1st ed. Princeton Lifesaver Study Guides. Princeton: Princeton University Press. https://press.princeton.edu/books/paperback/9780691172934/the-real-analysis-lifesaver.

Hardin, James W, and Joseph M Hilbe. 2018. Generalized Linear Models and Extensions. 4th ed. Stata Press.

Harrell, Frank E. 2015. Regression Modeling Strategies: With Applications to Linear Models, Logistic Regression, and Survival Analysis. 2nd ed. Springer. https://doi.org/10.1007/978-3-319-19425-7.

Hedeker, Donald R., and Robert D. Gibbons. 2006. Longitudinal Data Analysis. Wiley Series in Probability and Statistics. Hoboken, N.J: Wiley-Interscience.

Hogg, Robert V., Elliot A. Tanis, and Dale L. Zimmerman. 2015. Probability and Statistical Inference. Ninth edition. Boston: Pearson.

Hosmer, David W, Stanley Lemeshow, and Rodney X Sturdivant. 2013. Applied Logistic Regression. John Wiley & Sons. https://onlinelibrary.wiley.com/doi/book/10.1002/9781118548387.

Hulley, Stephen, Deborah Grady, Trudy Bush, Curt Furberg, David Herrington, Betty Riggs, Eric Vittinghoff, for the Heart, and Estrogen/progestin Replacement Study (HERS) Research Group. 1998. “Randomized Trial of Estrogen Plus Progestin for Secondary Prevention of Coronary Heart Disease in Postmenopausal Women.” JAMA : The Journal of the American Medical Association 280 (7): 605–13.

James, Gareth, Daniela Witten, Trevor Hastie, Robert Tibshirani, et al. 2013. An Introduction to Statistical Learning. Vol. 112. Springer. https://www.statlearning.com/.

Jewell, Nicholas P. 2003. Statistics for Epidemiology. Oxford, UK: Chapman; Hall/CRC. https://www.routledge.com/Statistics-for-Epidemiology/Jewell/p/book/9781584884330.

Jewell, Nicholas P, and Alan E Hubbard. 2016. Analysis of Longitudinal Studies in Epidemiology. Chapman & Hall/CRC Texts in Statistical Science. Taylor & Francis. https://books.google.com/books?id=-LoLPQAACAAJ.

Jiang, Jiming, and Thuan Nguyen. 2021. Linear and Generalized Linear Mixed Models and Their Applications. Second edition. Springer Series in Statistics. New York, NY: Springer. https://doi.org/10.1007/978-1-0716-1282-8.

Kalbfleisch, John D, and Ross L Prentice. 2011. The Statistical Analysis of Failure Time Data. John Wiley & Sons.

Kaplan, Daniel. 2022. MOSAIC Calculus. www.mosaic-web.org. www.mosaic-web.org.

Khuri, André I. 2003. Advanced Calculus with Applications in Statistics. John Wiley & Sons. https://www.wiley.com/en-us/Advanced+Calculus+with+Applications+in+Statistics%2C+2nd+Edition-p-9780471391043.

Klein, John P, and Melvin L Moeschberger. 2003. Survival Analysis: Techniques for Censored and Truncated Data. Vol. 1230. Springer. https://link.springer.com/book/10.1007/b97377.

Kleinbaum, David G, and Mitchel Klein. 2010. Logistic Regression: A Self-Learning Text. 3rd ed. Springer. https://link.springer.com/book/10.1007/978-1-4419-1742-3.

———. 2012. Survival Analysis: A Self-Learning Text. 3rd ed. Springer. https://link.springer.com/book/10.1007/978-1-4419-6646-9.

Kleinbaum, David G., Lawrence L. Kupper, and Hal Morgenstern. 1982. Epidemiologic Research : Principles and Quantitative Methods. Belmont, Calif: Lifetime Learning Publications.

———. 1983. Solutions Manual for Epidemiologic Research : Principles and Quantitative Methods. Belmont, Calif: Lifetime Learning Publications.

Kleinbaum, David G, Lawrence L Kupper, Azhar Nizam, K Muller, and ES Rosenberg. 2014. Applied Regression Analysis and Other Multivariable Methods. 5th ed. Cengage Learning. https://www.cengage.com/c/applied-regression-analysis-and-other-multivariable-methods-5e-kleinbaum/9781285051086/.

Kleinman, Ken, and Nicholas J Horton. 2009. SAS and r: Data Management, Statistical Analysis, and Graphics. Chapman; Hall/CRC. https://www.routledge.com/SAS-and-R-Data-Management-Statistical-Analysis-and-Graphics-Second-Edition/Kleinman-Horton/p/book/9781466584495.

Knuth, Donald E. 1984. “Literate Programming.” Comput. J. 27 (2): 97–111. https://doi.org/10.1093/comjnl/27.2.97.

Kuhn, Max, and Julia Silge. 2022. Tidy Modeling with r. " O’Reilly Media, Inc.". https://www.tmwr.org/.

Kutner, Michael H, Christopher J Nachtsheim, John Neter, and William Li. 2005. Applied Linear Statistical Models. McGraw-Hill.

Kutoyants, Yury A. 2023. Introduction to the Statistics of Poisson Processes and Applications. Springer Nature. https://link.springer.com/book/10.1007/978-3-031-37054-0.

Lawrance, Rachael, Evgeny Degtyarev, Philip Griffiths, Peter Trask, Helen Lau, Denise D’Alessio, Ingolf Griebsch, Gudrun Wallenstein, Kim Cocks, and Kaspar Rufibach. 2020. “What Is an Estimand, and How Does It Relate to Quantifying the Effect of Treatment on Patient-Reported Quality of Life Outcomes in Clinical Trials?” Journal of Patient-Reported Outcomes 4 (1): 1–8. https://link.springer.com/article/10.1186/s41687-020-00218-5.

Lehmann, E. L. 1999. Elements of Large-Sample Theory. Springer Texts in Statistics. New York: Springer. https://doi.org/10.1007/b98855.

McCullagh, Peter, and J. A. Nelder. 1989. Generalized Linear Models. 2nd ed. Routledge. https://www.utstat.toronto.edu/~brunner/oldclass/2201s11/readings/glmbook.pdf.

McCulloch, Charles E, Searle Shayle R, and John M Neuhaus. 2008. Generalized, Linear, and Mixed Models. 2nd ed. Vol. 651. John Wiley & Sons.

McLachlan, Geoffrey J, and Thriyambakam Krishnan. 2007. The EM Algorithm and Extensions. 2nd ed. John Wiley & Sons. https://doi.org/10.1002/9780470191613.

Miller, Steven J. 2016. The Probability Lifesaver: Calculus Review Problems. https://web.williams.edu/Mathematics/sjmiller/public_html/probabilitylifesaver/index.htm#:~:text=http%3A//web.williams.edu/Mathematics/sjmiller/public_html/probabilitylifesaver/supplementalchap_calcreview.pdf.

———. 2017. The Probability Lifesaver : All the Tools You Need to Understand Chance. A Princeton Lifesaver Study Guide. Princeton: Princeton University Press. https://press.princeton.edu/books/hardcover/9780691149547/the-probability-lifesaver.

Molenberghs, Geert., and Geert. Verbeke. 2005. Models for Discrete Longitudinal Data. Springer Series in Statistics. New York: Springer Science+Business Media, Inc. https://doi.org/10.1007/0-387-28980-1.

Moore, Dirk F. 2016. Applied Survival Analysis Using R. Vol. 473. Springer. https://doi.org/10.1007/978-3-319-31245-3.

Muenchen, Robert A. 2011. R for SAS and SPSS Users. Springer Science & Business Media. https://link.springer.com/book/10.1007/978-1-4614-0685-3.

Myatt, Mark. 2022. Practical R for Epidemiologists. Online. https://practical-r.org/index.html.

Nahhas, Ramzi W. 2023. An Introduction to r for Research. https://bookdown.org/rwnahhas/IntroToR/.

———. 2024. Introduction to Regression Methods for Public Health Using R. CRC Press. https://www.bookdown.org/rwnahhas/RMPH/.

Nelder, John Ashworth, and Robert WM Wedderburn. 1972. “Generalized Linear Models.” Journal of the Royal Statistical Society Series A: Statistics in Society 135 (3): 370–84.

Newey, Whitney K, and Daniel McFadden. 1994. “Large Sample Estimation and Hypothesis Testing.” In Handbook of Econometrics, edited by Robert Engle and Dan McFadden, 4:2111–2245. Elsevier. https://doi.org/https://doi.org/10.1016/S1573-4412(05)80005-4.

Norton, Edward C., Bryan E. Dowd, Melissa M. Garrido, and Matthew L. Maciejewski. 2024. “Requiem for Odds Ratios.” Health Services Research 59 (4): e14337. https://doi.org/https://doi.org/10.1111/1475-6773.14337.

Pebesma, Edzer, and Roger Bivand. 2023. Spatial Data Science: With Applications in R. Boca Raton: Chapman; Hall/CRC. https://doi.org/10.1201/9780429459016.

Pohl, Moritz, Lukas Baumann, Rouven Behnisch, Marietta Kirchner, Johannes Krisam, and Anja Sander. 2021. “Estimands—A Basic Element for Clinical Trials.” Deutsches Ärzteblatt International 118 (51-52): 883–88. https://doi.org/10.3238/arztebl.m2021.0373.

Polin, Richard A, William W Fox, and Steven H Abman. 2011. Fetal and Neonatal Physiology. 4th ed. Elsevier health sciences.

Roback, Paul, and Julie Legler. 2021. Beyond Multiple Linear Regression: Applied Generalized Linear Models and Multilevel Models in r. Chapman; Hall/CRC. https://bookdown.org/roback/bookdown-BeyondMLR/.

Rodrigues, Bruno. 2023. Building Reproducible Analytical Pipelines with r. Online. https://raps-with-r.dev/.

Rosenman, Ray H, Richard J Brand, C David Jenkins, Meyer Friedman, Reuben Straus, and Moses Wurm. 1975. “Coronary Heart Disease in the Western Collaborative Group Study: Final Follow-up Experience of 8 1/2 Years.” JAMA 233 (8): 872–77. https://doi.org/10.1001/jama.1975.03260080034016.

Ross, Kevin. 2022. An Introduction to Bayesian Reasoning and Methods. Online. https://bookdown.org/kevin_davisross/bayesian-reasoning-and-methods/.

Rothman, Kenneth J., Timothy L. Lash, Tyler J. VanderWeele, and Sebastien Haneuse. 2021. Modern Epidemiology. Fourth edition. Philadelphia: Wolters Kluwer.

Sackett, David L, Jonathan J Deeks, and Doughs G Altman. 1996. “Down with Odds Ratios!” BMJ Evidence-Based Medicine 1 (6): 164.

Searle, Shayle R, and Andre I Khuri. 2017. Matrix Algebra Useful for Statistics. John Wiley & Sons.

Seber, George AF, and Alan J Lee. 2012. Linear Regression Analysis. 2nd ed. John Wiley & Sons. https://www.wiley.com/en-us/Linear+Regression+Analysis%2C+2nd+Edition-p-9781118274422.

Selvin, Steve. 2001. Epidemiologic Analysis: A Case-Oriented Approach. Oxford University Press.

———. 2004. Statistical Analysis of Epidemiologic Data. 3rd ed. Monographs in Epidemiology and Biostatistics ; v. 35. Oxford ; Oxford University Press.

Soch, Joram, ed. 2023. The Book of Statistical Proofs. Zenodo. https://doi.org/10.5281/ZENODO.4305949.

Suárez, Erick, Cynthia M Pérez, Roberto Rivera, and Melissa N Martı́nez. 2017. Applications of Regression Models in Epidemiology. John Wiley & Sons.

Van Buuren, Stef. 2018. Flexible Imputation of Missing Data. CRC press. https://stefvanbuuren.name/fimd/.

Venables, Bill. 2023. codingMatrices: Alternative Factor Coding Matrices for Linear Model Formulae (version 0.4.0). https://CRAN.R-project.org/package=codingMatrices.

Verbeke, Geert, and Geert Molenberghs. 2000. Linear Mixed Models for Longitudinal Data. 1st ed. Springer Series in Statistics. New York, NY: SpringerLink (Online service); Springer. https://doi.org/10.1007/978-1-4419-0300-6.

Vittinghoff, Eric, David V Glidden, Stephen C Shiboski, and Charles E McCulloch. 2012. Regression Methods in Biostatistics: Linear, Logistic, Survival, and Repeated Measures Models. 2nd ed. Springer. https://doi.org/10.1007/978-1-4614-1353-0.

Wakefield, Jon. 2013. Bayesian and Frequentist Regression Methods. 1st ed. 2013. Springer Series in Statistics. New York, NY: Springer New York.

Weisberg, Sanford. 2005. Applied Linear Regression. Vol. 528. John Wiley & Sons.

Wickham, Hadley. 2019. Advanced r. Chapman; Hall/CRC. https://adv-r.hadley.nz/index.html.

———. 2021. Mastering Shiny. " O’Reilly Media, Inc.". https://mastering-shiny.org/.

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.

Wickham, Hadley, and Jennifer Bryan. 2023. R Packages. O’Reilly Media, Inc. https://r-pkgs.org/.

Wickham, Hadley, Mine Çetinkaya-Rundel, and Garrett Grolemund. 2023. R for Data Science. " O’Reilly Media, Inc.". https://r4ds.hadley.nz/.

Wood, Simon N. 2017. Generalized Additive Models: An Introduction with r. chapman; hall/CRC.

Woodward, Mark. 2013. Epidemiology: Study Design and Data Analysis. CRC press. https://www.routledge.com/Epidemiology-Study-Design-and-Data-Analysis-Third-Edition/Woodward/p/book/9781439839706.

Zeileis, Achim, Christian Kleiber, and Simon Jackman. 2008. “Regression Models for Count Data in R.” Journal of Statistical Software 27 (8). https://www.jstatsoft.org/v27/i08/.

Zuur, Alain F. 2009. Mixed Effects Models and Extensions in Ecology with r. Statistics for Biology and Health. New York ; Springer.