Field Guide to the R Mixed Model Wilderness
  1. References
  • Preface
  • 1  Introduction
  • 2  Zen and the Art of Statistical Analysis
  • 3  Mixed Model Background
  • 4  Model Prep & Workflow
  • Experiment designs
    • 5  Randomized Complete Block Design
    • 6  Factorial RCBD Design
    • 7  Split Plot Design
    • 8  Split-Split Plot Design
    • 9  Strip Plot Design
    • 10  Incomplete Block Design
    • 11  Latin Square Design
  • 12  Repeated Measures
  • 13  Marginal Means and Contrasts
  • 14  Variance and Variance Components
  • 15  Troubleshooting
  • 16  Additional Resources
  • References

References

Bates, Douglas, Martin Mächler, Ben Bolker, and Steve Walker. 2015. “Fitting Linear Mixed-Effects Models Using lme4.” Journal of Statistical Software 67 (1): 1–48. https://doi.org/10.18637/jss.v067.i01.
Bolker, Ben, and David Robinson. 2024. Broom.mixed: Tidying Methods for Mixed Models. https://CRAN.R-project.org/package=broom.mixed.
Broman, Karl W., and Kara H. Woo. 2018. “Data Organization in Spreadsheets.” The American Statistician 72 (1): 2–10. https://doi.org/10.1080/00031305.2017.1375989.
Dushoff, Jonathan, Morgan P. Kain, and Benjamin M. Bolker. 2019. “I Can See Clearly Now: Reinterpreting Statistical Significance.” Methods in Ecology and Evolution 10 (6): 756–59. https://doi.org/https://doi.org/10.1111/2041-210X.13159.
Greenland, Sander, Stephen J. Senn, Kenneth J. Rothman, John B. Carlin, Charles Poole, Steven N. Goodman, and Douglas G. Altman. 2016. “Statistical Tests, P Values, Confidence Intervals, and Power: A Guide to Misinterpretations.” European Journal of Epidemiology 31 (4): 337–50. https://doi.org/10.1007/s10654-016-0149-3.
Hartig, Florian. 2022. DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models. https://CRAN.R-project.org/package=DHARMa.
John, JA, and ER Williams. 1995. Cyclic and Computer Generated Designs. 2nd ed. New York: Chapman; Hall/CRC Press. https://doi.org/10.1201/b15075.
Kuznetsova, Alexandra, Per B. Brockhoff, and Rune H. B. Christensen. 2017. “lmerTest Package: Tests in Linear Mixed Effects Models.” Journal of Statistical Software 82 (13): 1–26. https://doi.org/10.18637/jss.v082.i13.
Lenth, Russell V. 2022. Emmeans: Estimated Marginal Means, Aka Least-Squares Means. https://CRAN.R-project.org/package=emmeans.
Lüdecke, Daniel, Mattan S. Ben-Shachar, Indrajeet Patil, Philip Waggoner, and Dominique Makowski. 2021. “performance: An R Package for Assessment, Comparison and Testing of Statistical Models.” Journal of Open Source Software 6 (60): 3139. https://doi.org/10.21105/joss.03139.
Nair, K. R. 1952. “Analysis of Partially Balanced Incomplete Block Designs Illustrated on the Simple Square and Rectangular Lattices.” Biometrics 8 (2): 122–55. https://doi.org/10.2307/3001929.
Patterson, H. D., and E. R. Williams. 1976. “A New Class of Resolvable Incomplete Block Designs.” Biometrika 63 (1): 83–92. https://doi.org/10.2307/2335087.
Pinheiro, José C., and Douglas M. Bates. 2000. Mixed-Effects Models in s and s-PLUS. New York: Springer. https://doi.org/10.1007/b98882.
Pinheiro, José, Douglas Bates, and R Core Team. 2023. Nlme: Linear and Nonlinear Mixed Effects Models. https://CRAN.R-project.org/package=nlme.
Wasserstein, Ronald L., and Nicole A. Lazar. 2016. “The ASA Statement on p-Values: Context, Process, and Purpose.” The American Statistician 70 (2): 129–33. https://doi.org/10.1080/00031305.2016.1154108.
Yates, F. 1936. “A New Method of Arranging Variety Trials Involving a Large Number of Varieties.” J Agric Sci 26: 424–55.
16  Additional Resources

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