Lectures

Schedule

Date Topic Slides Reading
Jan 9 Introduction

Smaldino and McElreath (2016)
Jan 16 Introduction to Quarto

Alston and Rick (2021)
Jan 23 Introduction to Github

Ivimey-Cook et al. (2023)
Jan 30 Generalized linear models (and revision of linear models)

Zuur et al. (2010)
Feb 6 Causal structure and model building

Cinelli et al. (2022), Wysocki et al. (2022)
Feb 13 Introduction to mixed-models

Harrison et al. (2018)
Reading week
Feb 27 Introduction to Bayesian analysis

Kruschke and Liddell (2018)
Mar 5 Generalised linear mixed models

Bolker et al. (2009)
Mar 12 Discussion on data and plans for written reports

Wasserstein and Lazar (2016)
Mar 19 Multivariate mixed models

Van de Pol and Wright (2009)
Mar 26

Schielzeth and Forstmeier (2009)
Apr 2

Forstmeier et al. (2017)

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References

Alston, J. M., and J. A. Rick. 2021. A Beginner’s Guide to Conducting Reproducible Research. The Bulletin of the Ecological Society of America 102:e01801.
Bolker, B. M., M. E. Brooks, C. J. Clark, S. W. Geange, J. R. Poulsen, M. H. H. Stevens, and J.-S. S. White. 2009. Generalized linear mixed models: A practical guide for ecology and evolution. Trends in Ecology and Evolution 24:127–135.
Cinelli, C., A. Forney, and J. Pearl. 2022. A Crash Course in Good and Bad Controls. Sociological Methods & Research:00491241221099552.
Forstmeier, W., E.-J. Wagenmakers, and T. H. Parker. 2017. Detecting and avoiding likely false-positive findings – a practical guide. Biological Reviews 92:1941–1968.
Harrison, X. A., L. Donaldson, M. E. Correa-Cano, J. Evans, D. N. Fisher, C. E. D. Goodwin, B. S. Robinson, D. J. Hodgson, and R. Inger. 2018. A brief introduction to mixed effects modelling and multi-model inference in ecology. PeerJ 6:e4794.
Ivimey-Cook, E. R., J. L. Pick, K. R. Bairos-Novak, A. Culina, E. Gould, M. Grainger, B. M. Marshall, D. Moreau, M. Paquet, R. Royauté, A. Sánchez-Tójar, I. Silva, and S. M. Windecker. 2023. Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology. Journal of Evolutionary Biology 36:1347–1356.
Kruschke, J. K., and T. M. Liddell. 2018. Bayesian data analysis for newcomers. Psychonomic Bulletin & Review 25:155–177.
Schielzeth, H., and W. Forstmeier. 2009. Conclusions beyond support: Overconfident estimates in mixed models. Behavioral Ecology 20:416–420.
Smaldino, P. E., and R. McElreath. 2016. The natural selection of bad science. Royal Society Open Science 3:160384.
Van de Pol, M., and J. Wright. 2009. A simple method for distinguishing within-versus between-subject effects using mixed models. Animal behaviour 77:753–758.
Wasserstein, R. L., and N. A. Lazar. 2016. The ASA Statement on p-Values: Context, Process, and Purpose. The American Statistician 70:129–133.
Wysocki, A. C., K. M. Lawson, and M. Rhemtulla. 2022. Statistical Control Requires Causal Justification. Advances in Methods and Practices in Psychological Science 5:25152459221095823.
Zuur, A. F., E. N. Ieno, and C. S. Elphick. 2010. A protocol for data exploration to avoid common statistical problems. Methods in Ecology and Evolution 1:3–14.