| Package | Version | Citation |
|---|---|---|
| abind | 1.4.5 | Plate and Heiberger (2016) |
| asreml | 4.2.0.302 | The VSNi Team (2023) |
| base | 4.3.3 | R Core Team (2024) |
| bookdown | 0.38 | Xie (2016); Xie (2024) |
| brms | 2.21.0 | Bürkner (2017); Bürkner (2018); Bürkner (2021) |
| gridExtra | 2.3 | Auguie (2017) |
| knitr | 1.45 | Xie (2014); Xie (2015); Xie (2023) |
| lme4 | 1.1.35.2 | Bates et al. (2015) |
| magick | 2.8.3 | Ooms (2024) |
| MCMCglmm | 2.35 | Hadfield (2010) |
| mvtnorm | 1.2.4 | Genz and Bretz (2009) |
| nadiv | 2.17.3 | Wolak (2012) |
| quarto | 1.4.1 | Allaire and Dervieux (2024) |
| rmarkdown | 2.26 | Xie et al. (2018); Xie et al. (2020); Allaire et al. (2024) |
| rptR | 0.9.22 | Stoffel et al. (2017) |
| tidyverse | 2.0.0 | Wickham et al. (2019) |
| visreg | 2.7.0 | Breheny and Burchett (2017) |
References
R packages
This book was produced using all the following R packages
Bibliography
Allaire, J., and C. Dervieux. 2024. quarto: R interface to
“Quarto” markdown publishing system.
Allaire, J., Y. Xie, C. Dervieux, J. McPherson, J. Luraschi, K. Ushey,
A. Atkins, H. Wickham, J. Cheng, W. Chang, and R. Iannone. 2024. rmarkdown: Dynamic documents for r.
Auguie, B. 2017. gridExtra: Miscellaneous functions for
“Grid” graphics.
Bates, D., M. Mächler, B. Bolker, and S. Walker. 2015. Fitting linear
mixed-effects models using lme4. Journal
of Statistical Software 67:1–48.
Breheny, P., and W. Burchett. 2017. Visualization of regression models
using visreg. The R Journal 9:56–71.
Bürkner, P.-C. 2017. brms: An R package for
Bayesian multilevel models using Stan.
Journal of Statistical Software 80:1–28.
Bürkner, P.-C. 2018. Advanced
Bayesian multilevel modeling with the R
package brms. The R Journal 10:395–411.
Bürkner, P.-C. 2021. Bayesian item response
modeling in R with brms and
Stan. Journal of Statistical Software 100:1–54.
Genz, A., and F. Bretz. 2009. Computation of multivariate normal and t
probabilities. Springer-Verlag, Heidelberg.
Hadfield, J. D. 2010. MCMC
methods for multi-response generalized linear mixed models: The
MCMCglmm R package. Journal of Statistical
Software 33:1–22.
Ooms, J. 2024. magick: Advanced graphics and image-processing in
r.
Plate, T., and R. Heiberger. 2016. abind: Combine multidimensional arrays.
R Core Team. 2024. R:
A language and environment for statistical computing. R Foundation
for Statistical Computing, Vienna, Austria.
Stoffel, M. A., S. Nakagawa, and H. Schielzeth. 2017. rptR: Repeatability estimation and variance
decomposition by generalized linear mixed-effects models. Methods in
Ecology and Evolution 8:1639???1644.
The VSNi Team. 2023. asreml: Fits linear mixed models using REML.
Wickham, H., M. Averick, J. Bryan, W. Chang, L. D. McGowan, R. François,
G. Grolemund, A. Hayes, L. Henry, J. Hester, M. Kuhn, T. L. Pedersen, E.
Miller, S. M. Bache, K. Müller, J. Ooms, D. Robinson, D. P. Seidel, V.
Spinu, K. Takahashi, D. Vaughan, C. Wilke, K. Woo, and H. Yutani. 2019.
Welcome to the tidyverse. Journal of Open Source Software
4:1686.
Wilson, A. J., D. Réale, M. N. Clements, M. M. Morrissey, E. Postma, C.
A. Walling, L. E. B. Kruuk, and D. H. Nussey. 2010. An ecologist’s
guide to the animal model. Journal of Animal Ecology 79:13–26.
Wolak, M. E. 2012. nadiv: An R package to create
relatedness matrices for estimating non-additive genetic variances in
animal models. Methods in Ecology and Evolution 3:792–796.
Xie, Y. 2014. knitr: A comprehensive tool
for reproducible research in R. in V. Stodden, F.
Leisch, and R. D. Peng, editors. Implementing reproducible computational
research. Chapman; Hall/CRC.
Xie, Y. 2015. Dynamic documents with
R and knitr. 2nd edition. Chapman; Hall/CRC, Boca
Raton, Florida.
Xie, Y. 2016. bookdown: Authoring books and technical documents
with R markdown. Chapman; Hall/CRC, Boca Raton,
Florida.
Xie, Y., J. J. Allaire, and G. Grolemund. 2018. R markdown: The definitive
guide. Chapman; Hall/CRC, Boca Raton, Florida.
Xie, Y., C. Dervieux, and E. Riederer. 2020. R markdown
cookbook. Chapman; Hall/CRC, Boca Raton, Florida.