References
Agostinelli, C., and U. Lund. 2022a. R Package
circular
: Circular Statistics (Version 0.4-95). CA: Department of Environmental Sciences, Informatics; Statistics, Ca’ Foscari University, Venice, Italy. UL: Department of Statistics, California Polytechnic State University, San Luis Obispo, California, USA. https://r-forge.r-project.org/projects/circular/.
———. 2022b. R Package
circular
: Circular Statistics (Version 0.4-95). CA: Department of Environmental Sciences, Informatics; Statistics, Ca’ Foscari University, Venice, Italy. UL: Department of Statistics, California Polytechnic State University, San Luis Obispo, California, USA. https://r-forge.r-project.org/projects/circular/.
Allaire, JJ, Yihui Xie, Christophe Dervieux, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, et al. 2024. rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown.
Auguie, Baptiste. 2017. gridExtra: Miscellaneous Functions for “Grid” Graphics. https://CRAN.R-project.org/package=gridExtra.
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.
Bürkner, Paul-Christian. 2017. “brms: An R Package for Bayesian Multilevel Models Using Stan.” Journal of Statistical Software 80 (1): 1–28. https://doi.org/10.18637/jss.v080.i01.
———. 2018. “Advanced Bayesian Multilevel Modeling with the R Package brms.” The R Journal 10 (1): 395–411. https://doi.org/10.32614/RJ-2018-017.
———. 2021a. “Bayesian Item Response Modeling in R with brms and Stan.” Journal of Statistical Software.
———. 2021b. “Bayesian Item Response Modeling in R with brms and Stan.” Journal of Statistical Software 100 (5): 1–54. https://doi.org/10.18637/jss.v100.i05.
Burnham, Kenneth P, and David R Anderson. 2002. Model Selection and Multimodel Inference. 2nd ed. New York, NY: Springer.
Burton, A Cole, Eric Neilson, Dario Moreira, Andrew Ladle, Robin Steenweg, Jason T Fisher, Erin Bayne, and Stan Boutin. 2015. “Wildlife Camera Trapping: A Review and Recommendations for Linking Surveys to Ecological Processes.” J. Appl. Ecol. 52 (3): 675–85.
de Valpine, Perry, Christopher Paciorek, Daniel Turek, Nick Michaud, Cliff Anderson-Bergman, Fritz Obermeyer, Claudia Wehrhahn Cortes, Abel Rodrìguez, Duncan Temple Lang, and Sally Paganin. 2022a. NIMBLE User Manual (version 0.12.2). https://doi.org/10.5281/zenodo.1211190.
———. 2022b. NIMBLE: MCMC, Particle Filtering, and Programmable Hierarchical Modeling (version 0.12.2). https://doi.org/10.5281/zenodo.1211190.
de Valpine, Perry, Daniel Turek, Christopher Paciorek, Cliff Anderson-Bergman, Duncan Temple Lang, and Ras Bodik. 2017. “Programming with Models: Writing Statistical Algorithms for General Model Structures with NIMBLE.” Journal of Computational and Graphical Statistics 26: 403–13. https://doi.org/10.1080/10618600.2016.1172487.
Dervieux, Christophe, JJ Allaire, Rich Iannone, Alison Presmanes Hill, and Yihui Xie. 2023. distill: “R Markdown” Format for Scientific and Technical Writing. https://CRAN.R-project.org/package=distill.
Ekstrøm, Claus Thorn. 2022. MESS: Miscellaneous Esoteric Statistical Scripts. https://CRAN.R-project.org/package=MESS.
Fieberg, John. 2024. Statistics for Ecologists: A Frequentist and Bayesian Treatment of Modern Regression Models. University of Minnesota Libraries Publishing. https://hdl.handle.net/11299/260227.
Fieberg, John, Randall H Rieger, Michael C Zicus, and Jonathan S Schildcrout. 2009. “Regression Modelling of Correlated Data in Ecology: Subject-Specific and Population Averaged Response Patterns.” J. Appl. Ecol. 46 (5): 1018–25.
Gerber, Brian D., Kadambari Devarajan, Zach J. Farris, and Mason Fidino. 2023. “A Model-Based Hypothesis Framework to Define and Estimate the Diel Niche via the Diel.niche’ r Package.” Journal of Animal Ecology 00: 0–15. https://doi.org/https://doi.org/10.1111/1365-2656.14035.
Hedeker, Donald, Stephen H C du Toit, Hakan Demirtas, and Robert D Gibbons. 2018. “A Note on Marginalization of Regression Parameters from Mixed Models of Binary Outcomes.” Biometrics 74 (1): 354–61.
Iannarilli, Fabiola. 2020. “Addressing Challenges in Camera-Trap Studies: Survey Designs for Multiple Species, Serial Dependence, and Site-to-Site Variability When Estimating Activity Patterns.” PhD thesis, Retrieved from the University of Minnesota Digital Conservancy. https://hdl.handle.net/11299/216384.
Iannarilli, Fabiola, Todd W Arnold, John Erb, and John R Fieberg. 2019. “Using Lorelograms to Measure and Model Correlation in Binary Data: Applications to Ecological Studies.” Methods Ecol. Evol. 10: 2153–62.
Iannarilli, Fabiola, John Erb, Todd W. Arnold, and John R. Fieberg. 2021. “Evaluating Species-Specific Responses to Camera-Trap Survey Designs.” Wildlife Biology 2021 (1). https://doi.org/10.2981/wlb.00726.
Iannarilli, Fabiola, Brian D. Gerber, John Erb, and John R. Fieberg. 2024. “A ‘How-to’ Guide for Estimating Animal Diel Activity Using Hierarchical Models.” Journal of Animal Ecology.
Kassambara, Alboukadel. 2023. ggpubr: “ggplot2” Based Publication Ready Plots. https://CRAN.R-project.org/package=ggpubr.
Kennedy, J. R. Oakleaf, C. M., and J. Kiesecker. 2019. “Managing the Middle: A Shift in Conservation Priorities Based on the Global Human Modification Gradient.” Global Change Biology 25 (3): 811–26. https://doi.org/10.1111/gcb.14549.
———. 2020. “Global Human Modification of Terrestrial Systems.” https://doi.org/10.7927/edbc-3z60.
Meredith, Mike, and Martin Ridout. 2021. Overlap: Estimates of Coefficient of Overlapping for Animal Activity Patterns. https://CRAN.R-project.org/package=overlap.
Meredith, Mike, Martin Ridout, and Liz A. D. Campbell. 2024. overlap: Estimates of Coefficient of Overlapping for Animal Activity Patterns. https://CRAN.R-project.org/package=overlap.
Niedballa, Jürgen, Rahel Sollmann, Alexandre Courtiol, and Andreas Wilting. 2016. “camtrapR: An r Package for Efficient Camera Trap Data Management.” Methods in Ecology and Evolution 7 (12): 1457–62. https://doi.org/10.1111/2041-210X.12600.
Oliveira-Santos, L G R, C A Zucco, and C Agostinelli. 2013. “Using Conditional Circular Kernel Density Functions to Test Hypotheses on Animal Circadian Activity.” Anim. Behav. 85: 269–80.
Pedersen, Eric J, David L Miller, Gavin L Simpson, and Noam Ross. 2019. “Hierarchical Generalized Additive Models in Ecology: An Introduction with Mgcv.” PeerJ 2019 (5).
Peral, Christopher, Marietjie Landman, and Graham I H Kerley. 2022. “The Inappropriate Use of Time‐to‐independence Biases Estimates of Activity Patterns of Free‐ranging Mammals Derived from Camera Traps.” Ecol. Evol. 12 (10).
R Core Team. 2022. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
———. 2024. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Rees, Matthew W, Brendan A Wintle, Jack H Pascoe, Mark Le Pla, Emma K Birnbaum, and Bronwyn A Hradsky. 2024. “Dynamic Shifts in Predator Diel Activity Patterns Across Landscapes and Threat Levels.” Oikos 2024 (3).
Ridout, Martin, and Matthew Linkie. 2009. “Estimating Overlap of Daily Activity Patterns from Camera Trap Data.” Journal of Agricultural, Biological, and Environmental Statistics 14 (3): 322–37.
Rizopoulos, Dimitris. 2022. GLMMadaptive: Generalized Linear Mixed Models Using Adaptive Gaussian Quadrature. https://CRAN.R-project.org/package=GLMMadaptive.
———. 2023. GLMMadaptive: Generalized Linear Mixed Models Using Adaptive Gaussian Quadrature. https://CRAN.R-project.org/package=GLMMadaptive.
Rowcliffe, J Marcus, Roland Kays, Bart Kranstauber, Chris Carbone, and Patrick A Jansen. 2014. “Quantifying Levels of Animal Activity Using Camera Trap Data.” Methods Ecol. Evol. 5: 1170–79.
Rowcliffe, M. 2022. Activity: Animal Activity Statistics. https://CRAN.R-project.org/package=activity.
Rowcliffe, Marcus. 2023. activity: Animal Activity Statistics. https://CRAN.R-project.org/package=activity.
Roy, Vivekananda. 2019. “Convergence Diagnostics for Markov Chain Monte Carlo,” September. https://arxiv.org/abs/1909.11827.
Thieurmel, Benoit, and Achraf Elmarhraoui. 2022. suncalc: Compute Sun Position, Sunlight Phases, Moon Position and Lunar Phase. https://CRAN.R-project.org/package=suncalc.
Vazquez, Carmen, J Marcus Rowcliffe, Kamiel Spoelstra, and Patrick A Jansen. 2019. “Comparing Diel Activity Patterns of Wildlife Across Latitudes and Seasons: Time Transformations Using Day Length.” Methods Ecol. Evol. 10 (12): 2057–66.
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.
Wood, S. N. 2017a. Generalized Additive Models: An Introduction with r. 2nd ed. Chapman; Hall/CRC.
Wood, S. N. 2003. “Thin-Plate Regression Splines.” Journal of the Royal Statistical Society (B) 65 (1): 95–114.
———. 2004. “Stable and Efficient Multiple Smoothing Parameter Estimation for Generalized Additive Models.” Journal of the American Statistical Association 99 (467): 673–86.
———. 2011. “Fast Stable Restricted Maximum Likelihood and Marginal Likelihood Estimation of Semiparametric Generalized Linear Models.” Journal of the Royal Statistical Society (B) 73 (1): 3–36.
———. 2017b. Generalized Additive Models: An Introduction with r. 2nd edition. Chapman; Hall/CRC.
Wood, S. N., N., Pya, and B. S"afken. 2016. “Smoothing Parameter and Model Selection for General Smooth Models (with Discussion).” Journal of the American Statistical Association 111: 1548–75.
Xie, Yihui. 2014. “knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.
———. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.
———. 2016a. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/bookdown.
———. 2016b. bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/bookdown.
———. 2024a. Bookdown: Authoring Books and Technical Documents with r Markdown. https://github.com/rstudio/bookdown.
———. 2024b. bookdown: Authoring Books and Technical Documents with r Markdown. https://github.com/rstudio/bookdown.
———. 2024c. knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/.
Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.
Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.
Zeileis, Achim, and Torsten Hothorn. 2002. “Diagnostic Checking in Regression Relationships.” R News 2 (3): 7–10. https://CRAN.R-project.org/doc/Rnews/.