Literature Cited

Alberti, E., G. Gioia, G. Sironi, S. Zanzani, P. Riccaboni, M. Magrini, and M. Manfredi. 2011. Elaphostrongylus cervi in a population of red deer (Cervus elaphus) and evidence of cerebrospinal nematodiasis in small ruminants in the province of Varese, Italy. Journal of Helminthology 85:313–318.

Anderson, M. J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology 26:32–46.

Bodin, N., H. Pethybridge, L. M. Duffy, A. Lorrain, V. Allain, J. M. Logan, F. Ménard, B. Graham, C. A. Choy, C. J. Somes, R. J. Olson, and J. W. Young. 2021. Global data set for nitrogen and carbon stable isotopes of tunas. Ecology 102:e03265.

Bolker, B. M. 2008. Ecological models and data in R. Princeton University Press, Princeton, New Jersey, USA.

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 & Evolution 24:127–135.

Borcard, D., F. Gillet, and P. Legendre. 2018. Numerical ecology with R. Springer, New York.

Box, G. E. P., and D. R. Cox. 1964. An analysis of transformations. Journal of the Royal Statistical Society: Series B (Methodological) 26:211–243.

Brieuc, M. S. O., C. D. Waters, D. P. Drinan, and K. A. Naish. 2018. A practical introduction to random forest for genetic association studies in ecology and evolution. Molecular Ecology Resources 18:755–766.

Broman, K. W., and K. H. Woo. 2018. Data organization in spreadsheets. The American Statistician 72:2–10.

Bubrig, L. T., J. M. Sutton, and J. L. Fierst. 2020. Caenorhabditis elegans dauers vary recovery in response to bacteria from natural habitat. Ecology and Evolution 10:9886–9895.

Burnham, K. P., and D. R. Anderson. 2004. Multimodel inference: Understanding AIC and BIC in model selection. Sociological methods & research 33:261–304.

Burnham, K., and D. Anderson. 2002. Model selection and multi-model inference: a practical information-theoretic approach. Springer-Verlag, New York.

Button, K. S., J. P. Ioannidis, C. Mokrysz, B. A. Nosek, J. Flint, E. S. Robinson, and M. R. Munafò. 2013. Power failure: why small sample size undermines the reliability of neuroscience. Nature Reviews Neuroscience 14:365–376.

Cade, B. S., and B. R. Noon. 2003. A gentle introduction to quantile regression for ecologists. Frontiers in Ecology and the Environment 1:412–420.

Carey, V. J. 2019. gee: Generalized estimation equation solver.

Carnell, R. 2019. Triangle: Provides the standard distribution functions for the triangle distribution.

Chivers, D. J., and C. M. Hladik. 1980. Morphology of the gastrointestinal tract in primates: Comparisons with other mammals in relation to diet. Journal of Morphology 166:337–386.

Clarke, K. R. 1993. Non-parametric multivariate analyses of changes in community structure. Australian journal of ecology 18:117–143.

Clarke, K. R., P. J. Somerfield, and M. G. Chapman. 2006. On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages. Journal of Experimental Marine Biology and Ecology 330:55–80.

Cutler, D. R., T. C. Edwards, K. H. Beard, A. Cutler, K. T. Hess, J. Gibson, and J. J. Lawler. 2007. Random forests for classification in ecology. Ecology 88:2783–2792.

Dalgaard, P. 2002. Introductory statistics with R. Springer Science+Business Media.

De’ath, G. 2007. Boosted trees for ecological modeling and prediction. Ecology 88:243–251.

De’ath, G., and K. E. Fabricius. 2000. Classification and regression trees: A powerful yet simple technique for ecological data analysis. Ecology 81:3178–3192.

De Solla, S. R., P. A. Martin, K. J. Fernie, B. J. Park, and G. Mayne. 2006. Effects of environmentally relevant concentrations of atrazine on gonadal development of snapping turtles (Chelydra serpentina). Environmental Toxicology and Chemistry: An International Journal 25:520–526.

Dormann, C. F., J. Elith, S. Bacher, C. Buchmann, G. Carl, G. Carré, J. R. G. Marquéz, B. Gruber, B. Lafourcade, P. J. Leitão, T. Münkemüller, C. McClean, P. E. Osborne, B. Reineking, B. Schröder, A. K. Skidmore, D. Zurell, and S. Lautenbach. 2013. Collinearity: A review of methods to deal with it and a simulation study evaluating their performance. Ecography 36:27–46.

Elith, J., and J. Leathwick. 2017. Boosted regression trees for ecological modeling. R Documentation. Available online: https://cran.r-project.org/web/packages/dismo/vignettes/brt.pdf (accessed on 2021-12-23).

Elith, J., J. R. Leathwick, and T. Hastie. 2008. A working guide to boosted regression trees. Journal of Animal Ecology 77:802–813.

Faurby, S., M. Davis, R. Ø. Pedersen, S. D. Schowanek, A. Antonelli, and J.-C. Svenning. 2018. PHYLACINE 1.2: The phylogenetic atlas of mammal macroecology. Ecology 99:2626.

Foucault, Q., A. Wieser, A.-M. Waldvogel, B. Feldmeyer, and M. Pfenninger. 2018. Rapid adaptation to high temperatures in Chironomus riparius. Ecology and Evolution 8:12780–12789.

Gelfand, A. E., and P. Vounatsou. 2003. Proper multivariate conditional autoregressive models for spatial data analysis. Biostatistics 4:11–15.

Gould, S. J. 1974. The origin and function of ’bizarre’ structures: Antler size and skull size in the ’irish elk,’ Megaloceros giganteus. Evolution 28:191–220.

Green, N. S., S. Li, J. D. Maul, and J. P. Overmyer. 2022. Natural and anthropogenic factors and their interactions drive stream community integrity in a North American river basin at a large spatial scale. Science of the Total Environment 835:155344.

Green, N. S., M. L. Wildhaber, and J. L. Albers. 2019. Potential responses of the Lower Missouri River shovelnose sturgeon (Scaphirhynchus platorynchus) population to a commercial fishing ban. Journal of Applied Ichthyology 35:370–377.

Green, N. S., M. L. Wildhaber, and J. L. Albers. 2021. Effectiveness of a distance sampling from roads program for white-tailed deer in the National Capital Region parks. Natural Resource Report, National Park Service, Fort Collins, Colorado.

Green, N. S., M. L. Wildhaber, J. L. Albers, T. W. Pettit, and M. J. Hooper. 2020. Efficient mammal biodiversity surveys for ecological restoration monitoring. Integrated Environmental Assessment and Management.

Grolemund, G., and H. Wickham. 2011. Dates and times made easy with lubridate. Journal of Statistical Software 40:1–25.

Head, M. L., L. Holman, R. Lanfear, A. T. Kahn, and M. D. Jennions. 2015. The extent and consequences of p-hacking in science. PLoS Biology 13:e1002106.

Hill, M. O. 1979. A FORTRAN program for arranging multivariate data in an ordered two-way table by classification of the individuals and attributes. TWINSPAN.

Hobbs, N. T., and R. Hilborn. 2006. Alternatives to statistical hypothesis testing in ecology: a guide to self teaching. Ecological Applications 16:5–19.

Højsgaard, S., U. Halekoh, and J. Yan. 2006. The R package geepack for generalized estimating equations. Journal of statistical software 15:1–11.

Hurlbert, S. H. 1984. Pseudoreplication and the design of ecological field experiments. Ecological Monographs 54:187–211.

Hutcheon, J. M., J. A. W. Kirsch, and T. G. Jr. 2002. A comparative analysis of brain size in relation to foraging ecology and phylogeny in the Chiroptera. Brain, behavior and evolution 60:165–180.

Inderjit, J. C. Streibig, and M. Olofsdotter. 2002. Joint action of phenolic acid mixtures and its significance in allelopathy research. Physiologia Plantarum 114:422–428.

James, G., D. Witten, T. Hastie, and R. Tibshirani. 2013. An introduction to statistical learning. 7th edition. Springer.

Jensen, A. J., R. P. Kelly, E. C. Anderson, W. H. Satterthwaite, A. O. Shelton, and E. J. Ward. (n.d.). Introducing zoid: a mixture model and R package for modeling proportional data with zeros and ones in ecology. Ecology:e3804.

Jones, D. T. 2019. Setting the standards for machine learning in biology. Nature Reviews Molecular Cell Biology 20:659–660.

Kan, A. 2017. Machine learning applications in cell image analysis. Immunology and Cell Biology 95:525–530.

Kéry, M. 2002. Inferring the absence of a species: a case study of snakes. The Journal of Wildlife Management:330–338.

Kéry, M. 2010. Introduction to WinBUGS for ecologists: Bayesian approach to regression, ANOVA, mixed models and related analyses. Academic Press.

Kirchman, D. L., X. A. G. Morán, and H. Ducklow. 2009. Microbial growth in the polar oceans—role of temperature and potential impact of climate change. Nature Reviews Microbiology 7:451–459.

Kirchner, B. N., N. S. Green, D. A. Sergeant, J. N. Mink, and K. T. Wilkins. 2011. Responses of small mammals and vegetation to a prescribed burn in a tallgrass blackland prairie. The American Midland Naturalist 166:112–125.

Koenker, R. 2021. Quantreg: Quantile regression.

Kuehn, I., and C. F. Dormann. 2012. Less than eight (and a half) misconceptions of spatial analysis. Journal of Biogeography 39:995–998.

Kunz, B. K., J. H. Waddle, and N. S. Green. 2019. Amphibian monitoring in hardwood forests: Optimizing methods for contaminant-based compensatory restorations. Integrated environmental assessment and management.

Kuznetsova, A., P. B. Brockhoff, and R. H. B. Christensen. 2017. lmerTest package: Tests in linear mixed effects models. Journal of Statistical Software 82:1–26.

Lazic, S. E., C. J. Clarke-Williams, and M. R. Munafò. 2018. What exactly is ‘N’in cell culture and animal experiments? PLoS Biology 16:e2005282.

Lebreton, J.-D., K. P. Burnham, J. Clobert, and D. R. Anderson. 1992. Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological Monographs 62:67–118.

Legendre, P., and L. Legendre. 2012. Numerical ecology. Elsevier, Amsterdam.

Leonard, E. M., and C. M. Wood. 2013. Acute toxicity, critical body residues, Michaelis–Menten analysis of bioaccumulation, and ionoregulatory disturbance in response to waterborne nickel in four invertebrates: Chironomus riparius, Lymnaea stagnalis, Lumbriculus variegatus and Daphnia pulex. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 158:10–21.

Liang, K.-Y., and S. L. Zeger. 1986. Longitudinal data analysis using generalized linear models. Biometrika 73:13–22.

Link, W. A., E. Cam, J. D. Nichols, and E. G. Cooch. 2002. Of BUGS and birds: Markov chain Monte Carlo for hierarchical modeling in wildlife research. The Journal of Wildlife Management:277–291.

Ludwig, J. A., J. F. Reynolds, L. QUARTET, and J. Reynolds. 1988. Statistical ecology: a primer in methods and computing. John Wiley & Sons.

Lunn, D., D. Spiegelhalter, A. Thomas, and N. Best. 2009. The BUGS project: evolution, critique and future directions. Statistics in Medicine 28:3049–3067.

Makin, T. R., and J.-J. O. de Xivry. 2019. Science forum: Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. Elife 8:e48175.

Mangiafico, S. 2021. rcompanion: Functions to support extension education program evaluation.

Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer research 27:209–220.

McCarthy, M. A. 2007. Bayesian methods for ecology. Cambridge University Press, Cambridge, United Kingdom.

McCune, B., J. B. Grace, and D. L. Urban. 2002. Analysis of ecological communities. MjM software design, Gleneden Beach, Oregon, USA.

Nelder, J. A., and R. W. M. Wedderburn. 1972. Generalized linear models. Journal of the Royal Statistical Society: Series A (General) 135:370.

Penone, C., A. D. Davidson, K. T. Shoemaker, M. Di Marco, C. Rondinini, T. M. Brooks, B. E. Young, C. H. Graham, and G. C. Costa. 2014. Imputation of missing data in life-history trait datasets: Which approach performs the best? Methods in Ecology and Evolution 5:961–970.

Pethybridge, H., C. A. Choy, J. M. Logan, V. Allain, A. Lorrain, N. Bodin, C. J. Somes, J. Young, F. Ménard, C. Langlais, L. Duffy, A. J. Hobday, P. Kuhnert, B. Fry, C. Menkes, and R. J. Olson. 2018. A global meta-analysis of marine predator nitrogen stable isotopes: Relationships between trophic structure and environmental conditions. Global Ecology and Biogeography 27:1043–1055.

Plummer, M. 2003. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Pages 1–10 Proceedings of the 3rd international workshop on distributed statistical computing. Vienna, Austria.

Plummer, M. 2021. rjags: Bayesian graphical models using MCMC.

Ritz, C., F. Baty, J. C. Streibig, and D. Gerhard. 2015. Dose-response analysis using R. PLoS ONE 10:e0146021.

Roleček, J., L. Tichý, D. Zelený, and M. Chytrý. 2009. Modified TWINSPAN classification in which the hierarchy respects cluster heterogeneity. Journal of Vegetation Science 20:596–602.

Schabenberger, O., and F. J. Pierce. 2001. Contemporary statistical models for the plant and soil sciences. CRC press, Boca Raton, Florida, USA.

Smith, F. A., and S. K. Lyons. 2013. Animal body size: Linking pattern and process across space, time, and taxonomic group. University of Chicago Press, Chicago.

Spector, P. 2008. Data manipulation with R. Springer Science+Business Media, New York.

Spiess, A.-N. 2018. propagate: Propagation of uncertainty.

Spiess, A.-N., and N. Neumeyer. 2010. An evaluation of \(R^2\) as an inadequate measure for nonlinear models in pharmacological and biochemical research: A Monte Carlo approach. BMC Pharmacology 10.

Su, Y.-S., and Masanao Yajima. 2021. R2jags: Using R to run ’JAGS’.

Tarca, A. L., V. J. Carey, X. Chen, R. Romero, and S. Drăghici. 2007. Machine learning and its applications to biology. PLoS Computational Biology 3:e116.

Therneau, T., and B. Atkinson. 2019. rpart: Recursive partitioning and regression trees.

Tufte, E. 2001. The visual display of quantitative information. Cheshire: Graphic Press.–2001.–213 p.

Turner, H., and D. Firth. 2020. Generalized nonlinear models in R: An overview of the gnm package.

Venables, W. N., and B. D. Ripley. 2002. Modern applied statistics with S. Fourth. Springer, New York.

Vicente, J., Y. Fierro, and C. Gortazar. 2005. Seasonal dynamics of the fecal excretion of Elaphostrongylus cervi (Nematoda, Metastrongyloidea) first-stage larvae in Iberian red deer (Cervus elaphus hispanicus) from southern Spain. Parasitology Research 95:60–64.

Ward, J. H. 1963. Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association 58:236–244.

Warton, D. I., and F. K. C. Hui. 2011. The arcsine is asinine: The analysis of proportions in ecology. Ecology 92:3–10.

Wasserstein, R. L., and N. A. Lazar. 2016. The ASA statement on p-values: Context, process, and purpose. Taylor & Francis.

Werner, J., and E. M. Griebeler. 2014. Allometries of maximum growth rate versus body mass at maximum growth indicate that non-avian dinosaurs had growth rates typical of fast growing ectothermic sauropsids. PloS ONE 9:e88834.

White, J. W., A. Rassweiler, J. F. Samhouri, A. C. Stier, and C. White. 2014. Ecologists should not use statistical significance tests to interpret simulation model results. Oikos 123:385–388.

Whytock, R. C., J. Świeżewski, J. A. Zwerts, T. Bara-Słupski, A. F. Koumba Pambo, M. Rogala, L. Bahaa-el-din, K. Boekee, S. Brittain, A. W. Cardoso, and others. 2021. Robust ecological analysis of camera trap data labelled by a machine learning model. Methods in Ecology and Evolution.

Wickham, H. 2014. Tidy data. Journal of Statistical Software 59.

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.

Wood, S. N. 2017. Generalized additive models: An introduction with R. 2nd edition. CRC press.

Woodward, H. N., E. A. F. Fowler, J. O. Farlow, and J. R. Horner. 2015. Maiasaura, a model organism for extinct vertebrate population biology: A large sample statistical assessment of growth dynamics and survivorship. Paleobiology 41:503–527.

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.

Zuur, A. F., E. N. Ieno, and G. M. Smith. 2007. Analysing ecological data. Springer Science+Business Media, New York.

Zuur, A. F., E. N. Ieno, N. J. Walker, A. A. Saveliev, G. M. Smith, and others. 2009a. Mixed effects models and extensions in ecology with R. Springer, New York.

Zuur, A., E. N. Ieno, and E. Meesters. 2009b. A beginner’s guide to R. Springer Science+Business Media, New York.