This a more or less haphazard collection of papers we’ve run across while looking for good examples or studies to use as exercises. The list below is roughly organized into a few groups, such as single predictor models, multiple continuous predictors, etc.

The references below aren’t the result of a systematic search, but our own somewhat haphazard sampling, heavily stratified by how accessible the paper and its data are. Our goal was to use as much as possible papers that are open access (via the journal or on a paper-by-paper basis), so we used PlosOne extensively initially, broadening in recent years as open access spreads.

If you’re a student, these extra examples can give you practice at running particular kinds of models. You might want to pick and choose to find examples of the kinds of models you might be using. It’s also worth looking at the original paper, to see how the authors approached their analysis and interpretation.

If you’re an instructor, the examples can be useful in class to deepen students’ experience of particular kinds of models. You’ll probably already know that your students will want to use more of some book chapters than others, and these examples let you easily expand those chapters.

Note. These references are offered as is. They are papers that were initial candidates for inclusion in the book and our teaching resources, but which were omitted at the final stage. This omission was for a variety of reasons - balance across disciplines, numbers of examples required for a topic. Some were also omitted because we struggled with the data files; it is unfortunately not common for online data to be a large data set, a subset of which appeared in analyses. Other papers were omitted if we struggled to replicate the analysis. The list below hasn’t been filtered by the reason we didn’t use each paper. In one sense it’s caveat emptor, even though you aren’t buying anything, but the variety of issues we encountered makes the papers valuable for class exercises and discussions - it’s good for students to discover how difficult it can be to check analyses even when there are good intentions. It may also be that in using real world examples, students devise better ways of analysing particular case studies. We suspect that many of us who’ve been publishing for a while have a catalogue of papers for which better analyses could be suggested :-)

We encourage users of the book to contribute additional examples - contact us through qkstats.com or Github with suggestions and we’ll add them.

Continuous response variables

Single predictor models

Booth and Evans (2011)

Haramura et al. (2016)

Hulbert et al. (2002)

Kurnath, Merz, and Dearing (2016)

Nobata et al. (2011)

C. M. Schmidt and Hood (2012)

Seitz, Lipcius, and Hines (2016)

Shu et al. (2015)

Thom and Clayton (2013)

Wiezik et al. (2015)

Multiple categorical predictors with fixed effects

Alba et al. (2014)

Arndt, Peterson, and Cain (2015)

Cramp et al. (2014)

Hostetler, Phillips, and Ryabinin (2016)

Espinoza-Romo et al. (2018)

Garland and Kimbro (2015)

Poureslami et al. (2010)

Thom and Clayton (2013)

Multiple continuous predictors

Bolger et al. (1997)

Crichton et al. (2023)

Dlugosz et al. (2013); also includes data for multivariate analysis (MDS, Anosim/Permanova)

Giosa, Mammides, and Zotos (2018)

Gutiérrez et al. (2012)

Huey et al. (2009)

Martin and Thomas (2011)

McGuire, Jonasson, and Guglielmo (2014)

J. P. Schmidt and Drake (2011) (boosted regression trees)

Mixed models: nesting and covariates

Bailey et al. (2017)

Cram et al. (2015)

Cramp et al. (2014)

Didiano, Johnson, and Duval (2016)

Ferrarezi et al. (2019) Note: cited as example in book, but data don’t seem to be at link in paper.

Haramura et al. (2016) Data are for observational units; could also be treated as single factor design with data condensed to experimental units.

Höhn, Lucas, and Thatje (2017)

Jacob, Tozzi, and Willenborg (2017)

Li et al. (2015)

Morissette et al. (2018)

Nudds, Codd, and Sellers (2009)

Pánková, Raabová, and Münzbergová (2014)

Ranåker et al. (2014)

C. M. Schmidt and Hood (2012)

Luter et al. (2016)

More models for correlated data

Bailey et al. (2017)

Dalziel et al. (2015)

Davies et al. (2015)

Dickson and Mitchell (2010)

Fernández, Springthorpe, and Hedrick (2012)

Hoye and Buttemer (2011)

Kurnath, Merz, and Dearing (2016)

Low-Décarie, Bell, and Fussmann (2015)

Mehring et al. (2015)

Navarro et al. (2022)

Morissette et al. (2018)

Reynolds et al. (2016)

Sirman et al. (2023)

Troyer and Turner (2015)

Seitz, Lipcius, and Hines (2016)

Other response variables

Simple logistic and Poisson responses

(bolger1997?)

Ceacero et al. (2015)

Li et al. (2015)

French and Westoby (1996)

Posthumus, Koprowski, and Steidl (2015)

Savage et al. (2016)

Schry et al. (2014)

Binomial responses

Cramp et al. (2014) (infection prevalence data)

Dale and Frank (2014)

Farley et al. (2014)

French and Westoby (1996) This example is from the first edition, and you can get the data here

Milisenda et al. (2014)

Pánková, Raabová, and Münzbergová (2014)

Scofield and Mattila (2015)

GLMMs & GAMs

Braulik et al. (2014)

Mols and Visser (2007)

Keslinka et al. (2019)

Tamura et al. (2020)

Multivariate analyses

Bender et al. (2015)

Hartman et al. (2019)

Hutto and Barrett (2021)

Campione and Evans (2011)

Krosnick et al. (2017)

Landová et al. (2021)

Newman, Manning, and Anderson (2015), which was used for Box 10.5, also includes datasets suitable for cluster analysis, MDS, and permanova/anosim

Noonan, Kluibenschedl, and Fabricius (2018)

Schulz et al. (2020)

Tegtman and Magrath (2020)

van der Stap, Coolen, and Lindeboom (2016)

Yvon-Durocher et al. (2015)

References

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Dale, Adam G., and Steven D. Frank. 2014. “The Effects of Urban Warming on Herbivore Abundance and Street Tree Condition.” PLoS ONE 9 (7). https://doi.org/f6h6s2.
Dalziel, Anne C., Nicolas Martin, Martin Laporte, Helga Guderley, and Louis Bernatchez. 2015. “Adaptation and Acclimation of Aerobic Exercise Physiology in Lake Whitefish Ecotypes (Coregonus Clupeaformis).” Evolution 69 (8): 2167–86. https://doi.org/f7ptnz.
Davies, Scott, Sisi Gao, Shelley Valle, Stephanie Bittner, Pierce Hutton, Simone L. Meddle, and Pierre Deviche. 2015. “Negative Energy Balance in a Male Songbird, the Abert’s Towhee, Constrains the Testicular Endocrine Response to Luteinizing Hormone Stimulation.” Journal of Experimental Biology 218 (17): 2685–93. https://doi.org/f7qfs6.
Dickson, T. L., and C. E. Mitchell. 2010. “Herbivore and Fungal Pathogen Exclusion Affects the Seed Production of Four Common Grassland Species.” PLoS One 5 (8): e12022. https://doi.org/cjgb8t.
Didiano, Teresa J., Marc T. J. Johnson, and Tim P. Duval. 2016. “Disentangling the Effects of Precipitation Amount and Frequency on the Performance of 14 Grassland Species.” Plos One 11 (9). https://doi.org/f9rkgk.
Dlugosz, Elizabeth M., Mark A. Chappell, Thomas H. Meek, Paulina Szafrańska, Karol Zub, Marek Konarzewski, James H. Jones, et al. 2013. “Phylogenetic Analysis of Mammalian Maximal Oxygen Consumption During Exercise.” Journal of Experimental Biology. https://doi.org/10.1242/jeb.088914.
Espinoza-Romo, B. A., J. C. Sainz-Hernández, C. P. Ley-Quiñónez, C. E. Hart, R. Leal-Moreno, A. A. Aguirre, and A. A. Zavala-Norzagaray. 2018. “Blood Biochemistry of Olive Ridley (Lepidochelys Olivacea) Sea Turtles Foraging in Northern Sinaloa, Mexico.” Plos One 13 (7). https://doi.org/10.1371/journal.pone.0199825.
Farley, Jessica H., J. Paige Eveson, Tim L. O. Davis, Retno Andamari, Craig H. Proctor, Budi Nugraha, and Campbell R. Davies. 2014. “Demographic Structure, Sex Ratio and Growth Rates of Southern Bluefin Tuna (Thunnus Maccoyii) on the Spawning Ground.” PLoS ONE 9 (5). https://doi.org/f6bhtp.
Fernández, María José, Dwight Springthorpe, and Tyson L. Hedrick. 2012. “Neuromuscular and Biomechanical Compensation for Wing Asymmetry in Insect Hovering Flight.” Journal of Experimental Biology. https://doi.org/grq8s2.
Ferrarezi, Rhuanito S., Jawwad A. Qureshi, Alan L. Wright, Mark A. Ritenour, and Natalia P. F. Macan. 2019. “Citrus Production Under Screen as a Strategy to Protect Grapefruit Trees From Huanglongbing Disease.” Frontiers in Plant Science 10 (December): 1598. https://doi.org/ghmzfs.
French, K., and M. Westoby. 1996. “Vertebrate-Dispersed Species in a Fire-Prone Environment.” Australian Journal of Ecology 21 (4): 379–85. https://doi.org/bgkcp2.
Garland, Hanna G., and David L. Kimbro. 2015. “Drought Increases Consumer Pressure on Oyster Reefs in Florida, USA.” Plos One 10 (8). https://doi.org/10.1371/journal.pone.0125095.
Giosa, Efthymia, Christos Mammides, and Savvas Zotos. 2018. “The Importance of Artificial Wetlands for Birds: A Case Study from Cyprus.” Plos One 13 (5). https://doi.org/10.1371/journal.pone.0197286.
Gutiérrez, Jorge S., José M. Abad-Gómez, Juan M. Sánchez-Guzmán, Juan G. Navedo, and José A. Masero. 2012. “Avian BMR in Marine and Non-Marine Habitats: A Test Using Shorebirds.” PLoS ONE 7 (7). https://doi.org/10.1371/journal.pone.0042206.
Haramura, Takashi, Hirohiko Takeuchi, Michael R. Crossland, and Richard Shine. 2016. “Biotic Resistance to an Alien Amphibian: Larval Competition Between Japanese Frogs and Invasive Cane Toads.” Plos One 11 (6). https://doi.org/10.1371/journal.pone.0156396.
Hartman, Rosemary, Stacy Sherman, Dave Contreras, Alison Furler, and Ryan Kok. 2019. “Characterizing Macroinvertebrate Community Composition and Abundance in Freshwater Tidal Wetlands of the Sacramento-San Joaquin Delta.” Edited by Carina Zittra. PLOS ONE 14 (11): e0215421. https://doi.org/gp9zsh.
Höhn, Danja P., Cathy H. Lucas, and Sven Thatje. 2017. “Respiratory Response to Temperature of Three Populations of Aurelia Aurita Polyps in Northern Europe.” Plos One 12 (5). https://doi.org/f982hj.
Hostetler, C. M., T. J. Phillips, and A. E. Ryabinin. 2016. “Methamphetamine Consumption Inhibits Pair Bonding and Hypothalamic Oxytocin in Prairie Voles.” PLoS One 11 (7): e0158178. https://doi.org/10.1371/journal.pone.0158178.
Hoye, B J, and W A Buttemer. 2011. “Inexplicable Inefficiency of Avian Molt? Insights from an Opportunistically Breeding Arid-Zone Dpecies, Lichenostomus Penicillatus.” PLoS One 6 (2): e16230. https://doi.org/bszbq7.
Huey, Raymond B., Curtis A. Deutsch, Joshua J. Tewksbury, Laurie J. Vitt, Paul E. Hertz, Héctor J. Álvarez Pérez, and Theodore Garland. 2009. “Why Tropical Forest Lizards Are Vulnerable to Climate Warming.” Proceedings of the Royal Society B: Biological Sciences 276 (1664): 1939–48. https://doi.org/10.1098/rspb.2008.1957.
Hulbert, A. J., S. Faulks, W. A. Buttemer, and P. L. Else. 2002. “Acyl Composition of Muscle Membranes Varies with Body Size in Birds.” Journal of Experimental Biology 205 (22): 3561–69. https://doi.org/gr2pdf.
Hutto, David, and Kyle Barrett. 2021. “Do Urban Open Spaces Provide Refugia for Frogs in Urban Environments?” Plos One 16 (1). https://doi.org/gr2r9n.
Jacob, Cory E., Eric Tozzi, and Christian J. Willenborg. 2017. “Neighbour Presence, Not Identity, Influences Root and Shoot Allocation in Pea.” Plos One 12 (3). https://doi.org/f9tzqz.
Keslinka, Liliana Katarzyna, Katarzyna Wojczulanis-Jakubas, Dariusz Jakubas, and Grzegorz Neubauer. 2019. “Determinants of the Little Auk (Alle Alle) Breeding Colony Location and Size in W and NW Coast of Spitsbergen.” Plos One 14 (3). https://doi.org/gr2sgk.
Krosnick, Shawn E., Joshuah S. Perkin, Tim S. Schroeder, Lesley G. Campbell, Elizabeth B. Jackson, Silas C. Maynord, Christopher G. Waters, and Jeffrey S. Mitchell. 2017. “New Insights into Floral Morph Variation in Passiflora Incarnata L. (Passifloraceae) in Tennessee, U.S.A.” Flora 236–237: 115–25. https://doi.org/gr2rk6.
Kurnath, P., N. D. Merz, and M. D. Dearing. 2016. “Ambient Temperature Influences Tolerance to Plant Secondary Compounds in a Mammalian Herbivore.” Proceedings of the Royal Society B: Biological Sciences 283 (1822). https://doi.org/10.1098/rspb.2015.2387.
Landová, Eva, Markéta Janovcová, Iveta Štolhoferová, Silvie Rádlová, Petra Frýdlová, Kristýna Sedláčková, and Daniel Frynta. 2021. “Specificity of Spiders Among Fear- and Disgust-Eliciting Arthropods: Spiders Are Special, but Phobics Not so Much.” Plos One 16 (9). https://doi.org/gngp4h.
Li, Hong-Li, Yong-Yang Wang, Qian Zhang, Pu Wang, Ming-Xiang Zhang, and Fei-Hai Yu. 2015. “Vegetative Propagule Pressure and Water Depth Affect Biomass and Evenness of Submerged Macrophyte Communities.” Plos One 10 (11). https://doi.org/f8bw5m.
Low-Décarie, Etienne, Graham Bell, and Gregor F. Fussmann. 2015. “CO2 Alters Community Composition and Response to Nutrient Enrichment of Freshwater Phytoplankton.” Oecologia 177 (3): 875–83. https://doi.org/f63tdh.
Luter, Heidi M., Alan R. Duckworth, Carsten W. Wolff, Elizabeth Evans-Illidge, and Steve Whalan. 2016. “Recruitment Variability of Coral Reef Sessile Communities of the Far North Great Barrier Reef.” Plos One 11 (4). https://doi.org/f8w2zp.
Martin, Adam R., and Sean C. Thomas. 2011. “A Reassessment of Carbon Content in Tropical Trees.” PLoS ONE 6 (8). https://doi.org/c7zcnd.
McGuire, Liam P., Kristin A. Jonasson, and Christopher G. Guglielmo. 2014. “Bats on a Budget: Torpor-Assisted Migration Saves Time and Energy.” PLoS ONE 9 (12). https://doi.org/f62czd.
Mehring, Andrew S., Kevin A. Kuehn, Aaron Thompson, Catherine M. Pringle, Amy D. Rosemond, Matthew R. First, R. Richard Lowrance, George Vellidis, and David Whitehead. 2015. “Leaf Litter Nutrient Uptake in an Intermittent Blackwater River: Influence of Tree Species and Associated Biotic and Abiotic Drivers.” Functional Ecology 29 (6): 849–60. https://doi.org/f7jnsf.
Milisenda, Giacomo, Sara Rosa, Veronica L. Fuentes, Ferdinando Boero, Letterio Guglielmo, Jennifer E. Purcell, and Stefano Piraino. 2014. “Jellyfish as Prey: Frequency of Predation and Selective Foraging of Boops Boops (Vertebrata, Actinopterygii) on the Mauve Stinger Pelagia Noctiluca (Cnidaria, Scyphozoa).” PLoS ONE 9 (4). https://doi.org/gr2r9s.
Mols, Christel M. M., and Marcel E. Visser. 2007. “Great Tits (Parus Major) Reduce Caterpillar Damage in Commercial Apple Orchards.” PLoS ONE 2 (2). https://doi.org/dnphxv.
Morissette, Olivier, Pascal Sirois, Nigel P. Lester, Chris C. Wilson, and Louis Bernatchez. 2018. “Supplementation Stocking of Lake Trout (Salvelinus Namaycush) in Small Boreal Lakes: Ecotypes Influence on Growth and Condition.” Plos One 13 (7). https://doi.org/gdv546.
Navarro, Jocelyn, John M. Powers, Ayaka Paul, and Diane R. Campbell. 2022. “Phenotypic Plasticity and Selection on Leaf Traits in Response to Snowmelt Timing and Summer Precipitation.” New Phytologist 234 (4): 1477–90. https://doi.org/gsbcxg.
Newman, Ethan, John Manning, and Bruce Anderson. 2015. “Local Adaptation: Mechanical Fit Between Floral Ecotypes of Nerine Humilis (Amaryllidaceae) and Pollinator Communities: FLORAL ADAPTATION TO LOCAL POLLINATOR COMMUNITIES.” Evolution 69 (9): 2262–75. https://doi.org/f7vhm7.
Nobata, Shigenori, John A. Donald, Richard J. Balment, and Yoshio Takei. 2011. “Potent Cardiovascular Effects of Homologous Urotensin II (UII)-Related Peptide and UII in Unanesthetized Eels After Peripheral and Central Injections.” American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 300 (2): R437–46. https://doi.org/bnzww5.
Noonan, Sam H. C., Anna Kluibenschedl, and Katharina E. Fabricius. 2018. “Ocean Acidification Alters Early Successional Coral Reef Communities and Their Rates of Community Metabolism.” Plos One 13 (5). https://doi.org/gdmbbd.
Nudds, Robert L., Jonathan R. Codd, and William I. Sellers. 2009. “Evidence for a Mass Dependent Step-Change in the Scaling of Efficiency in Terrestrial Locomotion.” PLoS ONE 4 (9). https://doi.org/ds6d25.
Pánková, Hana, Jana Raabová, and Zuzana Münzbergová. 2014. “Mycorrhizal Symbiosis and Local Adaptation in Aster Amellus: A Field Transplant Experiment.” PLoS ONE 9 (4). https://doi.org/gr289z.
Posthumus, Erin E., John L. Koprowski, and Robert J. Steidl. 2015. “Red Squirrel Middens Influence Abundance but Not Diversity of Other Vertebrates.” Plos One 10 (4). https://doi.org/f7jwtd.
Poureslami, R., K. Raes, G. M. Turchini, G. Huyghebaert, and S. De Smet. 2010. “Effect of Diet, Sex and Age on Fatty Acid Metabolism in Broiler Chickens:n-3 Andn-6 PUFA.” British Journal of Nutrition 104 (2): 189–97. https://doi.org/ctdvkg.
Ranåker, Lynn, Jens Persson, Mikael Jönsson, P. Anders Nilsson, and Christer Brönmark. 2014. “Piscivore-Prey Fish Interactions: Mechanisms Behind Diurnal Patterns in Prey Selectivity in Brown and Clear Water.” PLoS ONE 9 (11). https://doi.org/f245rh.
Reynolds, Laura K., Katherine DuBois, Jessica M. Abbott, Susan L. Williams, and John J. Stachowicz. 2016. “Response of a Habitat-Forming Marine Plant to a Simulated Warming Event Is Delayed, Genotype Specific, and Varies with Phenology.” Plos One 11 (6). https://doi.org/gbppqs.
Savage, Anne, Len Thomas, Katie L. Feilen, Darren Kidney, Luis H. Soto, Mackenzie Pearson, Felix S. Medina, German Emeris, and Rosamira R. Guillen. 2016. “An Assessment of the Population of Cotton-Top Tamarins (Saguinus Oedipus) and Their Habitat in Colombia.” Plos One 11 (12). https://doi.org/gg4bsp.
Schmidt, Christina M., and Wendy R. Hood. 2012. “Calcium Availability Influences Litter Size and Sex Ratio in White-Footed Mice (Peromyscus Leucopus).” PLoS ONE 7 (8). https://doi.org/gr2892.
Schmidt, John Paul, and John M. Drake. 2011. “Time Since Introduction, Seed Mass, and Genome Size Predict Successful Invaders Among the Cultivated Vascular Plants of Hawaii.” PLoS ONE 6 (3). https://doi.org/bb2hs7.
Schry, Amie R., Melissa M. Norberg, Brenna B. Maddox, and Susan W. White. 2014. “Gender Matters: The Relationship Between Social Anxiety and Alcohol-Related Consequences.” PLoS ONE 9 (12). https://doi.org/f6x95v.
Schulz, Kailee, Philip W. Stevens, Jeffrey E. Hill, Alexis A. Trotter, Jared L. Ritch, Quenton M. Tuckett, and Joshua T. Patterson. 2020. “Coastal Restoration Evaluated Using Dominant Habitat Characteristics and Associated Fish Communities.” Plos One 15 (10). https://doi.org/gr2r9t.
Scofield, Hailey N., and Heather R. Mattila. 2015. “Honey Bee Workers That Are Pollen Stressed as Larvae Become Poor Foragers and Waggle Dancers as Adults.” Plos One 10 (4). https://doi.org/f7f2ns.
Seitz, Rochelle D., Romuald N. Lipcius, and Anson H. Hines. 2016. “Consumer Versus Resource Control and the Importance of Habitat Heterogeneity for Estuarine Bivalves.” Oikos 126 (1): 121–35. https://doi.org/f9mh38.
Shu, Yang, Qichang Mei, Justin Fernandez, Zhiyong Li, Neng Feng, and Yaodong Gu. 2015. “Foot Morphological Difference Between Habitually Shod and Unshod Runners.” Plos One 10 (7). https://doi.org/f7vb2c.
Sirman, Aubrey E., Jacob E. Schmidt, Mark E. Clark, Jeffrey D. Kittilson, Wendy L. Reed, and Britt J. Heidinger. 2023. “Compensatory Growth Is Accompanied by Changes in Insulin-Like Growth Factor 1 but Not Markers of Cellular Aging in a Long-Lived Seabird.” The American Naturalist, May, 000–000. https://doi.org/gsbcwp.
Stap, Tim van der, Joop W. P. Coolen, and Han J. Lindeboom. 2016. “Marine Fouling Assemblages on Offshore Gas Platforms in the Southern North Sea: Effects of Depth and Distance from Shore on Biodiversity.” Plos One 11 (1). https://doi.org/gg3q7b.
Tamura, Momoka, Takayuki Ohgushi, Takashi Y. Ida, and Julia Koricheva. 2020. “Intraspecific Neighbourhood Effect: Population‐level Consequence of Aggregation of Highly Defended Plants.” Functional Ecology 34 (3): 597–605. https://doi.org/gr2893.
Tegtman, Natalie T., and Robert D. Magrath. 2020. “Discriminating Between Similar Alarm Calls of Contrasting Function.” Philosophical Transactions of the Royal Society B: Biological Sciences 375 (1802). https://doi.org/gr2894.
Thom, James M., and Nicola S. Clayton. 2013. “Re-Caching by Western Scrub-Jays (Aphelocoma Californica) Cannot Be Attributed to Stress.” PLoS ONE 8 (1). https://doi.org/f4h8nf.
Troyer, Rachael R., and Andrew M. Turner. 2015. “Chemosensory Perception of Predators by Larval Amphibians Depends on Water Quality.” Plos One 10 (6). https://doi.org/f7scr4.
Wiezik, Michal, Marek Svitok, Adela Wieziková, and Martin Dovčiak. 2015. “Identifying Shifts in Leaf-Litter Ant Assemblages (Hymenoptera: Formicidae) Across Ecosystem Boundaries Using Multiple Sampling Methods.” Plos One 10 (7). https://doi.org/f7z2tk.
Yvon-Durocher, Gabriel, Andrew P. Allen, Maria Cellamare, Matteo Dossena, Kevin J. Gaston, Maria Leitao, José M. Montoya, Daniel C. Reuman, Guy Woodward, and Mark Trimmer. 2015. “Five Years of Experimental Warming Increases the Biodiversity and Productivity of Phytoplankton.” PLOS Biology 13 (12). https://doi.org/f77rg6.