18.7 – References and suggested readings (Ch17 & 18)

References and suggested readings

Bewick V, Cheek L, Ball J (2005) Statistics review 14: Logistic regression. Critical Care 9:112-118.

Burraco, P., Valdés, A. E., & Orizaola, G. (2020). Metabolic costs of altered growth trajectories across life transitions in amphibians. The Journal of Animal Ecology, 89(3), 855–866.

Corn, C. A., & Hiesey, W. M. (1973). Altitudinal ecotypes in Hawaiian Metrosideros. American Journal of Botany 60(10): 991-1002.

Dobson, A. J., & Barnett, A. G. (2018). An introduction to generalized linear models. Chapman and Hall/CRC.

Faraway, J. J. Practical Regression and ANOVA with R 2002.

Felsenstein, J. (2003). Inferring Phylogenies. Sinauer Associates.

Gosner, Kenneth L. (1960). A simplified table for staging anuran embryos and larvae with notes on identification. Herpetologica 16 (3): 183–190. link to Wikipedia page

Head, M. L., Holman, L., Lanfear, R., Kahn, A. T., & Jennions, M. D. (2015). The extent and consequences of p-hacking in science. PLoS Biol, 13(3), e1002106.

LaBarbera M. (1989) Analyzing body size as a factor in ecology and evolution. Annual Review of Ecology and Systematics 29:97-117.

Legendre, P., & Desdevises, Y. (2009). Independent contrasts and regression through the origin. Journal of Theoretical Biology, 259(4), 727–743.

McArdle BH (2003) Lines, models, and errors: Regression in the field. Limnology and Oceanography 48:1363-1366.

McCullagh, P. 2002. What is a statistical model? The Annals of Statistics 30(5): 1225-1310.

Meeker WQ, Escobar LA (1995) Teaching about approximate confidence regions based on maximum likelihood estimation. American Statistician 49:48-53.

Montgomery, D. C., Peck, E. A., & Vining, G. G. (2021). Introduction to linear regression analysis, 6th edition. John Wiley & Sons.

O’Brien, R. M. (2007) A caution regarding rules of thumb for variance inflation factors. Quality & Quantity 41:673-690

Pawitan Y (2000) A Reminder of the Fallibility of the Wald Statistic: Likelihood Explanation. American Statistician 54:54-56.

Slinker Bryan K. & Glantz Stanton A Multiple Linear Regression: Accounting for Multiple Simultaneous Determinants of a Continuous Dependent Variable. Circulation, 2008, 117, 1732-1737

Stefan, A. M., & Schönbrodt, F. D. (2023). Big little lies: A compendium and simulation of p-hacking strategies. Royal Society Open Science, 10(2), 220346.

Warton DI, Wright IJ, Falster DS, Westoby M. (2006) Bivariate line-fitting methods for allometry. Biological Reviews 81: 259-291

Zuur, A. F., Ieno, E. N., Walker, N. J., Saveliev, A. A., & Smith, G. M. (2009). Mixed Effects Models and Extensions in Ecology with R. Springer.

Chapter 17 contents

Chapter 18 contents

 

16.7 – References and suggested readings

References and suggested readings

Anderson, N. W., & Zimmerman, F. J. (2024). Trends and structural factors affecting health equity in the United States at the local level, 1990–2019. SSM – Population Health, 26, 101675.

Bartko J (1976) On various intraclass reliability coefficients. Psychological Bulletin 83:762-765.

Benjamini Y, Hochberg Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B 57:289-300.

Bollen, K. A., & Diamantopoulos, A. (2015). In Defense of Causal-Formative Indicators: A Minority Report. Psychological Methods, 22(3), 581.

Brand J., Altman D (1997) Statistics notes: Cronbach’s alpha. BMJ 314:572.

Braveman, P., & Gottlieb, L. (2014). The Social Determinants of Health: It’s Time to Consider the Causes of the Causes. Public Health Reports, 129(Suppl 2), 19.

Bruton, A, and Conway, J. H., and Holgate, S. T. 2000 Reliability: What is it and how is it measured? Physiotherapy 86:94-99

Cook, D. A., & Beckman, T. J. (2006). Current Concepts in Validity and Reliability for Psychometric Instruments: Theory and Application. The American Journal of Medicine, 119(2), 166.e7-166.e16.

Cooper, R. L., Ramesh, A., Radix, A. E., Reuben, J. S., Juarez, P. D., Holder, C. L., Belton, A. S., Brown, K. Y., Mena, L. A., & Matthews-Juarez, P. (2023). Affirming and Inclusive Care Training for Medical Students and Residents to Reduce Health Disparities Experienced by Sexual and Gender Minorities: A Systematic Review. Transgender Health, 8(4), 307–327.

Crawford, R. (1977). You are Dangerous to Your Health: The Ideology and Politics of Victim Blaming. International Journal of Health Services, 7(4), 663–680.

Cronbach L. (1951) Coefficient alpha and the internal structure of tests. Psychometrika 16:297-334.

Davidson, M. (2017). Vaccination as a cause of autism—Myths and controversies. Dialogues in Clinical Neuroscience, 19(4), 403–407.

Doornick J. A., HanseDiamantopoulos, A., & Winklhofer, H. M. (2001). Index Construction with Formative Indicators: An Alternative to Scale Development. Journal of Marketing Research, 38(2), 269–277.

Espinosa, J., Stevens, J. R., Alberghina, D., Alway, H. E., Barela, J. D., Bogese, M., & et al. (2023). ManyDogs 1: A Multi-Lab Replication Study of Dogs’ Pointing Comprehension. Animal behavior and cognition, 10(3), 232–286.

Goertzen, J. R., & Cribbie, R. A. (2010). Detecting a lack of association: An equivalence testing approach. British Journal of Mathematical and Statistical Psychology, 63(3), 527-537.

Greenland, S. (2001). Ecologic versus individual-level sources of bias in ecologic estimates of contextual health effects. International journal of epidemiology, 30(6), 1343-1350.

Hu, P., Jiao, R., Jin, L., & Xiong, M. (2018). Application of Causal Inference to Genomic Analysis: Advances in Methodology. Frontiers in Genetics, 9, 238.

Kleinberg, S., & Hripcsak, G. (2011). A review of causal inference for biomedical informatics. Journal of Biomedical Informatics, 44(6), 1102–1112.

Kruse, A., Stafilidis, S., & Tilp, M. (2017). Ultrasound and magnetic resonance imaging are not interchangeable to assess the Achilles tendon cross-sectional-area. European Journal of Applied Physiology, 117(1), 73-82.

Lee Rodgers, J., & Nicewander, W. A. (1988). Thirteen ways to look at the correlation coefficient. The American Statistician, 42(1), 59-66.

Makowski, D., Ben-Shachar, M. S., Patil, I., & Lüdecke, D. (2019). Methods and Algorithms for Correlation Analysis in R. Journal of Open Source Software, 5(51), 2306.

Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS 76:5269-5273.

Parascandola, M., & Weed, D. L. (2001). Causation in epidemiology. Journal of Epidemiology & Community Health, 55(12), 905–912.

Portnov, B. A., Dubnov, J., & Barchana, M. (2007). On ecological fallacy, assessment errors stemming from misguided variable selection, and the effect of aggregation on the outcome of epidemiological study. Journal of exposure science & environmental epidemiology, 17(1), 106-121.

Read, J. G., & Gorman, B. K. (2010). Gender and Health Inequality. Annual Review of Sociology, 36(Volume 36, 2010), 371–386.

Robinson W.S. Ecological correlations and the behavior of individuals. Am Sociol Rev 1950: 15: 351–357.

Schmitt N (1996) Uses and abuses of coefficient alpha. Psychological Assessment 8:350-353.

Shrout P, Fleiss J (1979) Intraclass correlations: uses in assessing rater reliability. Psychological Bulletin 86:420-428.

Sijtsma K (2009) On the use, the misuse, and the very limited usefulness of Cronbach’s alpha. Psychometrika 74:107-120.

Székely, G. J., Rizzo, M. L., & Bakirov, N. K. (2007). Measuring and testing dependence by correlation of distances. The annals of statistics, 35(6), 2769-2794.

U.S. Pet Ownership & Demographics Sourcebook (2012) American Veterinary Association.

Wang Kong, C., Green, J., Hamity, C., & Jackson, A. (2022). Health Disparity Measurement Among Asian American, Native Hawaiian, and Pacific Islander Populations Across the United States. Health Equity, 6(1), 533–539.

Wetzels, R. & Wagenmakers, E.-J. (2012) A default Bayesian hypothesis test for correlations and partial correlations. Psychon Bull Rev 19: 1057-1064

Wilson C (2014) It’s True: Liberals Like Cats More Than Conservatives Do. Time Magazine online (https://time.com/8293/its-true-liberals-like-cats-more-than-conservatives-do/)

Zou K. H., Tuncali K., Silverman S. G. (2003) Correlation and linear regression. Radiology 227(3): 617-628.

Chapter 16, contents

15.4 – Chapter 15 – References

References and suggested readings

Bewick V, Cheek L, Ball J (2004) Statistics review 10: further nonparametric methods. Critical Care 8:196-199.

Fagerland MW, Sandvik L (2009) The Wilcoxon–Mann–Whitney test under scrutiny. Statistics in Medicine 28:1487-1497.

Feltovich N (2003) Nonparametric Tests of Differences in Medians: Comparison of the Wilcoxon–Mann–Whitney and Robust Rank-Order Tests. Experimental Economics 6:273-297

St‐Pierre, A. P., Shikon, V., & Schneider, D. C. (2018). Count data in biology—Data transformation or model reformation?. Ecology and evolution, 8(6), 3077-3085.

Whitley E, Ball J (2002) Statistics review 6: Nonparametric methods. Critical Care 6:509-513

Chapter 15 contents

14.9 – Chapter 14 – References

References and suggested readings

Hills, M., & Armitage, P. (1979). The two-period cross-over clinical trial. British Journal of Clinical Pharmacology, 8(1), 7–20.

Hills, M., & Armitage, P. (2004). The two-period cross-over clinical trial. British Journal of Clinical Pharmacology, 58(7), S717–S719.

Meijer, J. H., & Robbers, Y. (2014). Wheel running in the wild. Proceedings of the Royal Society B: Biological Sciences, 281(1786), 20140210.

Mills, E. J., Chan, A.-W., Wu, P., Vail, A., Guyatt, G. H., & Altman, D. G. (2009). Design, analysis, and presentation of crossover trials. Trials, 10(1), 27.

National Research Council. (2005). Mathematics and 21st century biology. National Academies Press.

O’Connor, C. M., Norris, D. R., Crossin, G. T., & Cooke, S. J. (2014). Biological carryover effects: Linking common concepts and mechanisms in ecology and evolution. Ecosphere, 5(3), art28.

Radzilani, F., Zinyemba, O., & Meijboom, R. (2025). Application of statistical design of experiment to identify key factors in cross coupling reactions. Scientific Reports, 15(1), 42800.

Vatcheva, K. P., Lee, M., McCormick, J. B., & Rahbar, M. H. (2015). The Effect of Ignoring Statistical Interactions in Regression Analyses Conducted in Epidemiologic Studies: An Example with Survival Analysis Using Cox Proportional Hazards Regression Model. Epidemiology, 6(1), 216.

See references in Chapter 12

Chapter 14 contents

13.5 – Chapter 13 – References

References and suggested readings

Cahoy, D. O. (2010). A bootstrap test for equality of variances. Computational statistics & data analysis, 54(10), 2306-2316.

Choi, P. T. (2005). Statistics for the reader: what to ask before believing the results. Canadian Journal of Anesthesia, 52(1), R46-R46.

Glass GV, Peckham PD, Sanders JR (1972) Consequences of Failure to Meet Assumptions Underlying the Fixed Effects Analyses of Variance and Covariance. Review of Educational Research 42:237-288

Hoekstra, R., Kiers, H., & Johnson, A. (2012). Are assumptions of well-known statistical techniques checked, and why (not)?. Frontiers in psychology, 3, 137.

Nakagawa S, Cuthill IC (2007) Effect size, confidence interval and statistical significance: a practical guide for biologists. Biological Review 82:591–605.

Olsen, C. H. (2003). Review of the use of statistics in infection and immunity. Infection and immunity, 71(12), 6689-6692.

Chapter 13, contents

12.8 – Chapter 12 – References

References and suggested readings

Asner, G., Martin, R., Keith, L., Heller, W., Hughes, M., Vaughn, N., … & Balzotti, C. (2018). A spectral mapping signature for the Rapid Ohia Death (ROD) pathogen in Hawaiian forests. Remote Sensing, 10(3), 404.

Bewick V, Cheek L, Ball J (2004) Statistics review 9: One-way analysis of variance. Critical Care 8:130–136.

Bewick V, Cheek L, Ball J (2004) Statistics review 9: One-way analysis of variance. Critical Care 8:130-136.

Boake CRB (1989) Repeatability: its role in evolutionary studies of mating behavior. Evolutionary Ecology 3:173-182.

Bokhorst, J.M., Blank, A., Lugli, A. et al. Assessment of individual tumor buds using keratin immunohistochemistry: moderate interobserver agreement suggests a role for machine learning. Mod Pathol 33, 825–833 (2020). https://doi.org/10.1038/s41379-019-0434-2

Burton P, Gurrin L, Sly P (1998) Extending the simple linear regression model to account for correlated responses : An introduction to generalized estimating equations and multi-level mixed modelling. Statistics in Medicine 17:1261-1291.

Cohen BH (2002) Calculating a factorial ANOVA from means and standard deviations. Understanding Statistics 1:191-203.

Corn CA, Hiesey WM. (1973) Altitudinal ecotypes in Hawaiian Metrosideros. No 10, US International Biology Program.

de Villemereuil, P., Gaggiotti, O. E., Mouterde, M., & Till-Bottraud, I. (2016). Common garden experiments in the genomic era: new perspectives and opportunities. Heredity, 116(3), 249.

Dohm MR (2002) Repeatability estimates do not always set an upper limit to heritability. Functional Ecology 16:273-280.

Falconer, D. S., & Mackay, T. F. C. (1996). Introduction to quantitative genetics. Longman Group.

Guisan A, Edwards Jr TC, Hastie T (2002) Generalized linear and generalized additive models in studies of species distributions: setting the scene. Ecological Modeling 157:89-100.

Goertzen, B. J., & Klaus, K. (2023). Is it actually reliable? Examining Statistical Methods for Inter-rater Reliability of a Rubric in Graduate Education. Research & Practice in Assessment, 18(2), 31.

Hayes, A. F., & Cai, L. (2007). Using heteroskedasticity-consistent standard error estimators in OLS regression: An introduction and software implementation. Behavior Research Methods, 39(4), 709–722.

Henrickson, M., Giwa, S., Hafford-Letchfield, T., Cocker, C., Mulé, N. J., Schaub, J., & Baril, A. (2020). Research Ethics with Gender and Sexually Diverse Persons. International Journal of Environmental Research and Public Health, 17(18), Article 18.

Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian journal of statistics, 65-70.

Hunter JE, Schmidt FL (2000) Fixed effects vs. random effects meta-analysis models: Implications for cumulative research knowledge. International Journal of Selection and Assessment 8:275-292

Jafari, M., & Ansari-Pour, N. (2019). Why, when and how to adjust your P values?. Cell Journal (Yakhteh), 20(4), 604.

Jeanmougin M, de Reynies A, Laetitia M, Paccard C, Nuel G, Guedj M (2010) Should we abandon the t-test in the analysis of gene expression microarray data: a comparison of variance modeling strategies. PloS One 5:e12336.

Jinyuan, L. I. U., Wan, T. A. N. G., Guanqin, C. H. E. N., Yin, L. U., & Changyong, F. E. N. G. (2016). Correlation and agreement: overview and clarification of competing concepts and measures. Shanghai archives of psychiatry, 28(2), 115.

Lessells B, & Boag PT (1987) Unrepeatable repeatabilities: A common mistake. Auk 104:116-121

Liljequist, D., Elfving, B., & Skavberg Roaldsen, K. (2019). Intraclass correlation–A discussion and demonstration of basic features. PloS one, 14(7), e0219854.

Ludbrook, J. (1998). Multiple comparison procedures updated. Clinical and Experimental Pharmacology and Physiology, 25(12), 1032–1037.

Matthews J. N., Altman D. G., Campbell M. J., Royston P. (1990) Analysis of serial measurements in medical research. BMJ 300:230-235.

McGraw, K. O., & Wong, S. P. (1996). Forming inferences about some intraclass correlation coefficients. Psychological methods, 1(1), 30.

Mitch, W. E., & Walser, M. (1977). Effects of oral neomycin and kanamycin in chronic uremic patients: II. Nitrogen balance. Kidney international, 11(2), 123-127.

Moore TJ, Conlin PR, Ard J,Svetkey LP (2001) DASH (Dietary Approaches to Stop Hypertension) Diet Is Effective Treatment for Stage 1 Isolated Systolic Hypertension. Hypertension 38: 155-158.

Mullis, M. N., Wright, K. M., Raj, A., Gatti, D. M., Reifsnyder, P. C., Flurkey, K., Archer, J. R., Robinson, L., Di Francesco, A., Svenson, K. L., Korstanje, R., Harrison, D. E., Ruby, J. G., & Churchill, G. A. (2025). Analysis of lifespan across diversity outbred mouse studies identifies multiple longevity-associated loci. Genetics, 230(4), iyaf081.

Nakagawa S, Cuthill IC (2007) Effect size, confidence interval and statistical significance: a practical guide for biologists. Biological Reviews 82:591-605.

Nuismer SL, Gandon S (2008) Moving beyond common-garden and transplant designs: Insight into the causes of local adaptation in species interactions. American Naturalist 171:658-668.

Okada, K. (2013). Is omega squared less biased? A comparison of three major effect size indices in one-way ANOVA. Behaviormetrika, 40(2), 129-147. (cited in Daniel Lakens blog)

Ruxton, G. D., & Beauchamp, G. (2008). Time for some a priori thinking about post hoc testing. Behavioral ecology, 19(3), 690-693.

Sauder, D. C., & DeMars, C. E. (2019). An Updated Recommendation for Multiple Comparisons. Advances in Methods and Practices in Psychological Science, 2(1), 26–44.

Shrout PE, Fleiss JL. (1979) Intraclass correlations: uses in assessing rater reliability. Psychological Bulletin 86:420-428.

Sokal RR, Rohlf FJ (1995) Biometry: The principles and practices of statistics in biological research, 3rd ed. WH Freeman.

Tobert, J. A., & Newman, C. B. (2016). Statin tolerability: In defence of placebo-controlled trials. European journal of preventive cardiology, 23(8), 891-896.

Whitley E, Ball J (2002) Statistics review 5: Comparison of means. Critical Care 6:424-428.

Wolak, M. E., Fairbairn, D. J., & Paulsen, Y. R. (2012). Guidelines for estimating repeatability. Methods in Ecology and Evolution, 3(1), 129-137.

Yoon, S., Baik, B., Park, T., & Nam, D. (2021). Powerful p-value combination methods to detect incomplete association. Scientific Reports, 11(1), 6980.

Chapter 12, contents

11.6 – Chapter 11 – References

References and suggested readings

Browner WS, Newman TB (1987) Are all significant P values created equal? The analogy between diagnostic tests and clinical research. JAMA 257:2459-2463.

Cohen J (1992) Statistical power analysis. Current directions in Psychological Science 1:98-101.

Colegrave, N., and Ruxton, Graeme D. (2003) Confidence intervals are a more useful complement to nonsignificant tests than are power calculations. Behavioral Ecology 14(3):446-447.

Durlak, J. A. (2009). How to Select, Calculate, and Interpret Effect Sizes. Journal of Pediatric Psychology, 34(9), 917–928.

Eng J (2003) Sample Size Estimation: How Many Individuals Should Be Studied? Radiology 227:309-313

Everitt BS, Hothorn T. (2007) A handbook of statistical analyses using R, 2nd edition. Chapman & Hall/CRC Press.

Ferguson, C. J. (2009). An effect size primer: A guide for clinicians and researchers. Professional Psychology: Research and Practice, 40(5), 532–538.

Freeman, E., Robson, E., Bates, B., & Sierra, K. (2008). Head first design patterns. ” O’Reilly Media, Inc.”.

Hansen WB, Collins LM (1994) Seven ways to increase power without increasing N, pp 184-195 in: Advances in Data Analysis for Prevention Intervention Research, Collins LM, Seitz LA (eds). NIDA Research Monograph 142.

Hedges, L. V. (1981). Distribution Theory for Glass’s Estimator of Effect size and Related Estimators. Journal of Educational Statistics, 6(2), 107–128.

Hoenig JM, Heisey DM (2001) The Abuse of Power: The Pervasive Fallacy of Power Calculations for Data Analysis. American Statistician 55:19-24.

Kanda Y (2013) Investigation of the freely available easy-to-use software ‘EZR’ for medical statistics. Bone marrow transplantation 48:452-458

Lakens, D. (2013). Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs. Frontiers in psychology, 4, 863.

Yuan K-H, Maxwell S (2005) On the Post Hoc Power in Testing Mean Differences. Journal of Educational and Behavioral Statistics 30(2):141-167

Zhang, Y., Hedo, R., Rivera, A., Rull, R., Richardson, S., & Tu, X. M. (2019). Post hoc power analysis: is it an informative and meaningful analysis?. General psychiatry, 32(4).

Chapter 11 contents

10.4 – Chapter 10 – References

References and suggested readings

Andergassen, U., Zebisch, M., Kölbl, A. C., König, A., Heublein, S., Schröder, L., … & Jeschke, U. (2016). Real-time qPCR-based detection of circulating tumor cells from blood samples of adjuvant breast cancer patients: A preliminary study. Breast Care, 11(3), 194-198.

Cohen J (1994) The Earth is round (P < 0.05). American Psychologist 49:991-1003.

Cowles M, Davis C (1982) On the origins of the .05 level of statistical significance. American Psychologist 37:553-558.

Driscoll et al (2000) An introduction to everyday statistics – 2. Journal of Accident & Emergency Medicine 17:274-281

Driscoll P (2009) Article 5. An introduction to estimation – 2: from z to t. Emergency Medical Journal 18:65-70.

Fagerland MW (2012) t-tests, non-parametric tests, and large studies—a paradox of statistical practice? BMC Medical Research Methodology 12:78

Whiteley and Ball (2002) Statistical review 5: Comparison of means. Critical Care 6:424-428.

Chapter 10 contents

 

9.7 – Chapter 9 – References

References and suggested readings

Agresti A (1992) A Survey of Exact Inference for Contingency Tables. Statistical Science 7(1):131-153.

Agresti, A. (2001). Exact inference for categorical data: recent advances and continuing controversies. Statistics in medicine 20(17-18): 2709-2722.

Apaydin, E. A., Maher, A. R., Shanman, R., Booth, M. S., Miles, J. N., Sorbero, M. E., & Hempel, S. (2016). A systematic review of St. John’s wort for major depressive disorder. Systematic reviews, 5(1), 148.

Bellinger D, Leviton A, Waternaux C, Needleman H, Rabinowitz M (1987) Longitudinal Analyses of Prenatal and Postnatal Lead Exposure and Early Cognitive Development. New England Journal of Medicine 316:1037-1043.

Bewick V, Cheek L, Ball, J (2003) Statistics review 8: Qualitative data — tests of association. Critical Care 8:46-53.

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Cohen J (1992) Statistical power analysis. Current directions in Psychological Science 1:98-101.

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Fagerland, M. W., Lydersen, S., & Laake, P. (2013). The McNemar test for binary matched-pairs data: mid-p and asymptotic are better than exact conditional. BMC medical research methodology, 13(1), 91.

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Kroonenberg, P. M., and Verbeek, A. (2018). The Tale of Cochran’s Rule: My Contingency Table has so Many Expected Values Smaller than 5, What Am I to Do? The American Statistician, 72(2), 175-183.

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Whitley E, Ball J (2002) Statistics review 3: Hypothesis testing and P values. Critical Care 6:222-225

Xiang J, Wünschmann S, Diekema DJ, Klinzman D, Patrick KD, George SL, Stapleton JT (2001) Effect of Coinfection with GB Virus C on Survival among Patients with HIV Infection. New England Journal of Medicine 345:707-714.

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Chapter 9 contents

8.7 – Chapter 8 – References

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