Personal & professional website of Patrick S. Phelan, medical & graduate student, statistics & philosophy enthusiast.

On this page I will collate various resources of interest, following David Schmidt’s creative example (now removed). Full-text PDF versions are linked where possible.


Blogs I attempt to keep up with (with variable motivation), listed alphabetically by primary author.

- Bååth. Publishable Stuff.
- Bartlett. The Stats Geek.
- Etz. The Etz-Files.
- Gandenberger. Greg Gandenberger – Data Scientist.
- Gelman et al. Statistical Modeling, Causal Inference, and Social Science.
- Harrell, Jr. Statistical Thinking.
- Kruschke. Doing Bayesian Data Analysis.
- Lakens. The 20% Statistician.
- Magnusson. R Psychologist.
- Mayo. Error Statistics Philosophy. With occasional guest posts from Stephen Senn!
- Morey. Richard D. Morey - Medium.
- Navarro. Danielle Navarro (A semi-professional blog).
- Rouder. Invariances.
- Schönbrodt. Felix Schönbrodt’s blog.
- van der Zee. The Skeptical Scientist.
- Wagenmakers et al. Bayesian Spectacles.
- Yanofsky. It's Chancy.


Mechanisms of Disease & Injury

- Redmon et al. (1992). Hypoglycemia due to a monoclonal insulin-binding antibody in multiple myeloma. N Engl J Med.
- Legendre et al. (1997). Transfer of symptomatic peanut allergy to the recipient of a combined liver-and-kidney transplant. N Engl J Med.
- Santucci et al. (1998). Interference with an implantable defibrillator by an electronic antitheft-surveillance device. N Engl J Med.
- Commins et al. (2009). Delayed anaphylaxis, angioedema, or urticaria after consumption of red meat in patients with IgE antibodies specific for galactose-α-1,3-galactose. J Allergy Clin Immunol.
- Muehlenbachs et al. (2015). Malignant transformation of Hymenolepsis nana in a human host. N Engl J Med.

Iatrogenesis

- Niederwieser et al. (1990). Inadvertent transmission of a donor’s acute myeloid leukemia in bone marrow transplantation for chronic myelocytic leukemia. N Engl J Med.
- Ridzon et al. (1997). Simultaneous transmission of human immunodeficiency virus and hepatitis C virus from a needle-stick injury. N Engl J Med.

Therapeutic Advances

- Willoughby, Jr. et al. (2005). Survival after treatment of rabies with induction of coma. N Engl J Med.
- Hargrove et al. (2013). Robotic leg control with EMG decoding in an amputee with nerve transfers. N Engl J Med.

The Berlin Patient

- Hütter et al. (2009). Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med.
- Allers et al. (2011). Evidence for the cure of HIV infection by CCR5Δ32/Δ32 stem cell transplantation. Blood.
- Yukl et al. (2013). Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient. PLoS Pathog.
- Brown (2015). I am the Berlin Patient: A personal reflection. AIDS Res Hum Retroviruses.


General

- Mattson & Dulaimy (2017). The 4 quadrants: Acute pathology in the abdomen and current imaging guidelines. Semin Ultrasound CT MR.
- Cifu (2017). Diagnostic errors and diagnostic calibration. JAMA.
- Cook et al. (2018). Management reasoning. Beyond the diagnosis. JAMA.

Dermatology

- Lowenstein & Sidlow (2018a). Cognitive and visual diagnostic errors in dermatology: part 1. Br J Dermatol.
- Lowenstein & Sidlow (2018b). Diagnostic heuristics in dermatology, part 2: metacognition and other fixes. Br J Dermatol.


- Kiene et al. (2013). In support of clinical case reports: A system of causality assessment. Glob Adv Health Med.
- Deaton & Cartwright (2018). Understanding and misunderstanding randomized controlled trials. Soc Sci Med.


- Yartsev (2018). Deranged Physiology.
- Reddi (2013). Why is saline so acidic (and does it really matter?) Int J Med Sci.


- Hartzband & Groopman (2011). The new language of medicine. N Engl J Med.
- Barsky (2017). The iatrogenic potential of the physician’s words. JAMA.
- Skolnik (2017). No wonder no one trusts us. JAMA Intern Med.


- Braithwaite (2013). EBM’s six dangerous words. JAMA.
- Ioannidis (2016). Evidence-based medicine has been hijacked: A report to David Sackett. J Clin Epidemiol.
- Nunan et al. (2017). Ten essential papers for the practice of evidence-based medicine. Evid Based Med.


Expert discussions on issues of medical consensus which are nonetheless portrayed as unresolved by detractors.

Cholesterol, Lipoproteins, Atherosclerotic Cardiovascular Disease (ASCVD), and Statin Therapy

- Collins et al. (2016). Interpretation of the evidence for the efficacy and safety of statin therapy. Lancet.
- Ference et al. (2017). Low-density lipoproteins cause atherosclerotic cardiovascular disease. 1. Evidence from genetic, epidemiologic, and clinical studies. A consensus statement from the European Atherosclerosis Society Consensus Panel. Eur Heart J.


"Where the philosopher ends, the physician begins." - Latin proverb

Epistemology & Philosophy of Science

- Goldman & Beddor (2016). Reliabilist Epistemology. Stanford Encyclopedia of Philosophy.
- Talbott (2016). Bayesian Epistemology. Stanford Encyclopedia of Philosophy.
- Chignell (2018). The ethics of belief. Stanford Encyclopedia of Philosophy.
- Reiss & Sprenger (2017). Scientific objectivity. Stanford Encyclopedia of Philosophy.

Ethics

- Ethics Unwrapped. McCombs School of Business, University of Texas at Austin.
- Savelescu et al. (2018). Philosophical medical ethics: more necessary than ever. J Med Ethics.

Rationalism & Rationality

- Kelly (2018). The need for a rationalist turn in evidence‐based medicine. J Eval Clin Pract.
- Djulbegovic et al. (2018). Rational decision making in medicine: Implications for overuse and underuse. J Eval Clin Pract.

Stanford Encyclopedia of Philosophy
An incredible resource for learning and studying philosophy from outside the field, with a number of entries relevant to the study of medicine (some selected examples below).

- Reiss & Ankeny (2016). Philosophy of medicine.
- DeGrazia (2017). The definition of death.
- Eyal (2012). Informed consent.
- Archard (2016). Children’s rights.
- Allen (2016). Privacy and medicine.


Diet & Nutrition

- The Nutrition Source. Harvard T. H. Chan School of Public Health.
- Micronutrient Information Center. Linus Pauling Institute, Oregon State University.

Information for Medical Decision-Making

- Patient Education. UpToDate.


"A subject which most statisticians find difficult but in which nearly all physicians are expert." - Stephen Senn

Introductions

- Gandenberger (2014). An introduction to likelihoodist, Bayesian, and frequentist methods.
- Motulsky (2017). Intuitive Biostatistics. A nonmathematical guide to statistical thinking. Oxford University Press.
- Kunin et al. (2018). Seeing Theory. Brown University.

General

- Silberzahn et al. (2018). Many analysts, one data set: Making transparent how variations in analytic choices affect results. Adv Methods Pract Psychol Sci.
"...one of [the] most important studies published this century." - Harlan Krumholz

Graphics

- Wagenmakers & Gronau (2018). A compendium of clean graphs in R.

Misconceptions
This article from a group of prominent statisticians and epidemiologists provides an extensive list of common and subtle misconceptions about foundational concepts in orthodox statistics.

- Greenland et al. (2016). Statistical tests, P values, confidence intervals, and power: A guide to misinterpretations. Eur J Epidemiol.

Frequentist Statistics

Null Hypothesis Significance Testing (NHST)

- Cohen (1994). The earth is round (p < .05). Am Psychol.
- Sterne & Davey Smith (2001). Sifting the evidence–What’s wrong with significance tests? BMJ.
- Gigerenzer (2004). Mindless statistics. J Socio Econ.
- Amrhein et al. (2017). The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research. PeerJ.
- Benjamin et al. (2018). Redefine statistical significance. Nat Hum Behav.
- Lakens et al. (2018). Justify your alpha. Nat Hum Behav.
- McShane et al. (2018). Abandon statistical significance. arXiv [preprint].

Power

- Hoenig & Heisey (2001). The abuse of power: The pervasive fallacy of power calculations for data analysis. Am Stat.
- Senn (2014). Delta Force: To what extent is clinical relevance relevant?. Error Statistics Philosophy [blog].
- Wagenmakers et al. (2015). A power fallacy. Behav Res.
- Lazic (2018). Four simple ways to increase power without increasing the sample size. Lab Anim.

Confidence Intervals
This sequence of four articles in the Psychonomic Bulletin & Review (plus a bonus blog post) explores the common understanding, underlying theory, and shortcomings in applicability of classical confidence intervals.

- Hoekstra et al. (2014). Robust misinterpretation of confidence intervals.
- Miller & Ulrich (2016). Interpreting confidence intervals: A comment on Hoekstra, Morey, Rouder, and Wagenmakers (2014).
- Morey et al. (2016). Continued misinterpretation of confidence intervals: response to Miller and Ulrich.
- Morey et al. (2016). The fallacy of placing confidence in confidence intervals.
- Morey (2016). Stop saying confidence intervals are "better" than p values. BayesFactor [blog].

Likelihood

- Gandenberger (2015). A new proof of the likelihood principle. Brit J Phil Sci.
- Etz (2018). Introduction to the concept of likelihood and its applications. Adv Methods Pract Psychol Sci.

Bayesian Statistics

Introductions

- Wagenmakers et al. (2016). Bayesian benefits for the pragmatic researcher. Curr Dir Psychol Sci.
My favorite introduction to Bayesian inference.
"Nooooooo, just make it stop, please!" - Andrew Gelman on the value of this paper.

- Dienes & Mclatchie (2018). Four reasons to prefer Bayesian analyses over significance testing. Psychon Bull Rev.
- Wagenmakers et al. (2018). Bayesian inference for psychology. Part I: Theoretical advantages and practical ramifications. Psychon Bull Rev.

Bayes Factors

- Ly et al. (2016a). Harold Jeffreys’s default Bayes factor hypothesis tests: Explanation, extension, and application in psychology. J Math Psychol.
- Robert (2016). The expected demise of the Bayes factor. J Math Psychol.
- Ly et al. (2016b). An evaluation of alternative methods for testing hypotheses, from the perspective of Harold Jeffreys. J Math Psychol.
- Schönbrodt & Wagenmakers (2018). Bayes factor design analysis: Planning for compelling evidence. Psychon Bull Rev.
- Navarro (2018). A personal essay on Bayes factors. Danielle Navarro (A semi-professional blog) [blog].
- Gronau & Wagenmakers (2019). Rejoinder: More limitations of Bayesian leave-one-out cross-validation. Comput Brain Behav.

In Medicine

- Hoekstra et al. (2018). Bayesian reanalysis of null results reported in medicine: Strong yet variable evidence for the absence of treatment effects. PLoS ONE.

Miscellaneous

- Bååth (2015). The non-parametric bootstrap as a Bayesian model. Publishable Stuff [blog].
- Harrell, Jr. (2018). My journal from frequentist to Bayesian statistics. Statistical Thinking [blog].