Sources Primary literature & methodology references

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Every method in BioStat Quest links to primary literature. This page is the full index — filter by branch, search by keyword, jump straight to the citation you need.

— methods — citations — branches — R packages referenced
Standing on the shoulders of
Hernán & Robins causal Altman clinical Rothman & Greenland epi VanderWeele mediation · E-value Pearl causality Agresti categorical Efron & Tibshirani bootstrap · selection Gelman regression · Bayes McElreath Bayes Harrell modeling
42 of 42 visible
Foundations #

Descriptive Statistics & Distributions

  • Altman, Practical Statistics for Medical Research
  • Tukey, Exploratory Data Analysis
R summaryskimrgtsummary
Foundations #

Central Tendency (Mean, Median, Mode)

  • Tukey, Exploratory Data Analysis
  • Wilcox, Introduction to Robust Estimation and Hypothesis Testing
R mean()median()DescTools::Mode
Foundations #

Measures of Spread (SD, Variance, IQR, CV, Range)

  • Altman, Practical Statistics for Medical Research
  • Tukey, Exploratory Data Analysis
R sd()var()IQR()range()
Foundations #

The Normal Distribution & z-Scores

  • Casella & Berger, Statistical Inference
  • Altman, Practical Statistics for Medical Research
R pnorm()qnorm()scale()
Foundations #

Variable Types & Measurement Scales

  • Stevens (1946), 'On the Theory of Scales of Measurement'
  • Agresti, Analysis of Ordinal Categorical Data
R factor()ordered()MASS::polrordinal::clm
Probability #

Central Limit Theorem & Sampling Distributions

  • Feller, An Introduction to Probability Theory and Its Applications
  • Casella & Berger, Statistical Inference
R replicate(10000, mean(rexp(30)))
Probability #

Common Probability Distributions

  • Ross, Introduction to Probability Models
  • Casella & Berger, Statistical Inference
R dbinom/pbinomdpois/ppoisdnorm/pnormdexp/pexp
Estimation & Inference #

Student's t-test (One-sample, Two-sample, Paired)

  • Student (1908); Welch (1947)
  • Wasserstein & Lazar (2016), 'The ASA statement on p-values'
R t.testeffectsize::cohens_d
Estimation & Inference #

Chi-square Test (Independence / Goodness-of-fit)

  • Pearson (1900)
  • Agresti, Categorical Data Analysis
R chisq.testfisher.testmcnemar.testrcompanion::cramerV
Estimation & Inference #

One-way / Factorial ANOVA

  • Fisher (1925)
  • Maxwell & Delaney, Designing Experiments and Analyzing Data
  • Welch / Brown-Forsythe alternatives under heteroscedasticity
R aovlm + anovaemmeansafex
Estimation & Inference #

Confidence Intervals & Standard Errors

  • Altman et al., Statistics with Confidence (BMJ Books)
  • Greenland et al. (2016), 'Statistical tests, P values, confidence intervals'
R confintconfint.defaultboot
Estimation & Inference #

Bootstrap Resampling

  • Efron & Tibshirani, An Introduction to the Bootstrap
  • Davison & Hinkley, Bootstrap Methods and their Application
R boot::bootboot::boot.cirsample
Estimation & Inference #

Null Hypothesis Significance Testing

  • Wasserstein & Lazar (2016), 'The ASA Statement on p-Values'
  • Greenland et al. (2016), 'Statistical tests, P values, confidence intervals, and power'
  • Amrhein, Greenland & McShane (2019), 'Retire statistical significance'
Regression #

Linear Regression (OLS)

  • Weisberg, Applied Linear Regression
  • Harrell, Regression Modeling Strategies (Springer)
R lmperformance::check_modelbroom::tidy
Regression #

Logistic Regression

  • Hosmer, Lemeshow & Sturdivant, Applied Logistic Regression
  • Riley et al. (2020), sample size for binary outcome prediction
R glm(family=binomial)rms::lrmpROC
Regression #

Cox Proportional Hazards Regression

  • Therneau & Grambsch (2000), Modeling Survival Data: Extending the Cox Model
  • Hernán, 'The hazards of hazard ratios' (Epidemiology 2010)
R survival::coxphcox.zphggsurvfitsurvminer
Regression #

Kaplan–Meier & Log-rank Test

  • Kaplan & Meier (1958); Klein & Moeschberger textbook
  • Royston & Parmar (2013), 'Restricted mean survival time' — BMC MRM
R survival::survfitsurvdiffsurvminer::ggsurvplot
Regression #

Regression Diagnostics

  • Fox, Applied Regression Analysis and Generalized Linear Models
  • Hartig, DHARMa R package vignette
R plot(lm.fit)car::vifcar::influencePlotlmtest::dwtestDHARMa
Regression #

Model Selection (AIC, BIC, LASSO, Ridge, Elastic Net)

  • Burnham & Anderson, Model Selection and Multimodel Inference
  • Hastie, Tibshirani & Friedman, Elements of Statistical Learning, ch. 3, 7
R AIC()BIC()glmnetMASS::stepAIC
Regression #

Mixed-Effects & Longitudinal Models

  • Fitzmaurice, Laird & Ware, Applied Longitudinal Analysis
  • Gelman & Hill, Data Analysis Using Regression and Multilevel Models
R lme4::lmerlme4::glmernlme::lmegeepack::geeglmlmerTest
Design & Bias #

Study Design (RCT, Cohort, Case-Control, Cross-sectional)

  • Rothman, Greenland & Lash, Modern Epidemiology
  • Grimes & Schulz (2002), Lancet series on epidemiologic methods
STROBE checklist
Design & Bias #

Bias (Selection, Information, Confounding)

  • Rothman, Greenland & Lash, Modern Epidemiology — Chapter on Bias
  • Lash, Fox & Fink, Applying Quantitative Bias Analysis
  • Delgado-Rodríguez & Llorca (2004), J Epidemiol Community Health
Missing & Measurement #

Multiple Imputation by Chained Equations (MICE)

  • van Buuren (2018), Flexible Imputation of Missing Data
  • White, Royston & Wood (2011), 'Multiple imputation using chained equations'
R micemiceaddsmicemdjomo
FIMD (free online)
Missing & Measurement #

Cohen's Kappa (Inter-rater Agreement)

  • Cohen (1960); Landis & Koch (1977) benchmarks (<0.20 poor → >0.80 almost perfect)
  • Byrt, Bishop & Carlin (1993), 'Bias, prevalence and kappa'
R psych::cohen.kappairr::kappa2
Missing & Measurement #

Intraclass Correlation & Agreement

  • Shrout & Fleiss (1979); McGraw & Wong (1996)
  • Koo & Li (2016) guidelines for ICC reporting
R psych::ICCirr::icc
Missing & Measurement #

ROC Curves & AUC

  • Hanley & McNeil (1982); Pepe, The Statistical Evaluation of Medical Tests
  • DeLong et al. (1988) for correlated AUC comparison
R pROCROCRyardstick
Missing & Measurement #

Bland–Altman Limits of Agreement

  • Bland & Altman (1986), Lancet
  • Giavarina (2015), Biochemia Medica — practical guide
R blandrBlandAltmanLeh
Missing & Measurement #

Validity & Responsiveness of Measurement Scales

  • Streiner, Norman & Cairney, Health Measurement Scales
  • De Vet et al., Measurement in Medicine
COSMIN checklist
Causal #

Inverse Probability of Treatment Weighting (IPTW)

  • Hernán & Robins, Causal Inference: What If
  • Austin (2011), 'An Introduction to Propensity Score Methods'
R WeightItsurvey::svyglm
Causal #

Propensity Score Matching

  • Rosenbaum & Rubin (1983)
  • Stuart (2010), 'Matching methods for causal inference'
  • Austin (2011), Multivariable Behavioral Research
R MatchItcobalt
Causal #

E-value for Unmeasured Confounding

  • VanderWeele & Ding (2017), Annals of Internal Medicine
R EValue
E-value calculator
Causal #

Instrumental Variables (IV / 2SLS / Mendelian Randomisation)

  • Angrist & Pischke, Mostly Harmless Econometrics
  • Davey Smith & Ebrahim, 'Mendelian randomization' (IJE 2003)
R ivregAERTwoSampleMR
Causal #

Difference-in-Differences

  • Angrist & Pischke; Callaway & Sant'Anna (2021)
  • Roth et al. (2023), 'What's Trending in Difference-in-Differences?'
R didfixestDIDmultiplegtDYN
Causal #

Regression Discontinuity Design

  • Imbens & Lemieux (2008)
  • Cattaneo, Idrobo & Titiunik, A Practical Introduction to RDD
  • Lee & Lemieux (2010), JEL review
R rdrobustrddensity
Causal #

Target Trial Emulation

  • Hernán & Robins (2016), AJE; Hernán et al. (2022), 'A target trial approach'
  • Matthews et al. (2022), 'Target trial emulation: applying principles of randomized trials to observational studies'
R dplyr + survival + IPCW workflow
Causal #

Causal Mediation Analysis

  • VanderWeele (2015), Explanation in Causal Inference
  • Imai, Keele & Tingley (2010)
R mediationCMAverse
Causal #

Identifiability Assumptions for Causal Effects

  • Hernán & Robins, Causal Inference: What If
  • Pearl, Causality
  • Petersen & van der Laan (2014)
Advanced & Bayesian #

Power & Sample Size

  • Cohen (1988); Chow, Shao & Wang, Sample Size Calculations in Clinical Research
  • Schulz & Grimes (2005), 'Sample size calculations in randomised trials'
R pwrWebPowerlongpower
Advanced & Bayesian #

Multiple Testing Correction

  • Benjamini & Hochberg (1995)
  • Efron, Large-scale Inference
R p.adjustmultcomp
Advanced & Bayesian #

Meta-analysis (Fixed & Random Effects)

  • Borenstein et al., Introduction to Meta-Analysis
  • Higgins, Thompson et al., Cochrane Handbook
R metametafor
Advanced & Bayesian #

Bayesian Inference (Priors, Posteriors, Credible Intervals)

  • McElreath, Statistical Rethinking
  • Gelman et al., Bayesian Data Analysis
R brmsrstanarmcmdstanrposterior
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