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Methods in R: A topic reference for biomedical research and peer review

Notation

This page lists the symbols, conventions, and abbreviations used throughout the book. Where a chapter departs from these conventions locally, the chapter says so explicitly.

Greek symbols

Symbol Meaning
\(\alpha\) Type I error rate (significance threshold).
\(\beta\) Type II error rate; also a regression coefficient (context).
\(\mu\) Population mean.
\(\sigma\) Population standard deviation; \(\sigma^2\) for variance.
\(\pi\) Population proportion.
\(\theta\) Generic population parameter; \(\hat{\theta}\) for the estimator.
\(\tau^2\) Between-study variance in meta-analysis.
\(\rho\) Population correlation; intra-class correlation (ICC).
\(\lambda\) Rate parameter; eigenvalue (context).

Latin symbols

Symbol Meaning
\(n\) Sample size.
\(N\) Population size.
\(\bar{x}\) Sample mean.
\(s\) Sample standard deviation; \(s^2\) for variance.
\(\hat{p}\) Sample proportion.
\(\mathrm{SE}\) Standard error of an estimator.
\(p\) \(p\)-value.
\(L\), \(\ell\) Likelihood and log-likelihood.
\(I^2\) Heterogeneity statistic in meta-analysis.

Operators and notation

  • \(\sim\) — “is distributed as”.
  • \(\hat{\theta}\) — an estimator of the parameter \(\theta\).
  • \(X \perp Y\) — independence.
  • \(E[\cdot]\), \(\mathrm{Var}[\cdot]\) — expectation and variance.
  • \(X \mid Y\) — \(X\) given \(Y\) (conditional).

Abbreviations

Abbrev. Expansion
CI Confidence interval (frequentist); credible interval (Bayesian) — context disambiguates.
RR Relative risk (risk ratio).
OR Odds ratio.
HR Hazard ratio.
AUC Area under the (ROC) curve.
LR+ / LR− Positive / negative likelihood ratio.
PPV / NPV Positive / negative predictive value.
MLE Maximum likelihood estimator.
GLM Generalised linear model.
GLMM Generalised linear mixed model.
GEE Generalised estimating equation.
RCT Randomised controlled trial.
ITT Intention to treat.
PP Per protocol.
MI Multiple imputation.
FDR False discovery rate.
BH Benjamini–Hochberg (FDR procedure).
TRIPOD Transparent Reporting of a multivariable prediction model.
STROBE Strengthening the Reporting of Observational Studies in Epidemiology.
CONSORT Consolidated Standards of Reporting Trials.
PRISMA Preferred Reporting Items for Systematic Reviews and Meta-Analyses.
ARRIVE Animal Research: Reporting of In Vivo Experiments.
STARD Standards for Reporting of Diagnostic Accuracy.

Code conventions

  • The base R pipe |> is used throughout. Files mixing %>% and |> are flagged in GENERATION_LOG.md.
  • Package functions are written qualified the first time they appear in a chapter (dplyr::filter()), then bare on subsequent uses.
  • Code blocks shown in the rendered book are display-only; the book is built with eval = FALSE globally and verified to knit cleanly without side effects. To run a chunk yourself, copy it into an R session with the libraries cited in that section attached.
This book was built by the bookdown R package.