01
Foundations and Data Management
Measuring disease in populations — incidence, prevalence, person-time, rates and standardization; data cleaning and management in R — messy health data, missingness, dates, joins, deduplication, reshaping and documentation.
LabSet up an R project, import data and build an age-standardized rate table; then clean a messy multi-file dataset, resolve a many-to-many join, deduplicate and produce a before/after data-quality summary.
02
Epi Visualization and Study Designs I
Data visualization for epidemiology — grammar of graphics, epidemic curves, age-sex pyramids, heat plots and choropleths; cohort and cross-sectional studies — risk ratios, risk differences, attributable risk and 2x2 tables.
LabBuild an epidemic curve, age-sex pyramid, heat plot and choropleth of disease burden by state; construct 2x2 tables with epitools, compute RR/RD with confidence intervals and directly standardize rates.
03
Case-Control Studies and Statistical Inference
Case-control studies, bias and confounding — odds ratios, matching, DAGs, effect modification and Simpson's paradox; probability, hypothesis testing and confidence intervals — distributions, p-values, chi-square, Fisher, t-tests and Wilcoxon.
LabCalculate ORs and CIs with epitools, run Mantel-Haenszel stratified ORs with epiR and build a DAG with ggdag; simulate sampling distributions, run common statistical tests and build descriptive tables with gtsummary.
04
Regression and Multivariable Adjustment
Linear regression for epidemiological data — simple and multiple regression, confounding adjustment, diagnostics and interactions; logistic regression and multivariable adjustment — binary outcomes, adjusted odds ratios, model building, model fit and STROBE reporting.
LabFit lm() models with diagnostic and coefficient plots and gtsummary regression tables; fit glm(family = binomial), extract adjusted ORs and CIs with broom, and build Table 1 + Table 2 workflows.
05
Outbreak Modelling and Diagnostics
Epidemic modelling with EpiEstim and EpiNow2 — Rt, serial interval, reporting delays, nowcasting and short-term forecasting; diagnostic testing and screening — sensitivity, specificity, PPV, NPV, likelihood ratios, ROC curves and AUC.
LabEstimate time-varying Rt with EpiEstim and reproduce it with EpiNow2; build diagnostic 2x2 tables with epiR, create ROC curves and AUC with pROC, and simulate how PPV changes with disease prevalence.
06
Capstone Applied Analysis and Presentations
End-to-end applied outbreak/cohort case study integrating cleaning, descriptive epidemiology, 2x2 tables, regression and reproducible reporting; capstone presentations with peer critique and evidence-based feedback.
LabWork through an instructor-led applied outbreak/cohort case study and knit it into a reproducible report; present the independent capstone, respond to peer and instructor critique, and revise the final portfolio submission.