HVTI Recipes

Figures, tables, and R recipes for CORR manuscripts

Preface

Every figure in a CORR manuscript or presentation has been made before. The Kaplan-Meier curve with numbers at risk, the propensity-balance plot, the spaghetti plot of repeated echo measurements, the CONSORT diagram that opens the paper: we draw the same handful of figures over and over. This book collects them in one place, each with the code that produces it, so the next person who needs one starts from a working recipe instead of a blank script.

The recipes are built on the hvti* packages we maintain for this work, with ggplot2 underneath and a few specialist packages where they earn their place. Where a package gives you a helper, we use it. Where it does not (a plain density plot, a box plot), we fall back to bare ggplot2 and style it to match, so the figures look like they belong together regardless of how they were drawn.

Two ideas run through the whole book. First, a figure is built in two steps: a constructor prepares and validates the data, then plot() hands you a bare ggplot you finish with the usual +. That two-step shape is the figure pattern, not a universal one, though the tables keep the same division of labour between preparing the data and rendering it. Second, every example stands on its own. It generates its own sample data, so you can copy a chunk, run it, and see the figure before you point it at your own analysis. The aim is the one we hold for all of this team’s tooling: make the right path the easy path.

The chapters are grouped around the question in front of you. Start a reproducible analysis covers the packages and conventions. Describe the cohort moves from an inventory of the data to the distribution, relationship, and study-design figures that make that inventory clear. Analyze time-to-event outcomes handles survival, hazards, and additive hazard models. Explain predictive models reads the pieces of a forest fit. Finish and deliver the result carries a figure or table through its final styling and into a manuscript, poster, or slide.