Data in Hand

This part asks how raw files become an analysis dataset you can trust. It closes the first quarter, and its output, a checked and de-identified dataset, is the input to everything in the second.

• 10  Getting Data In: Files reads a clinical export with a full column specification and asserts against its usual pathologies.
• 11  APIs, Scraping, and Freezing What You Receive queries web interfaces with httr2 and freezes what was received.
• 12  Data Wrangling Essentials recodes per-site conventions and reports how many rows each step removes.
• 13  Factors, Strings, and Dates handles factors, free-text strings, and dates.
• 14  Joining and Reshaping predicts and checks the row count of every join.
• 15  Databases and SQL for Biostatisticians queries a database with SQL and dbplyr.
• 16  Plotting with ggplot2 and purrr builds figures with ggplot2 and many figures at once with purrr.
• 17  Missing Data: Diagnosis, Imputation, Reporting diagnoses missing data, imputes it with mice, and runs a sensitivity analysis.
• 18  De-identification in Practice applies the rules of 4  De-identification and Data Ethics to a release, with assertions that fail if an identifier survives.

If the quiz at the start of a chapter is easy, skip to the next.