Biostatistics Practicum
Biostatistics Practicum
Biostatistics Practicum
Copyright
Welcome
Preface
Conventions
1
Introduction
Reproducibility Mindset
2
Why Reproducible Research
3
De-identification and Data Ethics
4
Team Science for Biostatisticians
Data Science Workstation
5
Setting Up Your Workstation
6
The Unix Shell
7
Git and GitHub for Solo Developers
8
Git for Teams
9
Cloud Compute and Remote Servers
Reproducible Infrastructure
10
Research Compendia with rrtools
11
renv for Package Management
12
Docker for Reproducibility
13
The zzcollab Framework
14
Reproducible Pipelines with targets
Reproducible Reporting
15
Reproducible Reports with Quarto
16
Rmd Workflow: Conversions and Tables
Data Wrangling and Graphics
17
Getting Data In: Files, APIs, and Scraping
18
Data Wrangling Essentials
19
Factors, Strings, and Dates
20
Joining and Reshaping
21
Databases and SQL for Biostatisticians
22
Plotting with ggplot2 and purrr
23
Missing Data: Diagnosis, Imputation, Reporting
Analysis Practice
24
Statistical Analysis Plans
25
Clinical Data Standards: CDISC, SDTM, and ADaM
26
Testing Data Analysis Workflows
27
Continuous Integration with GitHub Actions
28
AI-Assisted Coding
29
SAS for R Programmers
Case Studies
30
Case Study: Palmer Penguins
31
Case Study: ADNI MCI Prediction
32
Communicating a Finished Analysis
Obligations and Synthesis
33
Federal Requirements and Deposition
34
Ethics Beyond Compliance
35
Course Synthesis and Review
References
Appendices
A
Alternative Wrangling Paradigms
B
The Peer-Program Survey
C
The rgtlab Software
Credits
Colophon
Biostatistics Practicum
Code
Reproducible analysis workflows for biostatisticians.
Copyright