Handbook
1
Welcome
1.1
add chapter
1.2
editing a chapter
1.3
compile handbook
2
Coding Standards
2.1
General overview
2.2
Helpful suggestions
3
Building a R package
3.1
Motivation
3.2
Preparation
3.2.1
Naming your R package
3.2.2
Checking
3.3
Minimal R Package
3.4
Additional Components
3.4.1
R code
R/
3.4.2
Documentation
3.4.3
Dependencies
3.4.4
License
3.4.5
README
3.4.6
Tests
3.4.7
Data
3.4.8
Compiled code
3.4.9
vignettes
3.5
Resources
4
Parallel computing
4.1
Introduction
4.2
What is parallel computing, anyway?
4.3
When is it a good idea?
4.4
Fundamentals
4.4.1
Types of parallelisms
4.4.2
What you need to know about Hardware
4.4.3
HPC in R
4.5
Parallel computing in R
4.5.1
The parallel package
4.5.2
parallel example 1: Parallel RNG
4.6
parallel example 2: Simulating
\(\pi\)
4.6.1
Speedup things with Rcpp + OpenMP
5
Testing
6
Profiling and benchmarking
6.1
Introduction
6.2
Profiling
6.2.1
Troubleshooting
6.3
Benchmarking
6.3.1
Slow code
6.3.2
Fast code - microbenchmarking
6.4
Additional resources
7
HPC
7.1
Keep yor library organized
7.2
Don’t hijack nodes
7.3
Keep tempfiles where they belong
7.4
Use links and not hard copies of large data
7.5
Be mindful about special configs for R packages
Published with bookdown
USC biostats R Handbook
5
Testing