Writing C++ code in R using the Rcpp package: Overcoming bottleneck in all v all comparison (CC055)
Sometimes we run out of tricks to accelerate our R code using built in functions, packages, and strategies. For these cases, Rcpp is a useful package that allows us to integrate C++ code into our R functions to speed up their execution. This episode is part of a larger arc of episodes investigating the sensitivity and specificity of amplicon sequence variants (ASVs), also known as exact sequence variants (ESVs). ASVs are growing in popularity for analyzing microbial communities using 16S rRNA gene sequences. Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make.
0:00 Introduction
7:21 Writing function using Rcpp
20:28 Integrating new function
25:04 Committing issue
26:21 Conclusion
The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2...
Rcpp resources
https://adv-r.hadley.nz/rcpp.html
https://teuder.github.io/rcpp4everyon...
