Benchmarking R functions for reading tsv files (CC291)

Reading data tables into R is a very common activity and there are many ways to do this in base R with read.delim or with the read_tsv function from readr, the vroom function from the vroom package, or the fread function from data.table. Pat will benchmark these four approaches and discuss the tradeoffs between speed and dependencies for package development. Then he implements readr::read_tsv with test driven development (TDD) to create a read_taxonomy function in his phylotypr R package. This episode is part of an ongoing effort to develop an R package that implements the naive Bayesian classifier.

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You can find my blog post for this episode at https://www.riffomonas.org/code_club/....

Check out the GitHub repository at the:
* Beginning of the episode: https://github.com/riffomonas/phyloty...
* End of the episode: https://github.com/riffomonas/phyloty...

#rstats #readr #vroom #data.table #read.delim #rdp #16S #classification #classifier #microbialecology #microbiome

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0:00 Introduction
3:30 Benchmarking methods for reading tsv files
24:23 Writing tests for read_taxonomy
28:18 Writing read_taxonomy function
32:09 Refactoring read_taxonomy
35:51 Package hygiene