Generating and classifying bootstrap replicates with test driven development (CC283)

Now that we have a kmer database, we are ready to classify our sequences using the Naive Bayesian approach. We'll start by refactoring some code that we used to make the database and then we'll generate and classify our bootstrap replicates. Of course, everything will be done using test driven development (TDD). This episode is part of an ongoing effort to develop an R package that implements the naive Bayesian classifier.

If you want to get a physical copy of R Packages: https://amzn.to/43pMR8L
If you want a free, online version of R packages: https://r-pkgs.org/

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 #refactor #testthat #tdd #microbenchmark #vectors #rdp #16S #classification #classifier #microbialecology #microbiome

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0:00 Introduction
4:32 Adding packages to DESCRIPTION file
8:20 Designing our classification function
10:55 Refactor generation of kmers from sequences
20:33 Generate bootstrap replicates of kmers
26:54 Classify kmers