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Refactoring R code to make it faster and more memory efficient (CC281)

Based on the extensive benchmarking Pat's been doing in recent episodes, it's now time to apply his results to get the code running without blowing out the required amount of RAM. Pat will use the test driven development (TDD) framework to refactor his code to have confidence that the improved code is correct. He also does a quick benchmarking comparison of table and tabulte. 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 Support Riffomonas by becoming a Patreon member!   / riffomonas   Want more practice on the concepts covered in Code Club? You can sign up for my weekly newsletter at https://shop.riffomonas.org/youtube to get practice problems, tips, and insights. If you're interested in purchasing a video workshop be sure to check out https://riffomonas.org/workshops/ You can also find complete tutorials for learning R with the tidyverse using... Microbial ecology data: https://www.riffomonas.org/minimalR/ General data: https://www.riffomonas.org/generalR/ 0:00 Introduction 1:26 Pinpointing where memory issue occurs 6:17 Refactoring detect_kmers 10:59 Refactoring detect_kmers_across_sequences 14:57 Refactoring calc_word_specific_priors 20:38 Benchmarking table and tabulate 26:00 Refactoring calc_genus_conditional_prob 30:43 Refactoring build_kmer_database 32:24 Will the vignette run without crashing? 35:04 Replace sapply with a for loop