1 Zhehao’s R Packages
After few years of using R, I learned more about R, and also about myself - I get extremely grumpy if I have to do the same work over and over. So I wrote them in functions and packaged them away so whatever details in those repetitive works won’t annoy me anymore.
It might sound sloppy, but currently I recommend install from the dev branch, latest fixes on bugs are published there. It might take a while until those fixed are merged to the main branch.
All packages can be installed from GitHub:
devtools::install_github("zzzhehao/<repo_name>", ref = "dev")1.1 Utilities
1.1.1 zhutilsr Basic Utilities
Basic utilities in R, handles database interactions, ggplot theming, general file management, custom logic, data wrangling, quality-checking, and cleaning. Dependency for most of my other packages.
1.1.2 zseq Genetic Sequence Handling & Analysis
Tools for sequence handling and analysis.
Importing and managing GenBank sequence and metadata via INSD XML file. Sequence I/O, metadata matching. Sanger sequence assembler (map to reference), alignment (local MAFFT) calculation, browsing, and editing, wrapper and interface to conventional tools (IQ-TREE, MrBayes, BEAST 2, ABGD, ASAP, GMYC, Gblocks), phylogenetic tree editing and visualization.
1.2 Topic-specific
1.2.1 rworms Taxonomist-friendly R Interface for WoRMS
Functions to retrieve taxonomy and distribution data from World Register of Marine Species.
This package currently doesn’t have an active dev branch:
devtools::install_github("zzhehao/rworms")Blog: