Function reference • schtools

schtools schtools-package: schtools: Schloss Lab Tools for Reproducible Microbiome Research

Microbiome

Handle microbiome-related data.

read_dist(): Read in lower left triangular matrix from file

read_tax(): Read in a taxonomy file and parse it to a wide dataframe

parse_tax(): Convert taxonomy strings into dataframe of labels based on taxonomic classification

calc_relabun(): Calculate OTU relative abundances from a shared file

pool_taxon_counts(): Pool OTU counts at a particular taxonomic level

R Markdown

Format publication-quality documents.

set_knitr_opts(): Set knitr chunk options & inline hook

inline_hook(): Inline hook for knitr to paste human-readable numbers and nice lists.

paste_oxford_list(): Create a prose string from a list or vector

format_number(): Format human-readable numbers.

ggplot2

Make your plots even prettier.

theme_lucas(): Sarah's go-to theme for ggplot2

theme_sovacool(): Kelly's go-to theme for ggplot2

Snakemake

Helpers for running R scripts from Snakemake.

log_snakemake(): Save output, messages, warnings, and errors to the Snakemake log file

get_wildcards_tbl(): Get the Snakemake wildcards as a tibble

Everything else

Useful tools for miscellaneous tasks.

close_enough(): Check whether two numeric vectors are close enough

is_nearly_whole(): Checks whether a number is near to a whole number

is_nondesc(): Check whether all elements given are sorted in non-descending order

load_deps(): Install & load packages