# Schloss Lab Tools for Reproducible Microbiome Research

## Documentation for package ‘schtools’ version 0.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

calc_relabun | Calculate OTU relative abundances from a shared file
close_enough | Check whether two numeric vectors are close enough for gov't work.
format_number | Format human-readable numbers.
get_wildcards_tbl | Get the Snakemake wildcards as a tibble
inline_hook | Inline hook for knitr to paste human-readable numbers and nice lists.
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
log_snakemake | Save output, messages, warnings, and errors to the Snakemake log file
parse_tax | Convert taxonomy strings into dataframe of labels based on taxonomic classification
paste_oxford_list | Create a prose string from a list or vector
pool_taxon_counts | Pool OTU counts at a particular taxonomic level
read_dist | Read in lower left triangular matrix from file
read_tax | Read in a taxonomy file and parse it to a wide dataframe
schtools | schtools: Schloss Lab Tools for Reproducible Microbiome Research
set_knitr_opts | Set knitr chunk options & inline hook
theme_lucas | Sarah's go-to theme for ggplot2
theme_sovacool | Kelly's go-to theme for ggplot2