Schloss Lab Tools for Reproducible Microbiome Research

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Documentation for package ‘schtools’ version 0.4.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calc_relabun	Calculate OTU relative abundances from a shared file
close_enough	Check whether two numeric vectors are close enough
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
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