NEWS.md

In schtools: Schloss Lab Tools for Reproducible Microbiome Research

schtools 0.4.1

• Minor bug fix in get_wildcards_tbl() (#48, @kelly-sovacool).
• Fix roxygen package doc syntax (https://github.com/r-lib/roxygen2/issues/1491, @kelly-sovacool).

schtools 0.4.0

• set_knitr_opts() now sets message to FALSE (#45, @kelly-sovacool).
• New function get_wildcards_tbl() returns the Snakemake wildcards list as a tibble (#46, @kelly-sovacool).

schtools 0.3.1

• Fixes for API changes in ggplot2 v3.4.0 and tidyselect v1.2.0 (#42, #44, @kelly-sovacool).
• pool_taxon_counts() now takes the taxon_level argument as a character rather than a data variable (#43, @kelly-sovacool).

schtools 0.3.0

• New function log_snakemake() redirects all output to a rule-specific log file when called by a Snakemake rule (#35, @kelly-sovacool).
• New function pool_taxon_counts() pools OTU counts at a particular taxonomic level (e.g. genus, phylum, etc.) to enable comparing analyses at different taxonomic resolutions, as seen in https://doi.org/10.1128/mbio.03161-21 (#37, @kelly-sovacool).
• New function calc_relabun() calculates OTU relative abundances (#38, @kelly-sovacool).
• New custom themes for ggplot2:
  • theme_sovacool() (#39, @kelly-sovacool)
  • theme_lucas() (#40, @sklucas)

schtools 0.2.1

• Improvements to parse_tax() (#32, @kelly-sovacool).
  • New column label_html provides HTML to correctly italicize genus names but not OTU labels.
  • Added an example to the intro vignette to demonstrate using this feature with ggtext.
  • Changed taxonomy data frame column names to lowercase and reordered them.
• Minor documentation improvements (#33, @kelly-sovacool).

schtools 0.1.1

• Refactored read_tax() (#30, @kelly-sovacool).
  • New function parse_tax() to separate the logic of reading and parsing taxonomy files.
  • read_tax() now accepts a sep parameter to handle different delim file types (e.g. csv or tsv).
• schtools now has a logo! (#31, @kelly-sovacool)

schtools 0.1.0

This is the first release version of schtools! 🎉

• You can now install schtools from CRAN!
• Added a NEWS.md file to track changes to the package.
• Major new functions:
• read_dist() (#10, @NLesniak)
• read_tax() (#22, @NLesniak)
• set_knitr_opts() (#21, @pschloss, @kelly-sovacool)
• inline_hook() (#21, @pschloss, @kelly-sovacool)
• paste_oxford_list() (#21, @pschloss, @kelly-sovacool)
• format_number() (#24, @pschloss, @kelly-sovacool)
• is_nearly_whole() (#24, @pschloss, @kelly-sovacool)
• close_enough() (#26, @kelly-sovacool)
• is_nondesc() (#28, @kelly-sovacool)
• New vignettes:
• introduction

schtools documentation built on Aug. 21, 2023, 5:10 p.m.