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development version

schtools 0.4.1

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