CHANGES IN chem16S 1.2.0 (2025-01-16)
-------------------------------------

- Update reference database to GTDB release 220.

- For GTDB release 220, map_taxa() maps from old to new names identified in
  post-curation cycle
  (https://data.gtdb.ecogenomic.org/releases/release220/220.0/RELEASE_NOTES.txt).

- Add get_metric_byrank() to return chemical metric for all taxa at a given
  rank, calculated by aggregating abundance-weighted amino acid compositions.

- Add `drop.groups` argument to read_RDP() with default of FALSE.
  Classification to non-prokaryotic groups was an issue with previous
  reference databases but not the GTDB, and dropping root- and domain-
  level classifications may lose information.

- Add 'rootrank' (Root) taxon to RefDB/GTDB_220/taxon_AA.csv.xz to permit
  complete mapping of RDP output with GTDB reference database.

- Elemental formulas (O2 and H2O) are no longer subscripted in documentation.

CHANGES IN chem16S 1.1.0 (2024-07-01)
-------------------------------------

- Change default reference database to GTDB version 214.

- Normalize file names in RefDB/RefSeq_206 and RefDB/GTDB_214 for easier
  programmatic access.

- Add 'xvar' and 'yvar' arguments to plot_metrics().

- Add 'Domain' as an allowed rank in ps_taxacounts().

- Move calc_metrics() and add_hull() to the canprot package, which is now
  imported by chem16S.

- A single 'metrics' argument replaces 'x' and 'y' in plot_ps_metrics2().

CHANGES IN chem16S 1.0.0 (2023-07-17)
-------------------------------------

- Add functions for integration with phyloseq: ps_taxacounts(), ps_metrics(),
  plot_ps_metrics(), and plot_ps_metrics2().

- Add vignettes: *Chemical metrics of reference proteomes*, *Integration of
  chem16S with phyloseq*, and *Plotting two chemical metrics*.

- Change default reference database from RefSeq to GTDB.

- Add metrics: nO2, GRAVY, pI, MW, length, H/C, N/C, O/C, and S/C.

- Rename readRDP() to read_RDP(), getmetrics() to get_metrics(), plotmet() to
  plot_metrics(), and other analogous changes to function names.

- First release on CRAN.

CHANGES IN chem16S 0.1.3 (2023-02-12)
-------------------------------------

- Add 'pt.open.col' argument to plotmet() for border color of open plot symbols.

- Add 'xlab' and 'ylab' arguments to plotmet().

CHANGES IN chem16S 0.1.2 (2022-10-24)
-------------------------------------

- Add reference proteomes for taxa based on the Genome Taxonomy Database (GTDB).

- Add 'return_AA' argument to getmetrics() to return amino acid composition.

- Add 'zero_AA' argument to getmetrics() to specify amino acids with
  abundances set to zero for calculating chemical metrics.

CHANGES IN chem16S 0.1.1 (2022-10-11)
-------------------------------------

- Add 'cex' argument to plotmet().

- Don't drop dimensions in readRDP().

- Change "estimated community proteomes" to "community reference proteomes".

CHANGES IN chem16S 0.1.0 (2022-07-04)
-------------------------------------

- First release on GitHub.
