NEWS in package ‘chem16S’

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Changes in version 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 version 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 version 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 version 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 version 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 version 0.1.0 (2022-07-04)

• First release on GitHub.