Changelog

Source: NEWS.md

jakR2 0.4

• Reworked alpha-diversity functions with corrected naming and Hill number framework
  • SIMPSON_EVENNESS renamed to GINI_SIMPSON (1 - D); SIMPSON_INVERSE renamed to SIMPSON_ENS (1/D)
  • New SIMPSON_ENS_EVENNESS column (ENS / S.obs)
  • SHANNON_E renamed to SHANNON_PIELOU; new SHANNON_EVENNESS column (ENS / S.obs)
• Added roxygen documentation for all package data objects
• Added @param entries for clusters and filter in the ft class
• Added testthat coverage for all alpha-diversity functions

jakR2 0.3

• A new S7 object called ft to hold feature tables
• methods for filtering based on min count and sample
• methods for OTU clustering
• some reusable regular expressions
• some new functions to work with multiple seqtab objects (seqtab_stats_bind and seqtab_stats_plot)
• better feature naming options for ft objects
• new obs_callout() function
• split jak_theme() into 6 smaller functions, with jak_theme() now being a wrapper around them

jakR2 0.2

• Helpful functions to create and work with palettes and colors
  • new order parameter for default, reverse and random palette order
  • blend_palette() to use monochromeR::generate_palette() blending
• Some jak_theme() tweaks
• Alpha-diversity metrics
• Session and package info utilities