Changes in version 0.3.5 (2025-08-27)                  

(August 26th, 2025)

  - Function combine_log now also reads and combine log files from
    BEAST2 and MCMCTREE
  - Added Z-transformation for functions plot_back_rates and
    plot_treerates_sgn
  - New function write_partitioned_alignments2 write alignment
    partitions as separate alignment files for various data types
  - New function clade_membershipdesignates clade membership for each
    tip for downstream analyses summarizing rates for each clade

                        Changes in version 0.3.3                        

(July 21st, 2023)

  - Function plot_back_rates corrected for MrBayes.
  - New warnings and import of MrBayes single {all} clock partition for
    plot_treerates_sgn.

                 Changes in version 0.3.2 (2022-11-03)                  

(October 31st, 2022)

  - New function plot_back_rates and updates on vignettes.

                        Changes in version 0.3.1                        

(OCtober 20th, 2022)

  - Bug fixes and adjustment of selection functions for BEAST2: old
    get_pwt_rates function exists now in two
    versionsget_pwt_rates_MrBayes and get_pwt_rates_BEAST2, and updates
    on plot_treerates_sgn to handle BEAST2.

                  Changes in version 0.3 (2022-08-19)                   

(August 1st, 2022)

Implementation of functions for BEAST2 data now complete!

  - Added function (write_partitioned_alignments) to write partitioned
    alignments based on the inferred clusters.
  - Added BEAST2 support for clock rate table import - old
    get_clockrate_table function exists now in two versions,
    get_clockrate_table_MrBayes and get_clockrate_table_BEAST2

                        Changes in version 0.2.1                        

(July 8th, 2022)

  - Added function (drop.dummy.mb) to remove "dummy" tip from Mr. Bayes
    summary trees and export tree accounting for metadata on the tips
    (for fully extinct clades).

                        Changes in version 0.2.0                        

(June 27th, 2022)

  - Added functions (drop.dummy.beast, offset.to.dummy,
    write.beast.treedata, offset.to.dummy.metadata) to handle trees with
    offsets as produced by the BEAST2 SA package for fully extinct
    clades
  - FBD functions can now handle BEAST2 log files produced by several
    packages (SA, BDSKY)
  - plot_treerates_sgn() function update: outputs chosen thresholds and
    estimated rate values for each threshold.

                        Changes in version 0.1.0                        

(May 12th, 2022)

  - First version!