Changes in version 1.2.1                        

CHANGES

  - Added functions to explore assembly and annotation statistics in a
    context: assembly and annotation stats for NCBI genomes can be
    extracted through the Datasets API and compared with user-defined
    values. New functions: get_genome_stats(), compare_genome_stats(),
    and plot_genome_stats().

                        Changes in version 1.1.8                        

CHANGES

  - Synteny assessment formula now also considers scale-free topology
    fit.

BUG FIXES

  - Reference-based orthogroup inference does not require the exact same
    set of species anymore.

                        Changes in version 1.1.7                        

BUG FIXES

  - Variable Duplications_50 of the duplications data frame was not
    matching variable Dups of the stats data frame in the output of
    read_orthofinder_stats()

NEW FEATURES

  - Replaced dispersal formula with a more meaningful and interpretable
    one.
  - Added a max_size param to plot_og_sizes() to ignore OGs larger than
    a specific size.

                        Changes in version 1.1.4                        

NEW FEATURES

  - Added option to scale scores by the maximum value

                        Changes in version 1.1.3                        

NEW FEATURES

  - Added a correction for overclustering in calculate_H() that
    penalizes protein domains in multiple orthogroups.
  - Updated vignette to provide a detailed explanation of how
    homogeneity scores are calculated.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Added a NEWS.md file to track changes to the package.