Skip to content

Latest commit

 

History

History
167 lines (115 loc) · 3.89 KB

CHANGES.md

File metadata and controls

167 lines (115 loc) · 3.89 KB
Raw

Version 0.2.11

Changes

  • Adding command-line tool msb2nex (and supporting code in parsing.py module) for converting msbayes-formatted configs and data to ecoevolity-formatted configs and data.

Version 0.2.10

Changes

  • Removing matplotlib dependencies on Latex.

Version 0.2.9

Changes

  • Adding option to command-line tools loci2nex and loci2phy to randomly subsample loci.

Version 0.2.8

Bug fixes

  • Fixing issue with pyco-sumevents where it would crash if any Bayes factors were "NA".

Version 0.2.7

Changes

  • Adding option to command-line tools loci2nex and loci2phy to convert names of sequence label. A CSV file can now be provided with the current seq labels in the first colum and the desired labels in the second.

Version 0.2.6

Changes

  • Adding pyco-dummy-data command-line tool for generating dummy biallelic data in YAML format. Such files are often useful as templates for running simulations with simcoevolity.

Version 0.2.5

Changes

  • Updating pyco-sumsims to allow mutlple summary-table files to plot from.
  • Updating pyco-sumevents to plot via matplotlib by default; can still choose to use R.
  • Updating posterior classes to summarize model distances (set-partitions distances); this uses the Hungarian (Munkres) algorithm via the Munkres package.
  • Updating logic in setup script to be more robust/portable.

Version 0.2.4

Changes

  • Fixing highlighting bug in plots of sumsims tool (highlighting estimates with poor ESS values, rather than good).

Version 0.2.3

Changes

  • Updating sumsims tool to make plotting more robust across matplotlib environments.
  • Adding option to plot directly from previous summary table produced by sumsims.

Version 0.2.2

Changes

  • Updating sumsims tool to avoid LaTeX dependencies.

Version 0.2.1

Changes

  • Updating sumsims tool to specify a backend for matplotlib (mpl.use("agg")). This should avoid the invalid DISPLAY environmental variable RuntimeError on some systems.

Version 0.2.0

Changes

  • Adding sumsims CLI tool for summarizing and plotting results of ecoevolity analyses on datasets simulated with simcoevolity.

  • Adding formatting options to CLI plotting tools for greater control over output plots.

  • Adding option to output violin plots for sumsizes and sumtimes tools.

  • Adding option to plotting tools to ignore (i.e., do not plot) specified comparisons.

  • Adding option to PosteriorSample class to store event times in coalescent units.

  • Posterior classes updated to keep track of models and number of events separately for divergence and demographic comparisons.

  • Adding option to randomly split loci from one dataset into two datasets. This option is offered by CLI tools for converting pyrad loci file or fasta files to a nexus or phylip alignment.

Version 0.1.2

Changes

  • Adding CLI option to specify colors for plotting the comparison of divergence-time densities.

  • Adding '--charsets' option to include include a 'sets' block that defines locus boundaries in output nexus files.

  • Adding CLI tools for converting fasta files (rather than just .loci files from iPyrad). There is now a fastas2alignment tool, which converts a bunch of fastas into a concatenated nexus or phylip file, and a fastas2 fastas tool which 'normalizes' a bunch of fasta files such that they all have the same set of sequences.

Version 0.1.1

Changes

  • Adding CLI tool for converting iPyrad loci files into input files for PyMsBayes.

Version 0.1.0

  • Initial release.