moire 3.5.0

New Features

• Implemented maximum runtime functionality (#34)
  • The user can now specify a maximum runtime for the MCMC. After the maximum runtime is reached, the MCMC will stop and the current state of the MCMC will be returned.
  • Enabled by setting max_runtime = {time in minutes} in run_mcmc()

Bug Fixes

• Fixed handling of NA values in allele frequency vector

  • NA values are now replaced with 0
  • Warning message added to alert users of potential MCMC chain issues or loci lacking diversity (#20)

• Fixed memory crash in prob_any_missing() function (#38)

Other Changes

• Modified data loading to ungroup input data when loading long form (#37)

• Updated citation and manuscript information

• Added OpenMP detection utility

• Implement logging of individual sample log likelihoods

  • May be useful for diagnosing issues with particular samples, such as those that come from different populations

moire 3.4.0

New features

• Implemented logging of latent genotypes (#14)
• Added new datasets: namibia_data and regional_allele_frequencies (#27)

Bug fixes and improvements

• Fixed handling of NA values in allele frequency vector (#20)
  • The code now replaces NA values with 0 and displays a warning message
• Updated vignette with code examples using the new datasets (#27)
• Various documentation updates and minor cleanup

Internal changes

• Modified src/Makevars to include ENABLE_PROFILER flag and link with -lprofiler (#24)
• Created new file src/profiler.cpp for profiling functions implementation (#24)
• Added start_profiler() and stop_profiler() functions for performance profiling (#24)

moire 3.3.2

Minor bugfix that corrects an issue with temperature gradient tuning when using parallel tempering.

moire 3.3.1

Minor bugfix that corrects an issue with parameter logging when not using parallel tempering.

moire 3.3.0

This is a minor revision that greatly improves the speed of the MCMC computationally, various bug fixes, and improvements to numerical stability when starting the MCMC.

v3.2.0

New release, see NEWS.md for details.

manuscript-release

Version of moire used in https://www.biorxiv.org/content/10.1101/2023.10.03.560769

v3.1.0

What's Changed

• Fix NaN Initialization / simplify usage by @m-murphy in #4
• Relatedness estimation implementation by @m-murphy in #5
• Add prior for relatedness, adaptive temperature scaling by @m-murphy in #6

Full Changelog: 2.2.0...3.1.0

v3.0.0-beta

What's Changed

• Fix NaN Initialization / simplify usage by @m-murphy in #4
• Relatedness estimation implementation by @m-murphy in #5

Full Changelog: 2.2.0...3.3.0-beta

v2.2.0

• Multiple chains implementation
• Various bug fixes