coala 0.4.0

• Adds the create_abc_param and create_abc_sumstat functions for converting the simulation results into the format needed for abc::abc function (#151).
• Improves the documentation significantly and adds more examples and links to help pages (#150).
• Changes name of get_population_indiviuals to get_population_individuals (#150).
• Adds an option to active_msms() to download msms' jar file (#153).
• Adds support for partial models. Now, arbitrary sets of features, loci, parameters and summary statistics can be combined via + and then be added to one or more models later (#155).

coala 0.3.0

Major improvements

• Support for more selection models, including ones for local adaptation (#137).
• Adds as.segsites.GENOME function that converts genetic data imported with the package PopGenome to coala's format (#139).

Small Changes

• Adds feat_ignore_singletons, which is a feature that makes coala ignore singletons when calculating the summary statistics (#138).
• Use ms from package phyclust instead of requiring that the binary is installed on the system (#140).
• Ensure that msms uses only one CPU core (#142).

coala 0.2.2

• Fixes the broken nucleotide diversity and Tajima's D summary statistics (#133).
• Adds support for calculating joint frequency spectra for more than two populations (#132).

coala 0.2.1

• Fixes a test that failed on R 3.1.x due to a bug in the tests code (#127).
• Fixes version requirement for testthat (#127).
• Adds the calc_sumstats_from_data function for calculating summary statistics from biological data (#124).
• Exports the functions related to segregating sites (#122).

coala 0.2.0

Major improvements

• Adds support for distribution independent repetitions on multiple CPU cores (#116).
• Improves support for polyploid models. The ploidy parameter is now provided in the coal_model instead of in feat_unphased (#115).
• Adds the MCMF summary statistic (#94).
• Adds support for the omega statistic using OmegaPlus (#109).

Small Changes

• Adds option to calculate iHS in sumstat_ihh() and made the statistic return a data.frame instead of a list.
• Adds optional support for calculating the JSFS per locus instead of globally (#112).
• Adds optional in-place transformation of summary statistics (#110).
• Adds support for simulating a fixed number of mutations with ms and msms (#19).
• Writes seq-gen output into memory instead of in files before it is parsed (#99).
• Adds optional support for parameter zero inflation for a deterministic fraction of loci instead of a random number. Can be used by setting random = FALSE in par_zero_inflation (#97).
• get_outgroup now returns NA if the model has no outgroup rather than throwing an error.

Bug Fixes

• Fixes the simulation of sizes changes in one populations models with msms (#105).
• Remove broken implementation of the nSL statistic (sumstat_nsl())
• Fixes site frequency calculation when an outgroup is present (#96).
• Fixes multiple errors that occurred in edge cases when calculating ihh (#98).

coala 0.1.1

• Fixes a memory corruption that occurred only in tests (#90).
• Updates README.md.
• Corrects various typos.

coala 0.1.0

• Initial release version
• Thanks to Ann Kathrin Huylmans for suggesting the name 'coala' and to Soumya Ranganathan for proofreading.