- 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).

- 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).

- 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).

- 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).

- 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).

- 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).

- 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.

- 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).

- Fixes a memory corruption that occurred only in tests (#90).
- Updates
`README.md`

. - Corrects various typos.

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