jaatha 2.7.0
============

* Implement a candidate loci approach for selection. So far only for internal
  testing.

* Allow for gamma distributed recombination and mutation rates
  between loci for genomic parameters (mutation and recombination rates).

* Bug fix: Fix two bugs with calculation of confidence intervals.

* Fix a harmless memory leak in experimental code (#19)



jaatha 2.6.0
============

* Switched unittests from RUnit to testthat

* Added a Rcpp function to parse tree from ms(ms) output for seqgen. This should
  make seqgen less platform dependent (it still requires a Unix platform).

* Add a subset parameter to Jaatha.confidenceIntervals that allows to distribute
  the calculation on multiple machines.

* Bug fix: in 2.5.1, the ms output file was not delete when using seq-gen. This can cause
  Jaatha to fail if the disk runs out of space (#14). 

* Bug fix: Fixed a severe bug in the `Jaatha.confidenceIntevals` function. There often
  parameters different from the maximum likelihood estimates were used to
  calculate the confidence intervals (#15). 



jaatha 2.5.1
============

* Made it possible to use seq-gen together with msms (Linux only).

* Bug fix: Fixed a bug that caused seq-gen to fail if the mutation parameter was not the
  last model parameter.



jaatha 2.5.0
============

* Fixed wrong description of N0 as size of the ancestral population in the documentation (#4)

* Fixed an bug with made jaatha abort when a point was slightly outside
  parameter range (#5)

* Fixed bug in calculation of JSFS introduced in 2.4-1 (#7)

* Now old simulations are actually reused (#8)

* It is no longer necessary to have a simulation program that can simulate all
  groups (#6)

* Different groups now really use different simulation programs

* Simplified internal simulation program interface

* Print dispatch for demographic model

* Modularized parsing of simulation output

* Models in different groups can now use different simulation software

* Now Jaatha simulates more data if it fails to fit the GLM

* Allow GLM more steps to converge

* Different Groups can now have different summary statistics

* Prioritizing system for simulations programs

* Removed additional tmp-folders

* Removed dependency on foreach

* Changed dependency from dplyr to reshape2

* Removed optional logging into a file



jaatha 2.4.0
==================

* Jaatha.initialSearch() now divides the parameter space by all axis in turn,
  which makes the number of block linear instead of exponential in the
  parameter number.  

* Add an optional border to smoothing type summary statistics with is fitted
  via traditional transformations.

* Using `dplyr` instead of `plyr` for converting JSFS into data frames because
  it is significantly faster.

* Striped unused components from the `glm` objects.



jaatha 2.3.0
============

* Removed `epsilon`. We now stop the refined search after the
  likelihood did not improve for 10 consecutive steps.

* Removed `weight` parameter to down-weight old simulations,
  because it had no measurable effect on the estimates.

* Support for multiple groups of loci

*  Possibility to smooth arrays of arbitrary dimension



jaatha 2.2.0
==================

* Added function for calculating BCa confidence intervals

* Added `rerun` option to initial & refined search 

* Switched form doMC to multicore for parallelization

* Support for multiple independent summary statistics, even though this is not 
  yet used in the default front end.

* Differentiated between unit and integration tests and moved the unit tests
  back into the package.

* Reworked the reusing of simulations from previous steps in the refined search.
  Now only simulations that actually are inside the current block are reused. 

* Removed the "score". We are always using the log-likelihood now.

* Added support for a new "poisson.smoothing" type of summary statistics. 

* Fixed problem with naming of temporary directories if Jaatha was executed
  multiple times in different threads

* Fixed problem with Rcpp in size_t on 64 bit windows

* Fixed warning messages in cpp files

* Updated Makevars



jaatha 2.1.0
==================

* Removed the "externalTheta" option to simplify further development

* Rewrote and cleaned up many of the internal functions

* Further separated Jaatha and Demographic Model to simplify use of Jaatha
  in other areas

* Added caching for log factorials

* Ported msFile2jsfs to Rcpp

* Removed vignettes from the package due to their long build time; The pdfs will
  be provided on Jaatha's homepage instead 

* Added citation information to the package  

* Added link to github repo to package description

* Removed unused optimization strategies

* Bugfix: Changed the example fasta file for compatibility with next ape version

* Bugfix: Fixed encoding issue with bibtex for the packages vignette

* Bugfix: Removed debug functions in C++ files that prevented installation on R-2.14



jaatha 2.0.0
==================

* Updated Documentation and Vignette

* New Feature: Added caching of ms and seqgen commands

* Changed Feature: Made use of /dev/shm optional

* Bugfix: Multiple tmp-dirs used during multicore refined search

* Bugfix: Multiple searches for seqgen binary if running on multiple cores

* Fixed a bug with one parameter models

* Added support for seqgen

* GLM fitting algorithm can now take more steps to converge

* Updated the vignette

* Ported seqgenFile2Jsfs.cc to Rcpp

* Added parallelization using doMC.

* Some improvements to the UI.

* Updated copyright information.

* Added import from ape.

* Updated the vignette.

* Use /dev/shm for temp files if available

* Added "folded" option to use a folded JSFS

* Added documentation for fasta2jsfs()

* Made fasta2jsfs calculate the folded JSFS if no outgroup is given.

* Reworked the demographic model class to be more flexible and consistent.
