ChangeLog

Changes from Version 2.0.1 to 2.0.2 [Nov 15 2016]

* Option maxgap modified (functions return NA value if not satisfied)
* Example data sets removed from the rehh package and included in the newly developed rehh.data package. The function make.example.files() was modified accordingly.

Changes from Version 2.0.0 to 2.0.1 [Oct 24 2016]

* Option maxgap added to the calc_ehh, calc_ehhs and scan_hh functions

Changes from Version 1.13 to 2.0.0 [July 30 2016]

* Major modification of the algorithm to explore haplotype variability (more than one order of magnitude faster), including parallelization
* Major modification of the data2haplohh function to improve reading efficiency and allele recoding. In addition, a new input data file format (haplotype.in.columns) is now available
* Computation of xp-EHH
* A vignette that details how to use the package is now included in the package
* Several other minor modifications in other functions

Changes from Version 1.12 to 1.13 [May 13 2015]

* Removing smartlegend() calls (deprecated in new version of gplot) in calc_ehh.R and fistribplot.R

Changes from Version 1.11 to 1.12 [Apr 7 2015]

* Minor modification of the CITATION file

Changes from Version 1.1 to 1.11 [Aug 25 2013]

* Minor modification of the distribplot.R file (call to plot.density was disabled)

Changes from Version 1.0 to 1.1 [Apr 25 2013]

* Minor modification of the rehh-package.Rd file

* Printing of the advance of each site out of the total SNPs scanned when using scan_hh() function was disabled to save time and simplify screen output (particularly relevant for large data sets).

* Minor bugs corrected in the ehh_utils.c and r_scan_hh.c codes. These bugs had no effect on the results.