Changes in version 3.2.3 (2026-01-30) - due to a change in the C<->R API in R version 4.6., resizing of vectors in calc_furcation() using deprecated C function SETLENGTH() has moved from C to R - added options "negativeThreshold" and "keepNA" in function calc_candidate_regions() - added examples for usage of calc_candidate_regions() Changes in version 3.2.2 (2021-09-15) - bug-fix: calc_candidate_regions() produced error if a chromosome contained only for a single site a score - omp libraries are included first in multi-thread C-code in order to comply to new release of Clang-13 Changes in version 3.2.1 (2020-11-09) - bug-fix: memory error in function calc_sfs_tests() Changes in version 3.2.0 (2020-11-01) - corrections and extensions of the vignettes - added inset between chromosomes in function manhattanplot() - added option to highlight specific markers in plot.haplohh() - function subset() can filter markers on maximum number of alleles - option to set maximal haplotype extension (in base pairs) in function scan_hh_full() - added function haplohh2sweepfinder() that extracts allele frequencies which can serve as input for the programs SweepFinder or SweeD - added function calc_sfs_tests() to calculate Tajima's D and Fay & Wu's H, allowing for data with missing values Changes in version 3.1.2 (2020-07-17) - added option to parse vcf files using package 'data.table' in order to avoid reliance on package 'vcfR' Changes in version 3.1.1 (2020-06-19) - option to use stepwise continuous EHH(S) curves for integration and plotting - refactored C-code for calculation of furcation trees - bug fix for false rendering of missing values in furcations of unphased data - bug fix: removed reliance of examples and tests on suggested packages - updated section on calc_ehh() in main vignette - added functions calc_pairwise_haplen() and scan_hh_full() Changes in version 3.1.0 (2020-03-04) - functions ies2xpehh() and ines2rsb(): - bug fix for unphased data and markers with no homozygous individuals - function manhattanplot(): - added option to plot absolute values - added option to highlight individual markers - function manhattanplot() and distribplot(qqplot=TRUE): - added option to rasterize plot (reduce number of plotted data points) - function calc_ehh(), calc_furcation() and plot.haplen(): - changed default order of alleles from their frequency to internal coding - all plot functions: - allow user to set plot margins - allow user to overwrite some plot parameters such as "xlab" and "ylab" - new plot function for (small) haplohh-objects - minor optimization of parallelization - additional comments about unphased data in the main vignette Changes in version 3.0.1 (2019-07-11) - bug-fix: memory allocation in C Changes in version 3.0.0 (2019-07-09) - Major refactoring of underlying C code and its interface to R - The package can now handle multi-allelic markers - Enabled data input from vcf files and the simulation program 'ms' - Calculation and visualization functions have been separated - Added support for handling unphased haplotypes and unpolarized markers - Output in form of matrices has been replaced by data frames - Simplified column names in data output (use only capital letters and underscores) - Improved visualization of furcation trees - Added visualization of shared haplotype lengths - Added simple function to delineate candidate regions of selection - Added options to yield virtually identical results with program hapbin - Made all plots more customizable - Added new vignette with in-depth discussion of example files - Disagreement between code and vignette about uni-lateral p-value for Rsb/XP-EHH has been cleared Changes in version 2.0.4 (2019-02-13) - Corrected implementation of maxgap in combination with discard_integration_at_border=FALSE - Added parameter scalegap - Included section about gaps in vignette, added details in comparison with hapbin, corrected rendering - Corrected paper title in CITATIONS Changes in version 2.0.3 (2019-02-04) - Bug corrected in the ihh2ihsplot (it lead to a crash when the freqbin argument was set to 0) - Inactivation of graphical display in multiple windows (i.e., plot.new calls) in the calc_ehh, calc_ehhs, ihsplot, rsbplot, xpehhplot and distribplot functions - Minor corrections in the manual pages Changes in version 2.0.2 (2016-11-18) - 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 in version 2.0.1 (2016-10-25) - Option maxgap added to the calc_ehh, calc_ehhs and scan_hh functions Changes in version 2.0.0 (2016-08-01) - 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 in version 1.13 (2015-05-13) - Removing smartlegend() calls (deprecated in new version of gplot) in calc_ehh.R and fistribplot.R Changes in version 1.12 (2015-04-07) - Minor modification of the CITATION file Changes in version 1.11 (2013-08-26) - Minor modification of the distribplot.R file (call to plot.density was disabled) Changes in version 1.1 (2013-04-26) - 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. Changes in version 1.0 (2012-03-15)