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rehh 3.2.2 (September 15, 2021)

• 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

rehh 3.2.1 (November 03, 2020)

• bug-fix: memory error in function calc_sfs_tests()

rehh 3.2.0 (October 30, 2020)

• 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

rehh 3.1.2 (July 17, 2020)

• added option to parse vcf files using package ‘data.table’ in order to avoid reliance on package ‘vcfR’

rehh 3.1.1 (June 19, 2020)

• 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()

rehh 3.1.0 (March 03, 2020)

• 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

rehh 3.0.1 (July 11, 2019)

• bug-fix: memory allocation in C

rehh 3.0.0 (July 08, 2019)

• 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

rehh 2.0.4 (February 13, 2019)

• 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

rehh 2.0.3 (June 12, 2017)

• 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

rehh 2.0.2 (November 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.

rehh 2.0.1 (October 24, 2016)

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

rehh 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

rehh 1.13 (May 13, 2015)

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

rehh 1.12 (April 7, 2015)

• Minor modification of the CITATION file

rehh 1.11 (August 25, 2013)

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

rehh 1.1 (April 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.

rehh 1.0 (March 15, 2012)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.