NEWS.md

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

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)

rehh documentation built on Sept. 15, 2021, 5:06 p.m.