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NEWS.md

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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)