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Changelog

Source: NEWS.md

statgenIBD 1.0.6.9000

  • Plotting didn’t work correctly for populations where there was a heterozygous probability in the IBD output. This is now corrected for plotType “allGeno”, “meanProbs”, and “totalCoverage”.
  • It is now possible to create a plot of plotType “singleGeno” when the position of the markers in the map have large values, i.e. when they are in base pairs.
  • A small bug in the concatenation of calcIBD objects with an identical number of genotypes is fixed.

statgenIBD 1.0.6

CRAN release: 2023-08-30

  • A bug in the plot function is fixed. The “singleGeno” plots now show the correct probabilities.
  • Functions no longer rely on soft-deprecated ggplot2 functions.

statgenIBD 1.0.5

CRAN release: 2022-09-04

  • Two new functions for writing (writeIBDs) and reading IBD (readIBDs) probabilities to a custom format have been added. The format is explained in a new vignette vignette("IBDFileFormat", package = "statgenIBD").
  • Two new plots are added for objects of class IBDprob, a plot showing the mean coverage of each parent across the population (plotType = "meanProbs") and a plot showing the total coverage of each parent (plotType = "totalCoverage").
  • Parent names in the output of calcIBD no longer have a leading “p”.
  • The function readRabbit, for reading output from the RABBIT software for computing IBDs for complex crosses, is moved here from statgenMPP.

statgenIBD 1.0.4

CRAN release: 2022-03-07

  • Increased speed of IBD calculations by improving an inefficient part of the algorithm.

statgenIBD 1.0.3

CRAN release: 2022-02-17

  • It is now possible to plot the pedigree of an object of class IBDprob by specifying plotType = "pedigree".
  • A small bug in the calculation of probabilities for populations C3 and C4 is fixed.

statgenIBD 1.0.2

CRAN release: 2021-12-10

  • It is now possible to specify chromosomes in character format, i.e. 1a, 1b, 1c as is common in certain crops.
  • The plot function for calculated IBD probabilities now has an extra option plotType that can have values “singleGeno”, for the original plot, and “allGeno” for a new plot showing probabilities for all genotypes in a single plot.
  • A bug that in some cases could lead to misnaming of the markers when combining multiple imputed populations is fixed.

statgenIBD 1.0.1

CRAN release: 2021-09-14

  • A bug where written Flapjack files could not be read is fixed.

statgenIBD 1.0.0

CRAN release: 2021-08-16

  • Initial CRAN version