statgenIBD 1.0.11

• readRabbit now also reads inputs when pedigree is not specified directly in input file.
• Internal changes to accommodate upcoming Rcpp release

statgenIBD 1.0.10

• No user visual changes.

statgenIBD 1.0.9

• Functions no longer rely on soft-deprecated ggplot2 functions.

statgenIBD 1.0.8

• readRabbit now reads input files produced by the open source version of RABBIT, available at https://github.com/Biometris/RABBIT

statgenIBD 1.0.7

• 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

• 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

• 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

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

statgenIBD 1.0.3

• 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

• 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

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

statgenIBD 1.0.0

• Initial CRAN version