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

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.

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.

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

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.

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.