forrel 1.7.0

New features

• The function checkPairwise() has undergone substantial revision, with plots implemented in both ggplot2 and plotly in addition to the default base plot. A summary of the main changes are:

  • a new argument plotType can be either "base" (default), "ggplot" or "plotly"
  • the plotting is now done in a separate function plotCP() which is also exported
  • a new argument ids, which when given restricts the checks to those individuals
  • the output column LR is renamed to GLR (generalised likelihood ratio)
  • new output column pedrel describing (in words) each relationship according to the pedigree. The descriptions are obtained with the verbalisr package
  • estimation of P-values for each pairwise relationship, by parametric bootstrap simulations. This feature is controlled through new arguments nsim, pvalThreshold and seed. By default nsim = 0, meaning that no simulations are performed. The P-values are stored in the output column pval.

• New function quickLR() performs the most common kinship tests (paternity and sibship) for a pair of individuals.

• New function ibdLoglik() computes the pairwise likelihood for given set IBD coefficients (kappa or delta).

• Improved progress bars using the pbapply package.

Other

• Removed (long deprecated) IBDtriangle(), replaced by ribd::ibdTriangle().

• Improved missingPersonPlot() appearance.

• In ibdEstimate(), more efficient data prep, and better removal of missing data.

• Refresh code in examples.