R package pedSimulate: Pedigree, genetic merit and phenotype simulation

Version: 0.0.3

Applying mortality to each generation separately rather than on selection candidates, which may come from more than a single generation.

Added function assortative for assortative/disassortative mating.
Added "-P" and "-PA" to arguments fsel and msel to select in opposite directions of "P" (phenotype) and "PA" (parent average).

Debugged the bug introduced in the previous version in the simulatePed function.

Major revision
Functions simulatePed and assortative were combined into simulatePed, and arguments fullsib and parentprogeny were removed.
Added function appendPed for simulating new generations from an existing pedigree and appending to it.
Added function fs_mate_finder for finding fullsib matings in the pedigree.
Added function hs_mate_finder for finding halfsib matings in the pedigree.
Added function pp_mate_finder for finding parent-progeny matings in the pedigree.

Added agrumnts f.order and m.order to simulatePed and appendPed functions.

A major debug: %in% (-overlap.s:0)+i-1 was performing differently from %in% ((-overlap.s:0)+i-1), similarly %in% (-overlap.d:0)+i-1 and %in% ((-overlap.d:0)+i-1).
Added function appendGen for simulating genotypes for an appended pedigree to an existing pedigree with genotypes.

Debugged function appendPed for making no updates to the existing pedigree (the pedigree upon which new generations are appended).
“Bijma, P. & Rutten, M. (2002)” gone missing on the web. References were added.