CRAN v2.16

2.16.0 Released to CRAN 10 May 2018

NEW

• roxygen2 documentation
• Return diagonal of Mendelian sampling variance matrix in makeAinv() and makeS()
  • These (or their inverses?) can be used in JAGS or BUGS when running a quantitative genetic mixed model

Small changes

• default action is to calculate log-determinant of matrices
  • switched from not calculating this by default

2.15.0

NEW

• Functions to construct sex-chromosomal dominance relatedness matrices
  • makeSd() and makeSdsim()
    • These are similar to what makeD() and makeDsim() accomplish for autosomes
    • The ouptut contains the Sd and Sdsim dominance relatedness matrices
    • The inverses of these can be obtained from Sdinv and Sdsiminv and used in a mixed model

Small changes

• proLik() improved/bug fixed to find confidence limits
  • previously would declare confidence limits found when they hadn't been
    • this was due to optimize() quitting too early with default tol argument
  • returns NA if confidence limits are not, in fact, found (e.g., for boundary parameters, variances that are not significantly greater than zero)
  • plot.proLik() now includes vertical lines to better visualize CIs
• use lower_bound algorithm for matrix lookup within c++ code
  • based on c++ std::lower_bound
    • affect makeAinv() and makeD()
  • greater speedup as A^-1 and D become more dense
• create default and class 'numPed' methods for genAssign() and prunePed()
  • can greatly trim down genAssign.numPed() code (and to some extent prunePed.numped())
  • this speeds up/uses less memory
  • since genAssign() and prunePed() are frequently called in many nadiv functions which operate on class 'numPed', this will have modest, but significant performance increases
  • thanks to profvis for bringing my attention to this!