removed 'asreml' from suggests in the package DESCRIPTION file.argument added that specifies output format of ggcontrib(), default is "matrix".argument now allows specified prefix for all identities in a pedigree generated from simPedHS() or simPedDFC().argument to drfx() so that arguments for the internal use of grfx() can be supplied to drfx(). updated grfx.Rd with an example illustrating the stdnorms argument.extended the warn argument to apply to the warning when incidence = NULL.grfx() now has a new argument to allow user to supply the standard normal deviates instead of generating them within the function.Added founderLine() which traces all individuals back to either the paternal or maternal founder.Added TDtT(), a function to take the TDT' Cholesky decomposition of a matrix (not currently exported).Examples can be seen in the makeAinv.Rd help file or by running the following commands in R:Īs a minimum 2.13.3 Released 4 June 2015 New.To implement, the pedigree must have phantom parent identities as unique rows and a matrix of probabilities of group membership for every phantom parent in every genetic group has to be supplied to the fuzz argument.Meaning, they can be assigned to more than one genetic group. Allows individuals' phantom parents to be assigned to genetic groups with a probability.Fuzzy classification of genetic groups to construct A^-1.thanks to profvis for bringing my attention to this!.since genAssign() and prunePed() are frequently called in many nadiv functions which operate on class 'numPed', this will have modest, but significant performance increases.
ASREML R BOUND CODE
can greatly trim down genAssign.numPed() code (and to some extent prunePed.numped()).create default and class 'numPed' methods for genAssign() and prunePed().greater speedup as A^-1 and D become more dense.use lower_bound algorithm for matrix lookup within c++ code.plot.proLik() now includes vertical lines to better visualize CIs.returns NA if confidence limits are not, in fact, found (e.g., for boundary parameters, variances that are not significantly greater than zero).this was due to optimize() quitting too early with default tol argument.previously would declare confidence limits found when they hadn't been.proLik() improved/bug fixed to find confidence limits.The inverses of these can be obtained from Sdinv and Sdsiminv and used in a mixed model.The ouptut contains the Sd and Sdsim dominance relatedness matrices.These are similar to what makeD() and makeDsim() accomplish for autosomes.Functions to construct sex-chromosomal dominance relatedness matrices.switched from not calculating this by default.default action is to calculate log-determinant of matrices.These (or their inverses?) can be used in JAGS or BUGS when running a quantitative genetic mixed model.Return diagonal of Mendelian sampling variance matrix in makeAinv() and makeS().
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