Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (< https://www.vsni.co.uk/software/asreml>).
R package that constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package for ASReml software.
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makeDsim()accomplish for autosomes
proLik()improved/bug fixed to find confidence limits
optimize()quitting too early with default
NAif 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
genAssign.numPed()code (and to some extent
prunePed()are frequently called in many nadiv functions which operate on class 'numPed', this will have modest, but significant performance increases
profvisfor bringing my attention to this!
makeAinv.Rdhelp file or by running the following commands in
?makeAinv # launches the help documentationexample(makeAinv) # runs the examples in the help documentation
* Notably, fuzzy classification can be set to 'null', where each phantom parent is assigned to one genetic group with probability=1. This produces the same **Astar** matrix as regular genetic group methods (without fuzzy classification). See this demonstrated in the examples of the help documentation.
makeAstarMult()function to create the inverse numerator relationship matrix with genetic groups (and possibly also fuzzy classification of genetic groups) through matrix multiplication instead of using direct algorithms to set this up.
makeAinv()to create Q and A^-1 directly, then multiplies these in such a way as to obtain Astar.
makeAstarMult.Rdhelp file or run them in
Rwith the command:
?makeAstarMult # launches the help documentationexample(makeAstarMult) # runs the examples in the help documentation
F2009.Rdor in R type:
simGG() function to simulate pedigree and phenotype when immigration occurs in a focal population
ggTutorial.Rdor in R type:
LRTest()is now an exported function to do log-likelihood ratio tests
new S3 generic and methods for
fuzz == NULLthen dispatch the method
fuzz == "matrix" | fuzz == "Matrix"then dispatch
fix issue with
proLik() and the confidence interval estimation
LRTest()as basis of
proLik()so consistently define log-likelihood ratio test statistics
ggcontrib()can now incorporate fuzzy classification of genetic groups
ggcontrib()have been changed. For more information and examples, read the help documentation
?ggcontrib # launches the help documentationexample(ggcontrib) # runs the examples in the help documentation
makeAinv()now can construct the augmented A-inverse matrix for genetic groups
makeAinv(), however, the defaults are set to produce the normal A-inverse. For more information and examples, read the help documentation
makeAinv.Rdor in R type:
?makeAinv # launches the help documentationexample("makeAinv") # runs the examples in the help documentation
makeAinv()- significant speed-up!
numPedfor pedigrees constructed by
is.numPed()) and re-ordering rows (
ronPed()) currently available
ronPed()instead of typical subsetting operators (e.g.,
'[') to retain the class attribute
numPed. For example:
nPed <- numPed(Mrode2)is.numPed(nPed) # TRUE# re-order using typical R functionsnPed_sub <- nPed[order(nPed[, 2], nPed[, 3]), ]is.numPed(nPed_sub) # FALSE; see help via ?'[' about dropping attributesclass(nPed_sub) # matrixnPed_subnadiv <- ronPed(nPed, order(nPed[, 2], nPed[, 3]))is.numPed(nPed_subnadiv) # TRUEclass(nPed_subnadiv) # numPed
Q1988from Quaas 1988 and (2)
Mrode3from Mrode (2005) chapter 3. See their descriptions in
Mrode3.Rdor in R type:
won't work! Must now type:
makeS(FG90, heterogametic = "0")
as a minimum
TDtT(), a function to take the TDT' Cholesky decomposition of a matrix (not currently exported).
founderLine()which traces all individuals back to either the paternal or maternal founder
grfx()now has a new argument to allow user to supply the standard normal deviates instead of generating them within the function.
incidence = NULL
drfx()so that arguments for the internal use of
grfx()can be supplied to
ggcontrib(), default is "matrix"
FALSEif the object (asreml) shows the log-likelihood did not converge
silent = FALSEagrument to
pcc()so that the default can be changed to not show messages
proLik()so that profile likelihoods should be "valleys" (instead of "hills", as they were in versions previous to 2.13.3)
makeA()to use inverse of cholesky factorization of the A-inverse matrix
base::chol2inv()to obtain A
prepPed()to prepare pedigrees for use in other functions
ggcontrib()so that genetic group contributions can be calculated
pcc()functions for the delta method and parameter value convergence checking, respectively, for asreml type REML models. Also added the pin.Rd and pcc.Rd help/documentation files.
pin()is not exported in this version (need
nadiv:::pin()to use it)
makeDufam(), but did not export it.
makeDomEpi()argument "Dinverse" to "invertD" to be similar to makeD()
constrainFun()so that only likelihood ratio test statistics of the constrained model returned if both the loglikelihood & parameter estimates have converged