WaterRunoff.dat         Data for an experiment to investigate the
                        quality of water runoff over time
Wheat.dat               Data for an experiment to investigate 25
                        varieties of wheat
addrm.terms.asrtests    Adds or removes the specified set terms from
                        either the fixed or random model and records
                        the change in a data.frame.
alldiffs                Forms an object of S3-class 'alldiffs' that
                        stores the predictions for a model fitted using
                        asreml, along with supplied statistics for all
                        pairwise differences.
angular                 Applies the angular transformation to
                        proportions.
angular.mod             Applies the modified angular transformation to
                        a vector of counts.
asremlPlus-deprecated   Deprecated Functions in Package asremlPlus
asremlPlus-package      Augments the Use of 'ASReml-R' in Fitting Mixed
                        Models
asrtests                Forms an object of S3-class 'asrtests' that
                        stores a fitted asreml object, a pseudo-anova
                        table for the fixed and a history of changes
                        and hypthesis testing used in obtaining the
                        model.
choose.model.asrtests   Determines the set of significant terms taking
                        into account the hierarchy or marginality
                        relations.
info.crit.asreml        Computes AIC and BIC for a model.
newfit.asreml           refits an asreml model with modified model
                        formula using either a call to 'update.asreml'
                        or a direct call to 'asreml'.
newrcov.asrtests        Fits a new rcov formula using 'asreml'.
num.recode              Recodes the unique values of a vector using the
                        values in a new vector.
permute.square          Permutes the rows and columns of a square
                        matrix.
permute.to.zero.lowertri
                        Permutes a square matrix until all the lower
                        triangular elements are zero.
plotvariofaces.asreml   plot empirical variogram faces, including
                        envelopes, from supplied residuals as described
                        by Stefanova, Smith & Cullis (2009)
power.transform         Perform a combination of a linear and power
                        transformation on a variable whose name is
                        given as a character string in 'var.name'. The
                        transformed variable is stored in the
                        'data.frame data'.
pred.present.asreml     This function forms the predictions for each
                        significant term and presents them in tables
                        and/or graphs.
predictiondiffs.asreml
                        Uses information in a supplied alldiffs object
                        to forms all pairwise differences between a set
                        of predictions, the p-values for a test of
                        whether the differences are significantly
                        different from zero, and the minimum, mean and
                        maximum LSD values, provided they are not
                        present in the suppplied alldiffs object.
predictionplot.asreml   This function plots the predictions for a term,
                        possibly with error bars.
predictparallel.asreml
                        Uses an asreml object and a wald.tab to form
                        the predictions and associated statistics for a
                        term. It stores the results in an object of
                        class alldifffs and may print the results.  It
                        can be used when a numeric vector and a factor
                        that have parallel values both occur in the
                        model and need to be taken into account.
print.alldiffs          Prints the values in an 'alldiffs' object in a
                        nice format.
print.asrtests          Prints the values in an 'asrtests' object
recalc.wald.tab.asrtests
                        Recalculates the denDF, F.inc and P values for
                        a table of Wald test statistics obtained using
                        'wald.asreml'
reml.lrt.asreml         Performs REML likelihood ratio test.
rmboundary.asrtests     Removes any boundary or singular variance
                        components from the fit stored in 'asreml.obj'
                        and records their removal in a data.frame.
setvarianceterms.asreml
                        allows the seting of constraints and initial
                        values for terms in the 'random' and 'rcov'
                        arguments of an 'asreml' call, with the
                        resulting call being evaluated.
sig.devn.reparam.asrtests
                        This function reparamterizes each random
                        (deviations) term involving 'devn.fac' to a
                        fixed term and ensures that the same term, with
                        'trend.num' replacing 'devn.fac', is included
                        if any other term with 'trend.num' is included
                        in 'terms'.
simulate.asreml         Produce sets of simulated data from a
                        multivariate normal distribtion and save
                        quantites related to the simulated data
testranfix.asrtests     Tests for a single fixed or random term in
                        model fitted using 'asreml'
testrcov.asrtests       Fits a new rcov formula using 'asreml' and
                        tests whether the change is significant.
testswapran.asrtests    Tests, using a REMLRT, whether the difference
                        between current random model and one in which
                        oldterms are dropped and newterms are added is
                        significant.
variofaces.asreml       plot empirical variogram faces, including
                        envelopes, as described by Stefanova, Smith &
                        Cullis (2009)
