ChickpeaEnd.dat         A large data set comprising the end of imaging
                        data from a chick pea experiment conducted in
                        high-throughput greenhouses
LSD.frame               Description of an LSD frame
Ladybird.dat            Data for an experiment to investigate whether
                        ladybirds transfer aphids
Oats.dat                Data for an experiment to investigate nitrogen
                        response of 3 oats varieties
R2adj.asreml            Calculates the adjusted coefficient of
                        determination for a specified combination of
                        fixed and random terms.
REMLRT.asreml           Performs a REML ratio test to compare two
                        models.
WaterRunoff.dat         Data for an experiment to investigate the
                        quality of water runoff over time
Wheat.dat               Data for a 1976 experiment to investigate 25
                        varieties of wheat
addBacktransforms.alldiffs
                        Adds or recalculates the backtransforms
                        component of an 'alldiffs.object'.
addSpatialModel.asrtests
                        Adds, to a supplied model, a spatial model that
                        accounts for local spatial variation.
addSpatialModelOnIC.asrtests
                        Uses information criteria to decide whether to
                        add a spatial model to account for local
                        spatial variation.
addto.test.summary      Adds a row to a 'test.summary' 'data.frame'.
allDifferences.data.frame
                        Using supplied predictions and standard errors
                        of pairwise differences or the variance matrix
                        of predictions, forms all pairwise differences
                        between the set of predictions, and p-values
                        for the differences.
alldiffs.object         Description of an alldiffs object
angular                 Applies the angular transformation to
                        proportions.
angular.mod             Applies the modified angular transformation to
                        a vector of counts.
as.alldiffs             Forms an 'alldiffs.object' from the supplied
                        predictions, along with those statistics,
                        associated with the predictions and their
                        pairwise differences, that have been supplied.
as.asrtests             Forms an asrtests object that stores (i) a
                        fitted asreml object, (ii) a pseudo-anova table
                        for the fixed terms and (iii) a history of
                        changes and hypothesis testing used in
                        obtaining the model.
as.predictions.frame    Forms a 'predictions.frame' from a
                        'data.frame', ensuring that the correct columns
                        are present.
asremlPlus-deprecated   Deprecated Functions in the Package asremlPlus
asremlPlus-package      Augments 'ASReml-R' in Fitting Mixed Models and
                        Packages Generally in Exploring Prediction
                        Differences
asremlPlusTips          The randomly-presented, startup tips.
asrtests.object         Description of an asrtests object
bootREMLRT.asreml       Uses the parametric bootstrap to calculate the
                        p-value for a REML ratio test to compare two
                        models.
changeModelOnIC.asrtests
                        Uses information criteria to decide whether to
                        change an already fitted model.
changeTerms.asrtests    Adds and drops terms from one or both of the
                        fixed or random model, replaces the residual
                        (rcov) model with a new model and changes
                        bounds or initial values of terms.
chooseModel             Determines the set of significant terms using
                        p-values and records the tests performed in a
                        'data.frame', taking into account the
                        marginality relations of terms.
chooseModel.asrtests    Determines and records the set of significant
                        terms using an 'asrtests.object', taking into
                        account the hierarchy or marginality relations
                        of the terms.
chooseModel.data.frame
                        Determines the set of significant terms from
                        results stored in a 'data.frame', taking into
                        account the marginality relations of terms and
                        recording the tests used in a 'data.frame'.
chooseSpatialModelOnIC.asrtests
                        Uses information criteria to choose the best
                        fitting spatial model for accounting for local
                        spatial variation.
convAsremlobj.asreml    Recreates an 'asreml' object so that it is
                        compatible with the currently loaded 'asreml'
                        version.
convEffectNames2DataFrame.asreml
                        Converts the effects names for a term stored in
                        the component of an 'asreml' object into a
                        'data.frame'.
estimateV.asreml        Forms the estimated variance, random or
                        residual matrix for the observations from the
                        variance parameter estimates.
exploreLSDs.alldiffs    Explores the computed LSD values for pairwise
                        differences between predictions.
facCombine.alldiffs     Combines several factors into one in the
                        components of an 'alldiffs.object'
facRecast.alldiffs      Reorders and/or revises the factor levels using
                        the order of old levels in 'levels.order' and
                        the new labels for the levels given in
                        'newlabels'. The values in 'levels.order' must
                        be unique.
facRename.alldiffs      Renames 'factor's in the 'prediction' component
                        of an 'alldiffs.object'.
findLSDminerrors.alldiffs
                        Find LSD values that minimize the number of
                        errors in pairwise comparisons of predictions.
getASRemlVersionLoaded
                        Finds the version of asreml that is loaded and
                        returns the initial characters in version.
getFormulae.asreml      Gets the formulae from an asreml object.
getTestEntry.asrtests   Gets the entry for a test recorded in the
                        test.summary data.frame of an 'asrtests.object'
getTestPvalue.asrtests
                        Gets the p-value for a test recorded in the
                        test.summary data.frame of an 'asrtests.object'
infoCriteria            Computes AIC and BIC for models.
is.alldiffs             Tests whether an object is of class alldiffs
is.asrtests             Tests whether an object is of class asrtests
is.predictions.frame    Tests whether an object is of class
                        predictions.frame
isCompoundSymmetric.matrix
                        Tests whether an object of class matrix is
                        compound symmetric
iterate.asrtests        Subject the fitted 'asreml.obj' stored in an
                        'asrtests.object' to further iterations of the
                        fitting process.
linTransform.alldiffs   Calculates a linear transformation of the
                        predictions stored in an 'alldiffs.object'.
loadASRemlVersion       Ensures that a specific version of 'asreml' is
                        loaded.
makeTPPSplineMats.data.frame
                        Make the spline basis matrices and data needed
                        to fit Tensor Product P-splines.
newfit.asreml           Refits an 'asreml' model with changed arguments
                        by extracting, modifying and evaluating its
                        'call' - an alternate to update.asreml.
num.recode              Recodes the unique values of a vector using the
                        values in a new vector.
pairdiffsTransform.alldiffs
                        Calculates the differences between nominated
                        pairs of predictions stored in an
                        'alldiffs.object'.
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.
pickLSDstatistics.alldiffs
                        Pick LSDstatistics whose values minimize the
                        number of errors in pairwise comparisons of
                        predictions.
plotLSDerrors.alldiffs
                        Plots a map of the errors that occur in using
                        the computed LSD values for pairwise
                        differences between predictions.
plotLSDerrors.data.frame
                        Plots a map of the supplied errors that occur
                        in using the computed LSD values for pairwise
                        differences between predictions.
plotLSDs.alldiffs       Plots a heat map of computed LSD values for
                        pairwise differences between predictions.
plotLSDs.data.frame     Plots a heat map of computed LSD-values for
                        pairwise differences between predictions.
plotPredictions.data.frame
                        Plots the predictions for a term, possibly with
                        error bars.
plotPvalues.alldiffs    Plots a heat map of p-values for pairwise
                        differences between predictions.
plotPvalues.data.frame
                        Plots a heat map of p-values for pairwise
                        differences between predictions.
plotVariofaces.data.frame
                        Plots empirical variogram faces, including
                        envelopes, from supplied residuals as described
                        by Stefanova, Smith & Cullis (2009).
powerTransform          Performs a combination of a linear and a power
                        transformation on a variable. The transformed
                        variable is stored in the 'data.frame data'.
predictPlus.asreml      Forms the predictions for a term, their
                        pairwise differences and associated statistics.
                        A factor having parallel values may occur in
                        the model and a linear transformation of the
                        predictions can be specified. It results in an
                        object of class alldifffs.
predictPresent.asreml   Forms the predictions for each of one or more
                        terms and presents them in tables and/or
                        graphs.
predictions.frame       Description of a predictions object
print.LSDdata           Prints the components of a list containing data
                        on the LSDs for all pairwise differences of
                        predictions.
print.alldiffs          Prints the values in an 'alldiffs.object' in a
                        nice format.
print.asrtests          Prints the values in an 'asrtests.object'
print.predictions.frame
                        Prints the values in a 'predictions.frame',
                        with or without title and heading.
print.test.summary      Prints a data.frame containing a test.summary.
print.wald.tab          Prints a data.frame containing a Wald or
                        pseudoanova table.
printFormulae.asreml    Prints the formulae from an asreml object.
ratioTransform.alldiffs
                        Calculates the ratios of nominated pairs of
                        predictions stored in an 'alldiffs.object'.
recalcLSD.alldiffs      Adds or recalculates the 'LSD.frame' that is a
                        component of an 'alldiffs.object'.
recalcWaldTab.asrtests
                        Recalculates the denDF, F.inc and P values for
                        a table of Wald test statistics obtained using
                        'wald.asreml'
redoErrorIntervals.alldiffs
                        Adds or replaces the error intervals stored in
                        a prediction component of an 'alldiffs.object'.
renewClassify.alldiffs
                        Renews the components in an 'alldiffs.object'
                        according to a new classify.
reparamSigDevn.asrtests
                        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'.
rmboundary.asrtests     Removes any boundary or singular variance
                        components from the fit stored in
                        'asrtests.obj' and records their removal in an
                        'asrtests.object'.
setvarianceterms.call   allows the setting of bounds and initial values
                        for terms in the 'random' and 'residual'
                        arguments of an 'asreml' call, with the
                        resulting call being evaluated.
simulate.asreml         Produce sets of simulated data from a
                        multivariate normal distribution and save
                        quantities related to the simulated data
sort.alldiffs           Sorts the components in an 'alldiffs.object'
                        according to the predicted values associated
                        with a factor.
sort.predictions.frame
                        Sorts a 'predictions.frame' according to the
                        predicted values associated with a factor.
subset.alldiffs         Subsets the components in an 'alldiffs.object'
                        according to the supplied condition.
subset.list             Forms a 'list' that contains a subset of the
                        components of the supplied 'list'.
testranfix.asrtests     Tests for a single fixed or random term in
                        model fitted using 'asreml' and records the
                        result in an 'asrtests.object'.
testresidual.asrtests   Fits a new residual formula, tests whether the
                        change is significant and records the result in
                        an 'asrtests.object'.
testswapran.asrtests    Tests, using a REMLRT, the significance of the
                        difference between the current random model and
                        one in which oldterms are dropped and newterms
                        are added.  The result is recorded in an
                        'asrtests.object'.
validAlldiffs           Checks that an object is a valid alldiffs
                        object.
validAsrtests           Checks that an object is a valid asrtests
                        object.
validPredictionsFrame   Checks that an object is a valid
                        predictions.frame.
variofaces.asreml       Plots empirical variogram faces, including
                        envelopes, as described by Stefanova, Smith &
                        Cullis (2009).
