R: Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

# Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

## Documentation for package ‘asremlPlus’ version 4.4.58

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E F G I L M N O P R S T V W

asremlPlus-package | Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

## -- A --

addBacktransforms | Adds or recalculates the backtransforms component of an 'alldiffs.object'.
addBacktransforms.alldiffs | Adds or recalculates the backtransforms component of an 'alldiffs.object'.
addrm.terms.asreml | Deprecated Functions in the Package asremlPlus
addrm.terms.asrtests | Deprecated Functions in the Package asremlPlus
addSpatialModel | Adds, to a supplied model, a spatial model that accounts for local spatial variation.
addSpatialModel.asrtests | Adds, to a supplied model, a spatial model that accounts for local spatial variation.
addSpatialModelOnIC | Uses information criteria to decide whether to add a spatial model to account 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 | 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.
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 | Deprecated Functions in the Package asremlPlus
alldiffs-class | Description of an alldiffs object
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 | Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences
asremlPlus-deprecated | Deprecated Functions in the Package asremlPlus
asremlPlusTips | The randomly-presented, startup tips.
asrtests | Deprecated Functions in the Package asremlPlus
asrtests-class | Description of an asrtests object
asrtests.object | Description of an asrtests object

## -- B --

bootREMLRT | Uses the parametric bootstrap to calculate the p-value for a REML ratio test to compare two models.
bootREMLRT.asreml | Uses the parametric bootstrap to calculate the p-value for a REML ratio test to compare two models.

## -- C --

changeModelOnIC | Uses information criteria to decide whether to change an already fitted model.
changeModelOnIC.asrtests | Uses information criteria to decide whether to change an already fitted model.
changeTerms | 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.
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.
ChickpeaEnd.dat | A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhouses
choose.model.asreml | Deprecated Functions in the Package asremlPlus
choose.model.asrtests | Deprecated Functions in the Package asremlPlus
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 | Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation.
chooseSpatialModelOnIC.asrtests | Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation.
convAsremlobj | Recreates an 'asreml' object so that it is compatible with the currently loaded 'asreml' version.
convAsremlobj.asreml | Recreates an 'asreml' object so that it is compatible with the currently loaded 'asreml' version.
convEffectNames2DataFrame | Converts the effects names for a term stored in the component of an 'asreml' object into a 'data.frame'.
convEffectNames2DataFrame.asreml | Converts the effects names for a term stored in the component of an 'asreml' object into a 'data.frame'.

## -- E --

estimateV | Forms the estimated variance, random or residual matrix for the observations from the variance parameter estimates.
estimateV.asreml | Forms the estimated variance, random or residual matrix for the observations from the variance parameter estimates.
exploreLSDs | Explores the computed LSD values for pairwise differences between predictions.
exploreLSDs.alldiffs | Explores the computed LSD values for pairwise differences between predictions.

## -- F --

facCombine | Combines several factors into one in the components of an 'alldiffs.object'
facCombine.alldiffs | Combines several factors into one in the components of an 'alldiffs.object'
facRecast | 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.
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.
facRecode | Deprecated Functions in the Package asremlPlus
facRecode.alldiffs | Deprecated Functions in the Package asremlPlus
facRename | Renames 'factor's in the 'prediction' component of an 'alldiffs.object'.
facRename.alldiffs | Renames 'factor's in the 'prediction' component of an 'alldiffs.object'.
findLSDminerrors | Find LSD values that minimize the number of errors in pairwise comparisons of predictions.
findLSDminerrors.alldiffs | Find LSD values that minimize the number of errors in pairwise comparisons of predictions.

## -- G --

getASRemlVersionLoaded | Finds the version of asreml that is loaded and returns the initial characters in version.
getFormulae | Gets the formulae from an asreml object.
getFormulae.asreml | Gets the formulae from an asreml object.
getTestEntry | Gets the entry for a test recorded in the test.summary data.frame of an 'asrtests.object'
getTestEntry.asrtests | Gets the entry for a test recorded in the test.summary data.frame of an 'asrtests.object'
getTestPvalue | Gets the p-value 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'

## -- I --

info.crit | Deprecated Functions in the Package asremlPlus
info.crit.asreml | Deprecated Functions in the Package asremlPlus
infoCriteria | Computes AIC and BIC for models.
infoCriteria.asreml | Computes AIC and BIC for models.
infoCriteria.list | 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 | Tests whether an object of class matrix is compound symmetric
isCompoundSymmetric.matrix | Tests whether an object of class matrix is compound symmetric
iterate | Subject the fitted 'asreml.obj' stored in an 'asrtests.object' to further iterations of the fitting process.
iterate.asrtests | Subject the fitted 'asreml.obj' stored in an 'asrtests.object' to further iterations of the fitting process.

## -- L --

Ladybird.dat | Data for an experiment to investigate whether ladybirds transfer aphids
linTransform | Calculates a linear transformation of the predictions stored in an 'alldiffs.object'.
linTransform.alldiffs | Calculates a linear transformation of the predictions stored in an 'alldiffs.object'.
loadASRemlVersion | Ensures that a specific version of 'asreml' is loaded.
LSD.frame | Description of an LSD frame

## -- M --

makeTPPSplineMats | Make the spline basis matrices and data needed to fit Tensor Product P-splines.
makeTPPSplineMats.data.frame | Make the spline basis matrices and data needed to fit Tensor Product P-splines.

## -- N --

newfit | Refits an 'asreml' model with changed arguments by extracting, modifying and evaluating its 'call' - an alternate to update.asreml.
newfit.asreml | Refits an 'asreml' model with changed arguments by extracting, modifying and evaluating its 'call' - an alternate to update.asreml.
newrcov.asrtests | Deprecated Functions in the Package asremlPlus
num.recode | Recodes the unique values of a vector using the values in a new vector.

## -- O --

Oats.dat | Data for an experiment to investigate nitrogen response of 3 oats varieties

## -- P --

pairdiffsTransform | Calculates the differences between nominated pairs of predictions stored in an 'alldiffs.object'.
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 | Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions.
pickLSDstatistics.alldiffs | Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions.
plotLSDerrors | Plots a map of the errors that occur in using the computed LSD values for pairwise differences between 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 | Plots a heat map of 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 | Plots the predictions for a term, possibly with error bars.
plotPredictions.data.frame | Plots the predictions for a term, possibly with error bars.
plotPvalues | Plots a heat map of p-values for pairwise differences between predictions.
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 | Plots empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009).
plotvariofaces.asreml | Deprecated Functions in the Package asremlPlus
plotVariofaces.data.frame | Plots empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009).
power.transform | Deprecated Functions in the Package asremlPlus
powerTransform | Performs a combination of a linear and a power transformation on a variable. The transformed variable is stored in the 'data.frame data'.
pred.present.asreml | Deprecated Functions in the Package asremlPlus
predictiondiffs.asreml | Deprecated Functions in the Package asremlPlus
predictionplot.asreml | Deprecated Functions in the Package asremlPlus
predictions.frame | Description of a predictions object
predictions.frame-class | Description of a predictions object
predictparallel.asreml | Deprecated Functions in the Package asremlPlus
predictPlus | 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.
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 | Forms the predictions for each of one or more terms and presents them in tables and/or graphs.
predictPresent.asreml | Forms the predictions for each of one or more terms and presents them in tables and/or graphs.
print.alldiffs | Prints the values in an 'alldiffs.object' in a nice format.
print.asrtests | Prints the values in an 'asrtests.object'
print.LSDdata | Prints the components of a list containing data on the LSDs for all pairwise differences of predictions.
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 | Prints the formulae from an asreml object.
printFormulae.asreml | Prints the formulae from an asreml object.

## -- R --

R2adj | Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms.
R2adj.asreml | Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms.
ratioTransform | Calculates the ratios of nominated pairs of predictions stored in an 'alldiffs.object'.
ratioTransform.alldiffs | Calculates the ratios of nominated pairs of predictions stored in an 'alldiffs.object'.
recalc.wald.tab.asreml | Deprecated Functions in the Package asremlPlus
recalc.wald.tab.asrtests | Deprecated Functions in the Package asremlPlus
recalcLSD | Adds or recalculates the 'LSD.frame' that is a component of an 'alldiffs.object'.
recalcLSD.alldiffs | Adds or recalculates the 'LSD.frame' that is a component of an 'alldiffs.object'.
recalcWaldTab | Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using 'wald.asreml'
recalcWaldTab.asrtests | Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using 'wald.asreml'
redoErrorIntervals | Adds or replaces the error intervals stored in a prediction component of an 'alldiffs.object'.
redoErrorIntervals.alldiffs | Adds or replaces the error intervals stored in a prediction component of an 'alldiffs.object'.
reml.lrt | Deprecated Functions in the Package asremlPlus
reml.lrt.asreml | Deprecated Functions in the Package asremlPlus
REMLRT | Performs a REML ratio test to compare two models.
REMLRT.asreml | Performs a REML ratio test to compare two models.
renewClassify | Renews the components in an 'alldiffs.object' according to a new classify.
renewClassify.alldiffs | Renews the components in an 'alldiffs.object' according to a new classify.
reorderClassify | Deprecated Functions in the Package asremlPlus
reorderClassify.alldiffs | Deprecated Functions in the Package asremlPlus
reparamSigDevn | 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'.
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 | Removes any boundary or singular variance components from the fit stored in 'asrtests.obj' and records their removal in an 'asrtests.object'.
rmboundary.asreml | Deprecated Functions in the Package asremlPlus
rmboundary.asrtests | Removes any boundary or singular variance components from the fit stored in 'asrtests.obj' and records their removal in an 'asrtests.object'.

## -- S --

setvarianceterms | 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.
setvarianceterms.asreml | Deprecated Functions in the Package asremlPlus
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.
sig.devn.reparam.asreml | Deprecated Functions in the Package asremlPlus
sig.devn.reparam.asrtests | Deprecated Functions in the Package asremlPlus
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'.

## -- T --

testranfix | Tests for a single fixed or random term in model fitted using 'asreml' and records the result in an 'asrtests.object'.
testranfix.asreml | Deprecated Functions in the Package asremlPlus
testranfix.asrtests | Tests for a single fixed or random term in model fitted using 'asreml' and records the result in an 'asrtests.object'.
testrcov.asreml | Deprecated Functions in the Package asremlPlus
testrcov.asrtests | Deprecated Functions in the Package asremlPlus
testresidual | Fits a new residual formula, tests whether the change is significant 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 | 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'.
testswapran.asreml | Deprecated Functions in the Package asremlPlus
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'.

## -- V --

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 | Plots empirical variogram faces, including envelopes, as described by Stefanova, Smith & Cullis (2009).
variofaces.asreml | Plots empirical variogram faces, including envelopes, as described by Stefanova, Smith & Cullis (2009).

## -- W --

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