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


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Documentation for package ‘asremlPlus’ version 4.3-19

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A B C E F G I L 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
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 hypthesis 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 the specified sets of terms from one or both of the fixed or random model and/or replaces the residual (rcov) model with a new model.
changeTerms.asrtests Adds and drops the specified sets of terms from one or both of the fixed or random model and/or replaces the residual (rcov) model with a new model.
ChickpeaEnd.dat A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughtput 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'.

-- 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'.

-- 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
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

-- N --

newfit Refits an asreml model with modified model formula using either a call to 'update.asreml' or a direct call to 'asreml'.
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 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.
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 --

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 distribtion and save quantites 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