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asremlPlus (version 4.4.48)

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

Description

Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The 'asreml' package provides a computationally efficient algorithm for fitting a wide range of linear mixed models using Residual Maximum Likelihood. It is a commercial package and a license for it can be purchased from 'VSNi' as 'asreml-R', who will supply a zip file for local installation/updating (see ). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from .

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Version

Install

install.packages('asremlPlus')

Monthly Downloads

1,030

Version

4.4.48

License

MIT + file LICENSE

Maintainer

Chris Brien

Last Published

April 6th, 2025

Functions in asremlPlus (4.4.48)

WaterRunoff.dat

Data for an experiment to investigate the quality of water runoff over time
Ladybird.dat

Data for an experiment to investigate whether ladybirds transfer aphids
R2adj.asreml

Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms.
addSpatialModel.asrtests

Adds, to a supplied model, a spatial model that accounts for local spatial variation.
Oats.dat

Data for an experiment to investigate nitrogen response of 3 oats varieties
addBacktransforms.alldiffs

Adds or recalculates the backtransforms component of an alldiffs.object.
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
REMLRT.asreml

Performs a REML ratio test to compare two models.
Wheat.dat

Data for a 1976 experiment to investigate 25 varieties of wheat
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.
asremlPlus-deprecated

Deprecated Functions in the Package asremlPlus
angular

Applies the angular transformation to proportions.
as.predictions.frame

Forms a predictions.frame from a data.frame, ensuring that the correct columns are present.
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.
angular.mod

Applies the modified angular transformation to a vector of counts.
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
asrtests.object

Description of an asrtests object
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

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.
asremlPlus-package

tools:::Rd_package_title("asremlPlus")
chooseModel.data.frame

chooseSpatialModelOnIC.asrtests

Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation.
bootREMLRT.asreml

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

The randomly-presented, startup tips.
convAsremlobj.asreml

Recreates an asreml object so that it is compatible with the currently loaded asreml version.
facRename.alldiffs

Renames factors in the prediction component of an alldiffs.object.
getTestEntry.asrtests

Gets the entry for a test recorded in the test.summary data.frame of an asrtests.object
getFormulae.asreml

Gets the formulae from an asreml object.
getASRemlVersionLoaded

Finds the version of asreml that is loaded and returns the initial characters in version.
convEffectNames2DataFrame.asreml

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.
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
estimateV.asreml

Forms the estimated variance, random or residual matrix for the observations from the variance parameter estimates.
is.alldiffs

Tests whether an object is of class alldiffs
linTransform.alldiffs

Calculates a linear transformation of the predictions stored in an alldiffs.object.
iterate.asrtests

Subject the fitted asreml.obj stored in an asrtests.object to further iterations of the fitting process.
is.asrtests

Tests whether an object is of class asrtests
loadASRemlVersion

Ensures that a specific version of asreml is loaded.
is.predictions.frame

Tests whether an object is of class predictions.frame
infoCriteria

Computes AIC and BIC for models.
getTestPvalue.asrtests

Gets the p-value for a test recorded in the test.summary data.frame of an asrtests.object
isCompoundSymmetric.matrix

Tests whether an object of class matrix is compound symmetric
makeTPPSplineMats.data.frame

Make the spline basis matrices and data needed to fit Tensor Product P-splines.
permute.to.zero.lowertri

Permutes a square matrix until all the lower triangular elements are zero.
pairdiffsTransform.alldiffs

Calculates the differences between nominated pairs of predictions stored in an alldiffs.object.
newfit.asreml

Refits an asreml model with changed arguments by extracting, modifying and evaluating its call - an alternate to update.asreml.
permute.square

Permutes the rows and columns of a square matrix.
plotLSDs.alldiffs

Plots a heat map of computed LSD values for pairwise differences between predictions.
pickLSDstatistics.alldiffs

Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions.
plotLSDs.data.frame

Plots a heat map of 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.
num.recode

Recodes the unique values of a vector using the values in a new vector.
plotPvalues.data.frame

Plots a heat map of p-values for pairwise differences between predictions.
print.alldiffs

Prints the values in an alldiffs.object in a nice format.
plotPredictions.data.frame

Plots the predictions for a term, possibly with error bars.
predictPresent.asreml

Forms the predictions for each of one or more terms and presents them in tables and/or graphs.
print.LSDdata

Prints the components of a list containing data on the LSDs for all pairwise differences of predictions.
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.
powerTransform

Performs a combination of a linear and a power transformation on a variable. The transformed variable is stored in the data.frame data.
predictions.frame

Description of a predictions object
plotPvalues.alldiffs

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).
recalcLSD.alldiffs

Adds or recalculates the LSD.frame that is a component of an alldiffs.object.
redoErrorIntervals.alldiffs

Adds or replaces the error intervals stored in a prediction component of an alldiffs.object.
print.asrtests

Prints the values in an asrtests.object
print.test.summary

Prints a data.frame containing a test.summary.
renewClassify.alldiffs

Renews the components in an alldiffs.object according to a new classify.
print.wald.tab

Prints a data.frame containing a Wald or pseudoanova table.
print.predictions.frame

Prints the values in a predictions.frame, with or without title and heading.
recalcWaldTab.asrtests

Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using wald.asreml
printFormulae.asreml

Prints the formulae from an asreml object.
ratioTransform.alldiffs

Calculates the ratios of nominated pairs of predictions stored in an alldiffs.object.
testranfix.asrtests

Tests for a single fixed or random term in model fitted using asreml and records the result 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.
subset.alldiffs

Subsets the components in an alldiffs.object according to the supplied condition.
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.
testresidual.asrtests

Fits a new residual formula, tests whether the change is significant and records the result in an asrtests.object.
subset.list

Forms a list that contains a subset of the components of the supplied list.
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.
simulate.asreml

Produce sets of simulated data from a multivariate normal distribution and save quantities related to the simulated data
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.
variofaces.asreml

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