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asremlPlus (version 4.4.49)

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

830

Version

4.4.49

License

MIT + file LICENSE

Maintainer

Chris Brien

Last Published

June 15th, 2025

Functions in asremlPlus (4.4.49)

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.
Oats.dat

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

Data for an experiment to investigate the quality of water runoff over time
LSD.frame

Description of an LSD frame
R2adj.asreml

Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms.
ChickpeaEnd.dat

A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhouses
REMLRT.asreml

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

Data for a 1976 experiment to investigate 25 varieties of wheat
Ladybird.dat

Data for an experiment to investigate whether ladybirds transfer aphids
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
angular

Applies the angular transformation to proportions.
angular.mod

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

Description of an alldiffs object
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.
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.
chooseModel.data.frame

changeModelOnIC.asrtests

Uses information criteria to decide whether to change an already fitted model.
asremlPlusTips

The randomly-presented, startup tips.
asremlPlus-package

tools:::Rd_package_title("asremlPlus")
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

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.
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.
asrtests.object

Description of an asrtests object
getASRemlVersionLoaded

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

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

Find LSD values that minimize the number of errors in pairwise comparisons of predictions.
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.
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.
getFormulae.asreml

Gets the formulae from an asreml object.
facRename.alldiffs

Renames factors in the prediction component of an alldiffs.object.
convEffectNames2DataFrame.asreml

isCompoundSymmetric.matrix

Tests whether an object of class matrix is compound symmetric
loadASRemlVersion

Ensures that a specific version of asreml is loaded.
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
is.asrtests

Tests whether an object is of class asrtests
linTransform.alldiffs

Calculates a linear transformation of the predictions stored in an alldiffs.object.
is.predictions.frame

Tests whether an object is of class predictions.frame
getTestEntry.asrtests

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

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

Tests whether an object is of class alldiffs
plotLSDerrors.data.frame

Plots a map of the supplied errors that occur in using the computed LSD values for pairwise differences between predictions.
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.to.zero.lowertri

Permutes a square matrix until all the lower triangular elements are zero.
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.
makeTPPSplineMats.data.frame

Make the spline basis matrices and data needed to fit Tensor Product P-splines.
plotLSDs.alldiffs

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.
pickLSDstatistics.alldiffs

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