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asremlPlus (version 4.4.46)

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

4.4.46

License

MIT + file LICENSE

Maintainer

Chris Brien

Last Published

February 17th, 2025

Functions in asremlPlus (4.4.46)

ChickpeaEnd.dat

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

WaterRunoff.dat

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

addBacktransforms.alldiffs

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

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.

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

Data for a 1976 experiment to investigate 25 varieties of wheat

Data for an experiment to investigate whether ladybirds transfer aphids

Performs a REML ratio test to compare two models.

Description of an LSD frame

addto.test.summary

Adds a row to a test.summary data.frame.

Forms an alldiffs.object from the supplied predictions, along with those statistics, associated with the predictions and their pairwise differences, that have been supplied.

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.

addSpatialModelOnIC.asrtests

Uses information criteria to decide whether to add a spatial model to account for local spatial variation.

as.predictions.frame

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

alldiffs.object

Description of an alldiffs object

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.

asremlPlus-deprecated

Deprecated Functions in the Package asremlPlus

Applies the modified angular transformation to a vector of counts.

Applies the angular transformation to proportions.

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.

changeModelOnIC.asrtests

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

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.

The randomly-presented, startup tips.

asremlPlus-package

tools:::Rd_package_title("asremlPlus")

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.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.

bootREMLRT.asreml

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

chooseSpatialModelOnIC.asrtests

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

asrtests.object

Description of an asrtests object

convEffectNames2DataFrame.asreml

Converts the effects names for a term stored in the component of an asreml object into a data.frame.

exploreLSDs.alldiffs

Explores the computed LSD values for pairwise differences between predictions.

estimateV.asreml

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

getTestEntry.asrtests

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

convAsremlobj.asreml

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

facCombine.alldiffs

Combines several factors into one in the components of an alldiffs.object

getFormulae.asreml

Gets the formulae from an asreml object.

facRename.alldiffs

Renames factors in the prediction component 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.

getASRemlVersionLoaded

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

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

Tests whether an object is of class alldiffs

getTestPvalue.asrtests

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

Tests whether an object is of class asrtests

isCompoundSymmetric.matrix

Tests whether an object of class matrix is compound symmetric

loadASRemlVersion

Ensures that a specific version of asreml is loaded.

iterate.asrtests

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

Computes AIC and BIC for models.

makeTPPSplineMats.data.frame

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

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.

plotLSDs.alldiffs

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

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.

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

plotLSDs.data.frame

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

Permutes the rows and columns of a square matrix.

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.

plotPredictions.data.frame

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

plotPvalues.data.frame

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

Prints the values in an alldiffs.object in a nice format.

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.

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

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

plotVariofaces.data.frame

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

plotPvalues.alldiffs

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

ratioTransform.alldiffs

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

printFormulae.asreml

Prints the formulae from an asreml object.

print.test.summary

Prints a data.frame containing a test.summary.

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

recalcWaldTab.asrtests

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

recalcLSD.alldiffs

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

print.predictions.frame

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

renewClassify.alldiffs

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

Prints the values in an asrtests.object

redoErrorIntervals.alldiffs

Adds or replaces the error intervals stored in a prediction component of 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.

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

testresidual.asrtests

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

simulate.asreml

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

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.

sort.predictions.frame

Sorts a predictions.frame according to the predicted values associated with a factor.

Sorts the components in an alldiffs.object according to the predicted values associated with a factor.

Checks that an object is a valid asrtests object.

validPredictionsFrame

Checks that an object is a valid predictions.frame.

Checks that an object is a valid alldiffs 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.

variofaces.asreml

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