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asremlPlus (version 4.3.45)

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. Also used to display, in tables and graphs, predictions obtained using any model fitting function and to explore differences between predictions. The content falls into the following natural groupings: (i) Data, (ii) Object manipulation functions, (iii) Model modification functions, (iv) Model testing functions, (v) Model diagnostics functions, (vi) Prediction production and presentation functions, (vii) Response transformation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). A history of the fitting of a sequence of models is kept in a data frame. Procedures are available for choosing models that conform to the hierarchy or marginality principle and for displaying predictions for significant terms in tables and graphs. The 'asreml' package provides a computationally efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It is a commercial package that 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

1,155

Version

4.3.45

License

MIT + file LICENSE

Maintainer

Chris Brien

Last Published

January 24th, 2023

Functions in asremlPlus (4.3.45)

addSpatialModel.asrtests

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

WaterRunoff.dat

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

addSpatialModelOnIC.asrtests

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

Description of an LSD frame

addBacktransforms.alldiffs

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

Data for a 1976 experiment to investigate 25 varieties of wheat

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

Performs a REML ratio test to compare two models.

ChickpeaEnd.dat

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

Data for an experiment to investigate whether ladybirds transfer aphids

addto.test.summary

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

asremlPlus-deprecated

Deprecated Functions in the Package asremlPlus

alldiffs.object

Description of an alldiffs object

as.predictions.frame

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

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.

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.

Applies the modified angular transformation to a vector of counts.

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-package

tools:::Rd_package_title("asremlPlus")

Applies the angular transformation to proportions.

chooseSpatialModelOnIC.asrtests

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

The randomly-presented, startup tips.

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.

asrtests.object

Description of an asrtests object

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.

estimateV.asreml

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

changeModelOnIC.asrtests

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

bootREMLRT.asreml

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

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.

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.

facRename.alldiffs

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

exploreLSDs.alldiffs

Explores the computed LSD values for pairwise differences between predictions.

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.

getFormulae.asreml

Gets the formulae from an asreml object.

getTestEntry.asrtests

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

loadASRemlVersion

Ensures that a specific version of asreml is loaded.

facCombine.alldiffs

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

getTestPvalue.asrtests

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

makeTPSPlineXZMats.data.frame

Make the objects needed to fit Tensor Product P-splines.

pairdiffsTransform.alldiffs

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

linTransform.alldiffs

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

Permutes the rows and columns of a square matrix.

Recodes the unique values of a vector using the values in a new vector.

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

plotPredictions.data.frame

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

permute.to.zero.lowertri

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

plotPvalues.alldiffs

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

pickLSDstatistics.alldiffs

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

Computes AIC and BIC for models.

Tests whether an object is of class alldiffs

plotLSDerrors.alldiffs

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

Tests whether an object is of class asrtests

plotLSDerrors.data.frame

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

iterate.asrtests

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

is.predictions.frame

Tests whether an object is of class predictions.frame

plotLSDs.alldiffs

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

plotPvalues.data.frame

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

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

plotLSDs.data.frame

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

print.test.summary

Prints a data.frame containing a test.summary.

plotVariofaces.data.frame

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

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.

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

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

predictPresent.asreml

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

predictions.frame

Description of a predictions object

Prints the values in an asrtests.object

print.predictions.frame

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

printFormulae.asreml

Prints the formulae from an asreml object.

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.

redoErrorIntervals.alldiffs

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

simulate.asreml

Produce sets of simulated data from a multivariate normal distribtion and save quantites related to the simulated data

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.

ratioTransform.alldiffs

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

renewClassify.alldiffs

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

rmboundary.asrtests

Removes any boundary or singular variance components from the fit stored in asrtests.obj and records their removal in an asrtests.object.

subset.alldiffs

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

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.

Checks that an object is a valid asrtests object.

testresidual.asrtests

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

testranfix.asrtests

Tests for a single fixed or random term in model fitted using asreml and records the result in an asrtests.object.

variofaces.asreml

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

validPredictionsFrame

Checks that an object is a valid predictions.frame.

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.

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

Checks that an object is a valid alldiffs object.