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asremlPlus (version 4.1-26)

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

Description

Assists in automating the testing of terms 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. 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 packages that can be purchased from 'VSNi' as 'asreml-R', who will supply a zip file for local installation/updating. 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

918

Version

4.1-26

License

MIT + file LICENSE

Maintainer

Chris Brien

Last Published

May 13th, 2019

Functions in asremlPlus (4.1-26)

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.

is.predictions.frame

Tests whether an object is of class predictions.frame

Tests whether an object is of class asrtests

as.predictions.frame

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

plotPvalues.data.frame

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

simulate.asreml

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

plotVariofaces.data.frame

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

asremlPlus-package

alldiffs.object

Description of an alldiffs object

asremlPlus-deprecated

Deprecated Functions in the Package asremlPlus

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.

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

loadASRemlVersion

Ensures that a specific version of asreml is loaded.

recalcLSD.alldiffs

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

linTransform.alldiffs

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

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.

recalcWaldTab.asrtests

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

The randomly-presented, startup tips.

asrtests.object

Description of an asrtests object

chooseModel.asrtests

Determines the set of significant terms taking into account the hierarchy or marginality relations and records the tests performed in an asrtests.object.

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

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.

estimateV.asreml

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

facCombine.alldiffs

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

infoCriteria.asreml

Computes AIC and BIC for a model.

bootREMLRT.asreml

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

getASRemlVersionLoaded

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

getTestPvalue.asrtests

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

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

Permutes the rows and columns of a square matrix.

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

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

Tests whether an object is of class alldiffs

redoErrorIntervals.alldiffs

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

rmboundary.asrtests

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

Prints the values in an asrtests.object

renewClassify.alldiffs

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

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.

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).

plotPredictions.data.frame

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

plotPvalues.alldiffs

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

predictPresent.asreml

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

testresidual.asrtests

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

predictions.frame

Description of a predictions object

permute.to.zero.lowertri

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

Checks that an object is a valid asrtests object.

validPredictionsFrame

Checks that an object is a valid predictions.frame.

print.predictions.frame

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

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.

Prints a Wald or pseudoanova table.

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.

Checks that an object is a valid alldiffs object.

Applies the angular transformation to proportions.

Data for an 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.

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.

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.

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

Applies the modified angular transformation to a vector of counts.