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asremlPlus (version 4.4.15)

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 a wide range of linear 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

4.4.15

License

MIT + file LICENSE

Maintainer

Chris Brien

Last Published

October 2nd, 2023

Functions in asremlPlus (4.4.15)

ChickpeaEnd.dat

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

addSpatialModelOnIC.asrtests

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

addSpatialModel.asrtests

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

Description of an LSD frame

Data for an experiment to investigate whether ladybirds transfer aphids

Data for a 1976 experiment to investigate 25 varieties of wheat

WaterRunoff.dat

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

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

addBacktransforms.alldiffs

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

Performs a REML ratio test to compare two models.

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.

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.

asremlPlus-deprecated

Deprecated Functions in the Package asremlPlus

as.predictions.frame

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

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

Applies the angular transformation to proportions.

asremlPlus-package

tools:::Rd_package_title("asremlPlus")

alldiffs.object

Description of an alldiffs object

addto.test.summary

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

The randomly-presented, startup tips.

convAsremlobj.asreml

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

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 intial values of terms.

chooseSpatialModelOnIC.asrtests

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

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.

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.

bootREMLRT.asreml

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

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.

asrtests.object

Description of an asrtests object

changeModelOnIC.asrtests

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

facCombine.alldiffs

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

Computes AIC and BIC for models.

facRename.alldiffs

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

getFormulae.asreml

Gets the formulae from an asreml 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.

getTestPvalue.asrtests

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

estimateV.asreml

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

getASRemlVersionLoaded

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

exploreLSDs.alldiffs

Explores the computed LSD values for pairwise differences between predictions.

getTestEntry.asrtests

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

Tests whether an object is of class alldiffs

loadASRemlVersion

Ensures that a specific version of asreml is loaded.

Tests whether an object is of class asrtests

pairdiffsTransform.alldiffs

Calculates the differences between nominated pairs of 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.predictions.frame

Tests whether an object is of class predictions.frame

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

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.

linTransform.alldiffs

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

pickLSDstatistics.alldiffs

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

plotLSDerrors.data.frame

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

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.

permute.to.zero.lowertri

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

plotPredictions.data.frame

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

plotLSDerrors.alldiffs

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

plotLSDs.alldiffs

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

plotPvalues.alldiffs

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

plotPvalues.data.frame

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).

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.

print.predictions.frame

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

print.test.summary

Prints a data.frame containing a test.summary.

predictions.frame

Description of a predictions object

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.

predictPresent.asreml

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

Prints the values in an asrtests.object

ratioTransform.alldiffs

Calculates the ratios of nominated pairs of predictions stored in 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.

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.

recalcWaldTab.asrtests

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

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.

printFormulae.asreml

Prints the formulae from an asreml object.

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

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.

renewClassify.alldiffs

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

Checks that an object is a valid alldiffs object.

sort.predictions.frame

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

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

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.

simulate.asreml

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

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.

Checks that an object is a valid 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.