Package: asremlPlus 4.4.38

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

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' <https://vsni.co.uk/> as 'asreml-R', who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from <http://chris.brien.name/rpackages/>.

Authors:Chris Brien [aut, cre]

asremlPlus_4.4.38.tar.gz
asremlPlus_4.4.38.zip(r-4.5)asremlPlus_4.4.38.zip(r-4.4)asremlPlus_4.4.38.zip(r-4.3)
asremlPlus_4.4.38.tgz(r-4.4-any)asremlPlus_4.4.38.tgz(r-4.3-any)
asremlPlus_4.4.38.tar.gz(r-4.5-noble)asremlPlus_4.4.38.tar.gz(r-4.4-noble)
asremlPlus_4.4.38.tgz(r-4.4-emscripten)asremlPlus_4.4.38.tgz(r-4.3-emscripten)
asremlPlus.pdf |asremlPlus.html✨
asremlPlus/json (API)
NEWS

# Install 'asremlPlus' in R:
install.packages('asremlPlus', repos = c('https://briencj.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/briencj/asremlplus/issues

Datasets:
  • ChickpeaEnd.dat - A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhouses
  • Ladybird.dat - Data for an experiment to investigate whether ladybirds transfer aphids
  • 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
  • Wheat.dat - Data for a 1976 experiment to investigate 25 varieties of wheat

On CRAN:

asremlmixed-models

159 exports 16 stars 3.62 score 163 dependencies 12 mentions 219 scripts 912 downloads

Last updated 29 days agofrom:0b713844cb. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 20 2024
R-4.5-winNOTEAug 20 2024
R-4.5-linuxNOTEAug 20 2024
R-4.4-winNOTEAug 20 2024
R-4.4-macNOTEAug 20 2024
R-4.3-winNOTEAug 20 2024
R-4.3-macNOTEAug 20 2024

Exports:addBacktransformsaddBacktransforms.alldiffsaddrm.terms.asremladdrm.terms.asrtestsaddSpatialModeladdSpatialModel.asrtestsaddSpatialModelOnICaddSpatialModelOnIC.asrtestsaddto.test.summaryallDifferencesallDifferences.data.framealldiffsangularangular.modas.alldiffsas.asrtestsas.predictions.frameasrtestsbootREMLRTbootREMLRT.asremlchangeModelOnICchangeModelOnIC.asrtestschangeTermschangeTerms.asrtestschoose.model.asremlchoose.model.asrtestschooseModelchooseModel.asrtestschooseModel.data.framechooseSpatialModelOnICchooseSpatialModelOnIC.asrtestsconvAsremlobjconvAsremlobj.asremlconvEffectNames2DataFrameconvEffectNames2DataFrame.asremlestimateVestimateV.asremlexploreLSDsexploreLSDs.alldiffsfacCombinefacCombine.alldiffsfacRecastfacRecast.alldiffsfacRecodefacRecode.alldiffsfacRenamefacRename.alldiffsgetASRemlVersionLoadedgetFormulaegetFormulae.asremlgetTestEntrygetTestEntry.asrtestsgetTestPvaluegetTestPvalue.asrtestsinfo.critinfo.crit.asremlinfoCriteriainfoCriteria.asremlinfoCriteria.listis.alldiffsis.asrtestsis.predictions.frameisCompoundSymmetricisCompoundSymmetric.matrixiterateiterate.asrtestslinTransformlinTransform.alldiffsloadASRemlVersionmakeTPPSplineMatsmakeTPPSplineMats.data.framenewfitnewfit.asremlnewrcov.asrtestsnum.recodepairdiffsTransformpairdiffsTransform.alldiffspermute.squarepermute.to.zero.lowertripickLSDstatisticspickLSDstatistics.alldiffsplotLSDerrorsplotLSDerrors.alldiffsplotLSDerrors.data.frameplotLSDsplotLSDs.alldiffsplotLSDs.data.frameplotPredictionsplotPredictions.data.frameplotPvaluesplotPvalues.alldiffsplotPvalues.data.frameplotVariofacesplotVariofaces.data.framepower.transformpowerTransformpred.present.asremlpredictiondiffs.asremlpredictparallel.asremlpredictPluspredictPlus.asremlpredictPresentpredictPresent.asremlprint.alldiffsprint.asrtestsprint.LSDdataprint.predictions.frameprint.test.summaryprint.wald.tabprintFormulaeprintFormulae.asremlR2adjR2adj.asremlratioTransformratioTransform.alldiffsrecalc.wald.tab.asremlrecalc.wald.tab.asrtestsrecalcLSDrecalcLSD.alldiffsrecalcWaldTabrecalcWaldTab.asrtestsredoErrorIntervalsredoErrorIntervals.alldiffsreml.lrtreml.lrt.asremlREMLRTREMLRT.asremlrenewClassifyrenewClassify.alldiffsreparamSigDevnreparamSigDevn.asrtestsrmboundaryrmboundary.asremlrmboundary.asrtestssetvariancetermssetvarianceterms.asremlsetvarianceterms.callsig.devn.reparam.asremlsig.devn.reparam.asrtestssimulate.asremlsort.alldiffssort.predictions.framesubset.alldiffssubset.listtestranfixtestranfix.asremltestranfix.asrteststestrcov.asremltestrcov.asrteststestresidualtestresidual.asrteststestswaprantestswapran.asremltestswapran.asrtestsvalidAlldiffsvalidAsrtestsvalidPredictionsFramevariofacesvariofaces.asreml

Dependencies:abindaskpassbackportsbase64encbitopsbootbrewbriobroombslibcachemcallrcarcarDatacaToolsclicliprcodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncredentialscurldaeDEoptimRDerivdescdevtoolsdiffobjdigestdoBydoParalleldownlitdplyrellipsisevaluatefansifarverfastmapfontawesomeforeachfsgenericsgertggplot2ggpubrggrepelggsciggsignifghgitcredsgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttr2iniisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminiUIminqamodelrmunsellnlmenloptrnnetnumDerivopdisDownsamplingopensslpbkrtestpbmcapplypillarpkgbuildpkgconfigpkgdownpkgloadplyrpolynompracmapraiseprettyunitsprocessxprofvispromisespspurrrqqconfqqplotrquantregR6raggrappdirsrcmdcheckRColorBrewerRcppRcppEigenrematch2remotesreshape2rlangrmarkdownrobustbaseroxygen2rprojrootrstatixrstudioapirversionssassscalessessioninfoshinysourcetoolsSparseMstickystringistringrsurvivalsyssystemfontstestthattextshapingtibbletidyrtidyselecttinytextryCatchLogtwosamplesurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzip

asremlPlus-manual

Rendered fromasremlPlus-manual.pdf.asisusingR.rsp::asison Aug 20 2024.

Last update: 2019-02-21
Started: 2019-02-21

Ladybird: a predictions example using asreml and asremlPlus

Rendered fromLadybird.asreml.pdf.asisusingR.rsp::asison Aug 20 2024.

Last update: 2020-01-27
Started: 2020-01-27

Ladybird: a predictions example using lm and asremlPlus

Rendered fromLadybird.lm.pdf.asisusingR.rsp::asison Aug 20 2024.

Last update: 2020-01-27
Started: 2020-01-27

Wheat: a full analysis of an experiment with spatial variation

Rendered fromWheat.analysis.pdf.asisusingR.rsp::asison Aug 20 2024.

Last update: 2020-02-08
Started: 2020-02-08

Wheat: using information criteria

Rendered fromWheat.infoCriteria.pdf.asisusingR.rsp::asison Aug 20 2024.

Last update: 2020-02-08
Started: 2020-02-08

WheatSpatialModels: a full analysis of an experiment that includes choosing local spatial variation models

Rendered fromWheatSpatialModels.pdf.asisusingR.rsp::asison Aug 20 2024.

Last update: 2023-06-13
Started: 2023-06-13

Readme and manuals

Help Manual

Help pageTopics
Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction DifferencesasremlPlus-package asremlPlus
Adds or recalculates the backtransforms component of an 'alldiffs.object'.addBacktransforms addBacktransforms.alldiffs
Adds, to a supplied model, a spatial model that accounts for local spatial variation.addSpatialModel addSpatialModel.asrtests
Uses information criteria to decide whether to add a spatial model to account for local spatial variation.addSpatialModelOnIC addSpatialModelOnIC.asrtests
Adds a row to a 'test.summary' 'data.frame'.addto.test.summary
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.allDifferences allDifferences.data.frame
Description of an alldiffs objectalldiffs-class alldiffs.object
Applies the angular transformation to proportions.angular
Applies the modified angular transformation to a vector of counts.angular.mod
Forms an 'alldiffs.object' from the supplied predictions, along with those statistics, associated with the predictions and their pairwise differences, that have been supplied.as.alldiffs
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.as.asrtests
Forms a 'predictions.frame' from a 'data.frame', ensuring that the correct columns are present.as.predictions.frame
Deprecated Functions in the Package asremlPlusaddrm.terms.asreml addrm.terms.asrtests alldiffs asremlPlus-deprecated asrtests choose.model.asreml choose.model.asrtests facRecode facRecode.alldiffs info.crit info.crit.asreml newrcov.asrtests plotvariofaces.asreml power.transform pred.present.asreml predictiondiffs.asreml predictionplot.asreml predictparallel.asreml recalc.wald.tab.asreml recalc.wald.tab.asrtests reml.lrt reml.lrt.asreml reorderClassify reorderClassify.alldiffs rmboundary.asreml setvarianceterms.asreml sig.devn.reparam.asreml sig.devn.reparam.asrtests testranfix.asreml testrcov.asreml testrcov.asrtests testswapran.asreml
The randomly-presented, startup tips.asremlPlusTips
Description of an asrtests objectasrtests-class asrtests.object
Uses the parametric bootstrap to calculate the p-value for a REML ratio test to compare two models.bootREMLRT bootREMLRT.asreml
Uses information criteria to decide whether to change an already fitted model.changeModelOnIC changeModelOnIC.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.changeTerms changeTerms.asrtests
A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhousesChickpeaEnd.dat
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.chooseModel
Determines and records the set of significant terms using an 'asrtests.object', taking into account the hierarchy or marginality relations of the terms.chooseModel.asrtests
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'.chooseModel.data.frame
Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation.chooseSpatialModelOnIC chooseSpatialModelOnIC.asrtests
Recreates an 'asreml' object so that it is compatible with the currently loaded 'asreml' version.convAsremlobj convAsremlobj.asreml
Converts the effects names for a term stored in the component of an 'asreml' object into a 'data.frame'.convEffectNames2DataFrame convEffectNames2DataFrame.asreml
Forms the estimated variance, random or residual matrix for the observations from the variance parameter estimates.estimateV estimateV.asreml
Explores the computed LSD values for pairwise differences between predictions.exploreLSDs exploreLSDs.alldiffs
Combines several factors into one in the components of an 'alldiffs.object'facCombine facCombine.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.facRecast facRecast.alldiffs
Renames 'factor's in the 'prediction' component of an 'alldiffs.object'.facRename facRename.alldiffs
Finds the version of asreml that is loaded and returns the initial characters in version.getASRemlVersionLoaded
Gets the formulae from an asreml object.getFormulae getFormulae.asreml
Gets the entry for a test recorded in the test.summary data.frame of an 'asrtests.object'getTestEntry getTestEntry.asrtests
Gets the p-value for a test recorded in the test.summary data.frame of an 'asrtests.object'getTestPvalue getTestPvalue.asrtests
Computes AIC and BIC for models.infoCriteria infoCriteria.asreml infoCriteria.list
Tests whether an object is of class alldiffsis.alldiffs
Tests whether an object is of class asrtestsis.asrtests
Tests whether an object is of class predictions.frameis.predictions.frame
Tests whether an object of class matrix is compound symmetricisCompoundSymmetric isCompoundSymmetric.matrix
Subject the fitted 'asreml.obj' stored in an 'asrtests.object' to further iterations of the fitting process.iterate iterate.asrtests
Data for an experiment to investigate whether ladybirds transfer aphidsLadybird.dat
Calculates a linear transformation of the predictions stored in an 'alldiffs.object'.linTransform linTransform.alldiffs
Ensures that a specific version of 'asreml' is loaded.loadASRemlVersion
Description of an LSD frameLSD.frame
Make the spline basis matrices and data needed to fit Tensor Product P-splines.makeTPPSplineMats makeTPPSplineMats.data.frame
Refits an 'asreml' model with changed arguments by extracting, modifying and evaluating its 'call' - an alternate to update.asreml.newfit newfit.asreml
Recodes the unique values of a vector using the values in a new vector.num.recode
Data for an experiment to investigate nitrogen response of 3 oats varietiesOats.dat
Calculates the differences between nominated pairs of predictions stored in an 'alldiffs.object'.pairdiffsTransform pairdiffsTransform.alldiffs
Permutes the rows and columns of a square matrix.permute.square
Permutes a square matrix until all the lower triangular elements are zero.permute.to.zero.lowertri
Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions.pickLSDstatistics pickLSDstatistics.alldiffs
Plots a map of the errors that occur in using the computed LSD values for pairwise differences between predictions.plotLSDerrors plotLSDerrors.alldiffs
Plots a map of the supplied errors that occur in using the computed LSD values for pairwise differences between predictions.plotLSDerrors.data.frame
Plots a heat map of computed LSD values for pairwise differences between predictions.plotLSDs plotLSDs.alldiffs
Plots a heat map of computed LSD-values for pairwise differences between predictions.plotLSDs.data.frame
Plots the predictions for a term, possibly with error bars.plotPredictions plotPredictions.data.frame
Plots a heat map of p-values for pairwise differences between predictions.plotPvalues plotPvalues.alldiffs
Plots a heat map of p-values for pairwise differences between predictions.plotPvalues.data.frame
Plots empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009).plotVariofaces plotVariofaces.data.frame
Performs a combination of a linear and a power transformation on a variable. The transformed variable is stored in the 'data.frame data'.powerTransform
Description of a predictions objectpredictions.frame predictions.frame-class
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.predictPlus predictPlus.asreml
Forms the predictions for each of one or more terms and presents them in tables and/or graphs.predictPresent predictPresent.asreml
Prints the values in an 'alldiffs.object' in a nice format.print.alldiffs
Prints the values in an 'asrtests.object'print.asrtests
Prints the components of a list containing data on the LSDs for all pairwise differences of predictions.print.LSDdata
Prints the values in a 'predictions.frame', with or without title and heading.print.predictions.frame
Prints a data.frame containing a test.summary.print.test.summary
Prints a data.frame containing a Wald or pseudoanova table.print.wald.tab
Prints the formulae from an asreml object.printFormulae printFormulae.asreml
Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms.R2adj R2adj.asreml
Calculates the ratios of nominated pairs of predictions stored in an 'alldiffs.object'.ratioTransform ratioTransform.alldiffs
Adds or recalculates the 'LSD.frame' that is a component of an 'alldiffs.object'.recalcLSD recalcLSD.alldiffs
Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using 'wald.asreml'recalcWaldTab recalcWaldTab.asrtests
Adds or replaces the error intervals stored in a prediction component of an 'alldiffs.object'.redoErrorIntervals redoErrorIntervals.alldiffs
Performs a REML ratio test to compare two models.REMLRT REMLRT.asreml
Renews the components in an 'alldiffs.object' according to a new classify.renewClassify renewClassify.alldiffs
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'.reparamSigDevn reparamSigDevn.asrtests
Removes any boundary or singular variance components from the fit stored in 'asrtests.obj' and records their removal in an 'asrtests.object'.rmboundary rmboundary.asrtests
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.setvarianceterms setvarianceterms.call
Produce sets of simulated data from a multivariate normal distribution and save quantities related to the simulated datasimulate.asreml
Sorts the components in an 'alldiffs.object' according to the predicted values associated with a factor.sort.alldiffs
Sorts a 'predictions.frame' according to the predicted values associated with a factor.sort.predictions.frame
Subsets the components in an 'alldiffs.object' according to the supplied condition.subset.alldiffs
Forms a 'list' that contains a subset of the components of the supplied 'list'.subset.list
Tests for a single fixed or random term in model fitted using 'asreml' and records the result in an 'asrtests.object'.testranfix testranfix.asrtests
Fits a new residual formula, tests whether the change is significant and records the result in an 'asrtests.object'.testresidual testresidual.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'.testswapran testswapran.asrtests
Checks that an object is a valid alldiffs object.validAlldiffs
Checks that an object is a valid asrtests object.validAsrtests
Checks that an object is a valid predictions.frame.validPredictionsFrame
Plots empirical variogram faces, including envelopes, as described by Stefanova, Smith & Cullis (2009).variofaces variofaces.asreml
Data for an experiment to investigate the quality of water runoff over timeWaterRunoff.dat
Data for a 1976 experiment to investigate 25 varieties of wheatWheat.dat