{
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  "Package": "asremlPlus",
  "Version": "4.4.62",
  "Date": "2026-05-19",
  "Title": "Augments 'ASReml-R' in Fitting Mixed Models and Packages\nGenerally in Exploring Prediction Differences",
  "Authors@R": "person(\"Chris\",\"Brien\", role = c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0000-0003-0581-1817\"),\nemail = \"chris.brien@adelaide.edu.au\")",
  "VignetteBuilder": "R.rsp",
  "SystemRequirements": "asreml",
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  "Description": "Assists in automating the selection of terms to include in\nmixed models when 'asreml' is used to fit the models.\nProcedures are available for choosing models that conform to\nthe hierarchy or marginality principle, for fitting and\nchoosing between two-dimensional spatial models using\ncorrelation, natural cubic smoothing spline and P-spline\nmodels. A history of the fitting of a sequence of models is\nkept in a data frame. Also used to compute functions and\ncontrasts of, to investigate differences between and to plot\npredictions obtained using any model fitting function. The\ncontent falls into the following natural groupings: (i) Data,\n(ii) Model modification functions, (iii) Model selection and\ndescription functions, (iv) Model diagnostics and simulation\nfunctions, (v) Prediction production and presentation\nfunctions, (vi) Response transformation functions, (vii) Object\nmanipulation functions, and (viii) Miscellaneous functions (for\nfurther details see 'asremlPlus-package' in help). The 'asreml'\npackage provides a computationally efficient algorithm for\nfitting a wide range of linear mixed models using Residual\nMaximum Likelihood. It is a commercial package and a license\nfor it can be purchased from 'VSNi' <https://vsni.co.uk/> as\n'asreml-R', who will supply a zip file for local\ninstallation/updating (see <https://asreml.kb.vsni.co.uk/>). It\nis not needed for functions that are methods for 'alldiffs' and\n'data.frame' objects. The package 'asremPlus' can also be\ninstalled from <http://chris.brien.name/rpackages/>.",
  "License": "MIT + file LICENSE",
  "URL": "http://chris.brien.name",
  "BugReports": "https://github.com/briencj/asremlPlus/issues",
  "NeedsCompilation": "no",
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  "Repository": "https://briencj.r-universe.dev",
  "Date/Publication": "2026-05-19 13:01:54 UTC",
  "RemoteUrl": "https://github.com/briencj/asremlplus",
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  "Packaged": {
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  "Author": "Chris Brien [aut, cre] (ORCID: <https://orcid.org/0000-0003-0581-1817>)",
  "Maintainer": "Chris Brien <chris.brien@adelaide.edu.au>",
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    "addBacktransforms.alldiffs",
    "addrm.terms.asreml",
    "addrm.terms.asrtests",
    "addSpatialModel",
    "addSpatialModel.asrtests",
    "addSpatialModelOnIC",
    "addSpatialModelOnIC.asrtests",
    "addto.test.summary",
    "allDifferences",
    "allDifferences.data.frame",
    "alldiffs",
    "angular",
    "angular.mod",
    "as.alldiffs",
    "as.asrtests",
    "as.predictions.frame",
    "asrtests",
    "bootREMLRT",
    "bootREMLRT.asreml",
    "changeModelOnIC",
    "changeModelOnIC.asrtests",
    "changeTerms",
    "changeTerms.asrtests",
    "choose.model.asreml",
    "choose.model.asrtests",
    "chooseModel",
    "chooseModel.asrtests",
    "chooseModel.data.frame",
    "chooseSpatialModelOnIC",
    "chooseSpatialModelOnIC.asrtests",
    "convAsremlobj",
    "convAsremlobj.asreml",
    "convEffectNames2DataFrame",
    "convEffectNames2DataFrame.asreml",
    "estimateV",
    "estimateV.asreml",
    "exploreLSDs",
    "exploreLSDs.alldiffs",
    "facCombine",
    "facCombine.alldiffs",
    "facRecast",
    "facRecast.alldiffs",
    "facRecode",
    "facRecode.alldiffs",
    "facRename",
    "facRename.alldiffs",
    "findLSDminerrors",
    "findLSDminerrors.alldiffs",
    "getASRemlVersionLoaded",
    "getFormulae",
    "getFormulae.asreml",
    "getTestEntry",
    "getTestEntry.asrtests",
    "getTestPvalue",
    "getTestPvalue.asrtests",
    "info.crit",
    "info.crit.asreml",
    "infoCriteria",
    "infoCriteria.asreml",
    "infoCriteria.list",
    "is.alldiffs",
    "is.asrtests",
    "is.predictions.frame",
    "isCompoundSymmetric",
    "isCompoundSymmetric.matrix",
    "iterate",
    "iterate.asrtests",
    "linTransform",
    "linTransform.alldiffs",
    "loadASRemlVersion",
    "makeTPPSplineMats",
    "makeTPPSplineMats.data.frame",
    "newfit",
    "newfit.asreml",
    "newrcov.asrtests",
    "num.recode",
    "pairdiffsTransform",
    "pairdiffsTransform.alldiffs",
    "permute.square",
    "permute.to.zero.lowertri",
    "pickLSDstatistics",
    "pickLSDstatistics.alldiffs",
    "plotLSDerrors",
    "plotLSDerrors.alldiffs",
    "plotLSDerrors.data.frame",
    "plotLSDs",
    "plotLSDs.alldiffs",
    "plotLSDs.data.frame",
    "plotPredictions",
    "plotPredictions.data.frame",
    "plotPvalues",
    "plotPvalues.alldiffs",
    "plotPvalues.data.frame",
    "plotVariofaces",
    "plotVariofaces.data.frame",
    "power.transform",
    "powerTransform",
    "pred.present.asreml",
    "predictiondiffs.asreml",
    "predictparallel.asreml",
    "predictPlus",
    "predictPlus.asreml",
    "predictPresent",
    "predictPresent.asreml",
    "print.alldiffs",
    "print.asrtests",
    "print.LSDdata",
    "print.predictions.frame",
    "print.test.summary",
    "print.wald.tab",
    "printFormulae",
    "printFormulae.asreml",
    "R2adj",
    "R2adj.asreml",
    "ratioTransform",
    "ratioTransform.alldiffs",
    "recalc.wald.tab.asreml",
    "recalc.wald.tab.asrtests",
    "recalcLSD",
    "recalcLSD.alldiffs",
    "recalcWaldTab",
    "recalcWaldTab.asrtests",
    "redoErrorIntervals",
    "redoErrorIntervals.alldiffs",
    "reml.lrt",
    "reml.lrt.asreml",
    "REMLRT",
    "REMLRT.asreml",
    "renewClassify",
    "renewClassify.alldiffs",
    "reparamSigDevn",
    "reparamSigDevn.asrtests",
    "rmboundary",
    "rmboundary.asreml",
    "rmboundary.asrtests",
    "setvarianceterms",
    "setvarianceterms.asreml",
    "setvarianceterms.call",
    "sig.devn.reparam.asreml",
    "sig.devn.reparam.asrtests",
    "simulate.asreml",
    "sort.alldiffs",
    "sort.predictions.frame",
    "subset.alldiffs",
    "subset.list",
    "testranfix",
    "testranfix.asreml",
    "testranfix.asrtests",
    "testrcov.asreml",
    "testrcov.asrtests",
    "testresidual",
    "testresidual.asrtests",
    "testswapran",
    "testswapran.asreml",
    "testswapran.asrtests",
    "validAlldiffs",
    "validPredictionsFrame",
    "variofaces",
    "variofaces.asreml"
  ],
  "_datasets": [
    {
      "name": "ChickpeaEnd.dat",
      "title": "A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhouses",
      "object": "ChickpeaEnd.dat",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Smarthouse",
        "Lane",
        "Position",
        "Zone",
        "Mainplot",
        "Subplot",
        "Replicate",
        "xLane",
        "xPosition",
        "Genotypes",
        "Treatments",
        "Biomass",
        "PlantHeight",
        "SenescenceRank",
        "TotalPods",
        "FilledPods",
        "EmptyPods",
        "SeedNo",
        "TotalSeedWt",
        "SeedWt100"
      ],
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Data for an experiment to investigate whether ladybirds transfer aphids",
      "object": "Ladybird.dat",
      "class": [
        "data.frame"
      ],
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        "Run",
        "Plant",
        "Host",
        "Ladybird",
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        "Live",
        "Infected",
        "logitP",
        "Prop"
      ],
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    },
    {
      "name": "Oats.dat",
      "title": "Data for an experiment to investigate nitrogen response of 3 oats varieties",
      "object": "Oats.dat",
      "class": [
        "data.frame"
      ],
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        "Blocks",
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        "Subplots",
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      "table": true,
      "tojson": true
    },
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      "title": "Data for an experiment to investigate the quality of water runoff over time",
      "object": "WaterRunoff.dat",
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      ],
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        "MainPlots",
        "SubPlots",
        "Pot",
        "Date",
        "Day",
        "xDay",
        "Sources",
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        "pH",
        "Turbidity",
        "log.Turbidity"
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      "table": true,
      "tojson": true
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    {
      "name": "Wheat.dat",
      "title": "Data for a 1976 experiment to investigate 25 varieties of wheat",
      "object": "Wheat.dat",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Rep",
        "Row",
        "Column",
        "WithinColPairs",
        "Variety",
        "yield"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "asremlPlus-package",
      "title": "Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences",
      "topics": [
        "asremlPlus-package",
        "asremlPlus"
      ]
    },
    {
      "page": "addBacktransforms.alldiffs",
      "title": "Adds or recalculates the backtransforms component of an 'alldiffs.object'.",
      "topics": [
        "addBacktransforms",
        "addBacktransforms.alldiffs"
      ]
    },
    {
      "page": "addSpatialModel.asrtests",
      "title": "Adds, to a supplied model, a spatial model that accounts for local spatial variation.",
      "topics": [
        "addSpatialModel",
        "addSpatialModel.asrtests"
      ]
    },
    {
      "page": "addSpatialModelOnIC.asrtests",
      "title": "Uses information criteria to decide whether to add a spatial model to account for local spatial variation.",
      "topics": [
        "addSpatialModelOnIC",
        "addSpatialModelOnIC.asrtests"
      ]
    },
    {
      "page": "addto.test.summary",
      "title": "Adds a row to a 'test.summary' 'data.frame'.",
      "topics": [
        "addto.test.summary"
      ]
    },
    {
      "page": "allDifferences.data.frame",
      "title": "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.",
      "topics": [
        "allDifferences",
        "allDifferences.data.frame"
      ]
    },
    {
      "page": "alldiffs.object",
      "title": "Description of an alldiffs object",
      "topics": [
        "alldiffs-class",
        "alldiffs.object"
      ]
    },
    {
      "page": "angular",
      "title": "Applies the angular transformation to proportions.",
      "topics": [
        "angular"
      ]
    },
    {
      "page": "angular.mod",
      "title": "Applies the modified angular transformation to a vector of counts.",
      "topics": [
        "angular.mod"
      ]
    },
    {
      "page": "as.alldiffs",
      "title": "Forms an 'alldiffs.object' from the supplied predictions, along with those statistics, associated with the predictions and their pairwise differences, that have been supplied.",
      "topics": [
        "as.alldiffs"
      ]
    },
    {
      "page": "as.asrtests",
      "title": "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.",
      "topics": [
        "as.asrtests"
      ]
    },
    {
      "page": "as.predictions.frame",
      "title": "Forms a 'predictions.frame' from a 'data.frame', ensuring that the correct columns are present.",
      "topics": [
        "as.predictions.frame"
      ]
    },
    {
      "page": "asremlPlus-deprecated",
      "title": "Deprecated Functions in the Package asremlPlus",
      "topics": [
        "addrm.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"
      ]
    },
    {
      "page": "asremlPlusTips",
      "title": "The randomly-presented, startup tips.",
      "topics": [
        "asremlPlusTips"
      ]
    },
    {
      "page": "asrtests.object",
      "title": "Description of an asrtests object",
      "topics": [
        "asrtests-class",
        "asrtests.object"
      ]
    },
    {
      "page": "bootREMLRT.asreml",
      "title": "Uses the parametric bootstrap to calculate the p-value for a REML ratio test to compare two models.",
      "topics": [
        "bootREMLRT",
        "bootREMLRT.asreml"
      ]
    },
    {
      "page": "changeModelOnIC.asrtests",
      "title": "Uses information criteria to decide whether to change an already fitted model.",
      "topics": [
        "changeModelOnIC",
        "changeModelOnIC.asrtests"
      ]
    },
    {
      "page": "changeTerms.asrtests",
      "title": "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.",
      "topics": [
        "changeTerms",
        "changeTerms.asrtests"
      ]
    },
    {
      "page": "ChickpeaEnd",
      "title": "A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhouses",
      "topics": [
        "ChickpeaEnd.dat"
      ]
    },
    {
      "page": "chooseModel",
      "title": "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.",
      "topics": [
        "chooseModel"
      ]
    },
    {
      "page": "chooseModel.asrtests",
      "title": "Determines and records the set of significant terms using an 'asrtests.object', taking into account the hierarchy or marginality relations of the terms.",
      "topics": [
        "chooseModel.asrtests"
      ]
    },
    {
      "page": "chooseModel.data.frame",
      "title": "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'.",
      "topics": [
        "chooseModel.data.frame"
      ]
    },
    {
      "page": "chooseSpatialModelOnIC.asrtests",
      "title": "Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation.",
      "topics": [
        "chooseSpatialModelOnIC",
        "chooseSpatialModelOnIC.asrtests"
      ]
    },
    {
      "page": "convAsremlobj.asreml",
      "title": "Recreates an 'asreml' object so that it is compatible with the currently loaded 'asreml' version.",
      "topics": [
        "convAsremlobj",
        "convAsremlobj.asreml"
      ]
    },
    {
      "page": "convEffectNames2DataFrame.asreml",
      "title": "Converts the effects names for a term stored in the component of an 'asreml' object into a 'data.frame'.",
      "topics": [
        "convEffectNames2DataFrame",
        "convEffectNames2DataFrame.asreml"
      ]
    },
    {
      "page": "estimateV.asreml",
      "title": "Forms the estimated variance, random or residual matrix for the observations from the variance parameter estimates.",
      "topics": [
        "estimateV",
        "estimateV.asreml"
      ]
    },
    {
      "page": "exploreLSDs.alldiffs",
      "title": "Explores the computed LSD values for pairwise differences between predictions.",
      "topics": [
        "exploreLSDs",
        "exploreLSDs.alldiffs"
      ]
    },
    {
      "page": "facCombine.alldiffs",
      "title": "Combines several factors into one in the components of an 'alldiffs.object'",
      "topics": [
        "facCombine",
        "facCombine.alldiffs"
      ]
    },
    {
      "page": "facRecast.alldiffs",
      "title": "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.",
      "topics": [
        "facRecast",
        "facRecast.alldiffs"
      ]
    },
    {
      "page": "facRename.alldiffs",
      "title": "Renames 'factor's in the 'prediction' component of an 'alldiffs.object'.",
      "topics": [
        "facRename",
        "facRename.alldiffs"
      ]
    },
    {
      "page": "findLSDminerrors.alldiffs",
      "title": "Find LSD values that minimize the number of errors in pairwise comparisons of predictions.",
      "topics": [
        "findLSDminerrors",
        "findLSDminerrors.alldiffs"
      ]
    },
    {
      "page": "getASRemlVersionLoaded",
      "title": "Finds the version of asreml that is loaded and returns the initial characters in version.",
      "topics": [
        "getASRemlVersionLoaded"
      ]
    },
    {
      "page": "getFormulae.asreml",
      "title": "Gets the formulae from an asreml object.",
      "topics": [
        "getFormulae",
        "getFormulae.asreml"
      ]
    },
    {
      "page": "getTestEntry.asrtests",
      "title": "Gets the entry for a test recorded in the test.summary data.frame of an 'asrtests.object'",
      "topics": [
        "getTestEntry",
        "getTestEntry.asrtests"
      ]
    },
    {
      "page": "getTestPvalue.asrtests",
      "title": "Gets the p-value for a test recorded in the test.summary data.frame of an 'asrtests.object'",
      "topics": [
        "getTestPvalue",
        "getTestPvalue.asrtests"
      ]
    },
    {
      "page": "infoCriteria.asreml",
      "title": "Computes AIC and BIC for models.",
      "topics": [
        "infoCriteria",
        "infoCriteria.asreml",
        "infoCriteria.list"
      ]
    },
    {
      "page": "is.alldiffs",
      "title": "Tests whether an object is of class alldiffs",
      "topics": [
        "is.alldiffs"
      ]
    },
    {
      "page": "is.asrtests",
      "title": "Tests whether an object is of class asrtests",
      "topics": [
        "is.asrtests"
      ]
    },
    {
      "page": "is.predictions.frame",
      "title": "Tests whether an object is of class predictions.frame",
      "topics": [
        "is.predictions.frame"
      ]
    },
    {
      "page": "isCompoundSymmetric.matrix",
      "title": "Tests whether an object of class matrix is compound symmetric",
      "topics": [
        "isCompoundSymmetric",
        "isCompoundSymmetric.matrix"
      ]
    },
    {
      "page": "iterate.asrtests",
      "title": "Subject the fitted 'asreml.obj' stored in an 'asrtests.object' to further iterations of the fitting process.",
      "topics": [
        "iterate",
        "iterate.asrtests"
      ]
    },
    {
      "page": "Ladybird.dat",
      "title": "Data for an experiment to investigate whether ladybirds transfer aphids",
      "topics": [
        "Ladybird.dat"
      ]
    },
    {
      "page": "linTransform.alldiffs",
      "title": "Calculates a linear transformation of the predictions stored in an 'alldiffs.object'.",
      "topics": [
        "linTransform",
        "linTransform.alldiffs"
      ]
    },
    {
      "page": "loadASRemlVersion",
      "title": "Ensures that a specific version of 'asreml' is loaded.",
      "topics": [
        "loadASRemlVersion"
      ]
    },
    {
      "page": "LSD.frame",
      "title": "Description of an LSD frame",
      "topics": [
        "LSD.frame"
      ]
    },
    {
      "page": "makeTPPSplineMats.data.frame",
      "title": "Make the spline basis matrices and data needed to fit Tensor Product P-splines.",
      "topics": [
        "makeTPPSplineMats",
        "makeTPPSplineMats.data.frame"
      ]
    },
    {
      "page": "newfit.asreml",
      "title": "Refits an 'asreml' model with changed arguments by extracting, modifying and evaluating its 'call' - an alternate to update.asreml.",
      "topics": [
        "newfit",
        "newfit.asreml"
      ]
    },
    {
      "page": "num.recode",
      "title": "Recodes the unique values of a vector using the values in a new vector.",
      "topics": [
        "num.recode"
      ]
    },
    {
      "page": "Oats.dat",
      "title": "Data for an experiment to investigate nitrogen response of 3 oats varieties",
      "topics": [
        "Oats.dat"
      ]
    },
    {
      "page": "pairdiffsTransform.alldiffs",
      "title": "Calculates the differences between nominated pairs of predictions stored in an 'alldiffs.object'.",
      "topics": [
        "pairdiffsTransform",
        "pairdiffsTransform.alldiffs"
      ]
    },
    {
      "page": "permute.square",
      "title": "Permutes the rows and columns of a square matrix.",
      "topics": [
        "permute.square"
      ]
    },
    {
      "page": "permute.to.zero.lowertri",
      "title": "Permutes a square matrix until all the lower triangular elements are zero.",
      "topics": [
        "permute.to.zero.lowertri"
      ]
    },
    {
      "page": "pickLSDstatistics.alldiffs",
      "title": "Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions.",
      "topics": [
        "pickLSDstatistics",
        "pickLSDstatistics.alldiffs"
      ]
    },
    {
      "page": "plotLSDerrors.alldiffs",
      "title": "Plots a map of the errors that occur in using the computed LSD values for pairwise differences between predictions.",
      "topics": [
        "plotLSDerrors",
        "plotLSDerrors.alldiffs"
      ]
    },
    {
      "page": "plotLSDerrors.data.frame",
      "title": "Plots a map of the supplied errors that occur in using the computed LSD values for pairwise differences between predictions.",
      "topics": [
        "plotLSDerrors.data.frame"
      ]
    },
    {
      "page": "plotLSDs.alldiffs",
      "title": "Plots a heat map of computed LSD values for pairwise differences between predictions.",
      "topics": [
        "plotLSDs",
        "plotLSDs.alldiffs"
      ]
    },
    {
      "page": "plotLSDs.data.frame",
      "title": "Plots a heat map of computed LSD-values for pairwise differences between predictions.",
      "topics": [
        "plotLSDs.data.frame"
      ]
    },
    {
      "page": "plotPredictions.data.frame",
      "title": "Plots the predictions for a term, possibly with error bars.",
      "topics": [
        "plotPredictions",
        "plotPredictions.data.frame"
      ]
    },
    {
      "page": "plotPvalues.alldiffs",
      "title": "Plots a heat map of p-values for pairwise differences between predictions.",
      "topics": [
        "plotPvalues",
        "plotPvalues.alldiffs"
      ]
    },
    {
      "page": "plotPvalues.data.frame",
      "title": "Plots a heat map of p-values for pairwise differences between predictions.",
      "topics": [
        "plotPvalues.data.frame"
      ]
    },
    {
      "page": "plotVariofaces.data.frame",
      "title": "Plots empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009).",
      "topics": [
        "plotVariofaces",
        "plotVariofaces.data.frame"
      ]
    },
    {
      "page": "powerTransform",
      "title": "Performs a combination of a linear and a power transformation on a variable. The transformed variable is stored in the 'data.frame data'.",
      "topics": [
        "powerTransform"
      ]
    },
    {
      "page": "predictions.frame",
      "title": "Description of a predictions object",
      "topics": [
        "predictions.frame",
        "predictions.frame-class"
      ]
    },
    {
      "page": "predictPlus.asreml",
      "title": "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.",
      "topics": [
        "predictPlus",
        "predictPlus.asreml"
      ]
    },
    {
      "page": "predictPresent.asreml",
      "title": "Forms the predictions for each of one or more terms and presents them in tables and/or graphs.",
      "topics": [
        "predictPresent",
        "predictPresent.asreml"
      ]
    },
    {
      "page": "print.alldiffs",
      "title": "Prints the values in an 'alldiffs.object' in a nice format.",
      "topics": [
        "print.alldiffs"
      ]
    },
    {
      "page": "print.asrtests",
      "title": "Prints the values in an 'asrtests.object'",
      "topics": [
        "print.asrtests"
      ]
    },
    {
      "page": "print.LSDdata",
      "title": "Prints the components of a list containing data on the LSDs for all pairwise differences of predictions.",
      "topics": [
        "print.LSDdata"
      ]
    },
    {
      "page": "print.predictions.frame",
      "title": "Prints the values in a 'predictions.frame', with or without title and heading.",
      "topics": [
        "print.predictions.frame"
      ]
    },
    {
      "page": "print.test.summary",
      "title": "Prints a data.frame containing a test.summary.",
      "topics": [
        "print.test.summary"
      ]
    },
    {
      "page": "print.wald.tab",
      "title": "Prints a data.frame containing a Wald or pseudoanova table.",
      "topics": [
        "print.wald.tab"
      ]
    },
    {
      "page": "printFormulae.asreml",
      "title": "Prints the formulae from an asreml object.",
      "topics": [
        "printFormulae",
        "printFormulae.asreml"
      ]
    },
    {
      "page": "R2adj.asreml",
      "title": "Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms.",
      "topics": [
        "R2adj",
        "R2adj.asreml"
      ]
    },
    {
      "page": "ratioTransform.alldiffs",
      "title": "Calculates the ratios of nominated pairs of predictions stored in an 'alldiffs.object'.",
      "topics": [
        "ratioTransform",
        "ratioTransform.alldiffs"
      ]
    },
    {
      "page": "recalcLSD.alldiffs",
      "title": "Adds or recalculates the 'LSD.frame' that is a component of an 'alldiffs.object'.",
      "topics": [
        "recalcLSD",
        "recalcLSD.alldiffs"
      ]
    },
    {
      "page": "recalcWaldTab.asrtests",
      "title": "Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using 'wald.asreml'",
      "topics": [
        "recalcWaldTab",
        "recalcWaldTab.asrtests"
      ]
    },
    {
      "page": "redoErrorIntervals.alldiffs",
      "title": "Adds or replaces the error intervals stored in a prediction component of an 'alldiffs.object'.",
      "topics": [
        "redoErrorIntervals",
        "redoErrorIntervals.alldiffs"
      ]
    },
    {
      "page": "REMLRT.asreml",
      "title": "Performs a REML ratio test to compare two models.",
      "topics": [
        "REMLRT",
        "REMLRT.asreml"
      ]
    },
    {
      "page": "renewClassify.alldiffs",
      "title": "Renews the components in an 'alldiffs.object' according to a new classify.",
      "topics": [
        "renewClassify",
        "renewClassify.alldiffs"
      ]
    },
    {
      "page": "reparamSigDevn.asrtests",
      "title": "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'.",
      "topics": [
        "reparamSigDevn",
        "reparamSigDevn.asrtests"
      ]
    },
    {
      "page": "rmboundary.asrtests",
      "title": "Removes any boundary or singular variance components from the fit stored in 'asrtests.obj' and records their removal in an 'asrtests.object'.",
      "topics": [
        "rmboundary",
        "rmboundary.asrtests"
      ]
    },
    {
      "page": "setvarianceterms.call",
      "title": "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.",
      "topics": [
        "setvarianceterms",
        "setvarianceterms.call"
      ]
    },
    {
      "page": "simulate.asreml",
      "title": "Produce sets of simulated data from a multivariate normal distribution and save quantities related to the simulated data",
      "topics": [
        "simulate.asreml"
      ]
    },
    {
      "page": "sort.alldiffs",
      "title": "Sorts the components in an 'alldiffs.object' according to the predicted values associated with a factor.",
      "topics": [
        "sort.alldiffs"
      ]
    },
    {
      "page": "sort.predictions.frame",
      "title": "Sorts a 'predictions.frame' according to the predicted values associated with a factor.",
      "topics": [
        "sort.predictions.frame"
      ]
    },
    {
      "page": "subset.alldiffs",
      "title": "Subsets the components in an 'alldiffs.object' according to the supplied condition.",
      "topics": [
        "subset.alldiffs"
      ]
    },
    {
      "page": "subset.list",
      "title": "Forms a 'list' that contains a subset of the components of the supplied 'list'.",
      "topics": [
        "subset.list"
      ]
    },
    {
      "page": "testranfix.asrtests",
      "title": "Tests for a single fixed or random term in model fitted using 'asreml' and records the result in an 'asrtests.object'.",
      "topics": [
        "testranfix",
        "testranfix.asrtests"
      ]
    },
    {
      "page": "testresidual.asrtests",
      "title": "Fits a new residual formula, tests whether the change is significant and records the result in an 'asrtests.object'.",
      "topics": [
        "testresidual",
        "testresidual.asrtests"
      ]
    },
    {
      "page": "testswapran.asrtests",
      "title": "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'.",
      "topics": [
        "testswapran",
        "testswapran.asrtests"
      ]
    },
    {
      "page": "validAlldiffs",
      "title": "Checks that an object is a valid alldiffs object.",
      "topics": [
        "validAlldiffs"
      ]
    },
    {
      "page": "validAsrtests",
      "title": "Checks that an object is a valid asrtests object.",
      "topics": [
        "validAsrtests"
      ]
    },
    {
      "page": "validPredictionsFrame",
      "title": "Checks that an object is a valid predictions.frame.",
      "topics": [
        "validPredictionsFrame"
      ]
    },
    {
      "page": "variofaces.asreml",
      "title": "Plots empirical variogram faces, including envelopes, as described by Stefanova, Smith & Cullis (2009).",
      "topics": [
        "variofaces",
        "variofaces.asreml"
      ]
    },
    {
      "page": "WaterRunoff.dat",
      "title": "Data for an experiment to investigate the quality of water runoff over time",
      "topics": [
        "WaterRunoff.dat"
      ]
    },
    {
      "page": "Wheat.dat",
      "title": "Data for a 1976 experiment to investigate 25 varieties of wheat",
      "topics": [
        "Wheat.dat"
      ]
    }
  ],
  "_readme": "https://github.com/briencj/asremlplus/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "backports",
    "base64enc",
    "bitops",
    "boot",
    "brew",
    "brio",
    "broom",
    "bslib",
    "cachem",
    "callr",
    "car",
    "carData",
    "caTools",
    "cli",
    "clipr",
    "codetools",
    "colorspace",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "credentials",
    "curl",
    "dae",
    "DEoptimR",
    "Deriv",
    "desc",
    "devtools",
    "diffobj",
    "digest",
    "doBy",
    "doParallel",
    "downlit",
    "dplyr",
    "ellipsis",
    "evaluate",
    "fansi",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "forecast",
    "Formula",
    "fracdiff",
    "fs",
    "generics",
    "gert",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
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