| addBacktransforms |
Adds or recalculates the backtransforms component of an 'alldiffs.object'. |
| addBacktransforms.alldiffs |
Adds or recalculates the backtransforms component of an 'alldiffs.object'. |
| addrm.terms.asreml |
Deprecated Functions in the Package asremlPlus |
| addrm.terms.asrtests |
Deprecated Functions in the Package asremlPlus |
| addSpatialModel |
Adds, to a supplied model, a spatial model that accounts for local spatial variation. |
| addSpatialModel.asrtests |
Adds, to a supplied model, a spatial model that accounts for local spatial variation. |
| addSpatialModelOnIC |
Uses information criteria to decide whether to add a spatial model to account for local spatial variation. |
| addSpatialModelOnIC.asrtests |
Uses information criteria to decide whether to add a spatial model to account for local spatial variation. |
| addto.test.summary |
Adds a row to a 'test.summary' 'data.frame'. |
| allDifferences |
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.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. |
| alldiffs |
Deprecated Functions in the Package asremlPlus |
| alldiffs-class |
Description of an alldiffs object |
| alldiffs.object |
Description of an alldiffs object |
| angular |
Applies the angular transformation to proportions. |
| angular.mod |
Applies the modified angular transformation to a vector of counts. |
| as.alldiffs |
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.asrtests |
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.predictions.frame |
Forms a 'predictions.frame' from a 'data.frame', ensuring that the correct columns are present. |
| asremlPlus |
Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences |
| asremlPlus-deprecated |
Deprecated Functions in the Package asremlPlus |
| asremlPlusTips |
The randomly-presented, startup tips. |
| asrtests |
Deprecated Functions in the Package asremlPlus |
| asrtests-class |
Description of an asrtests object |
| asrtests.object |
Description of an asrtests object |
| changeModelOnIC |
Uses information criteria to decide whether to change an already fitted model. |
| changeModelOnIC.asrtests |
Uses information criteria to decide whether to change an already fitted model. |
| changeTerms |
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.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. |
| ChickpeaEnd.dat |
A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhouses |
| choose.model.asreml |
Deprecated Functions in the Package asremlPlus |
| choose.model.asrtests |
Deprecated Functions in the Package asremlPlus |
| chooseModel |
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.asrtests |
Determines and records the set of significant terms using an 'asrtests.object', taking into account the hierarchy or marginality relations of the terms. |
| 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'. |
| chooseSpatialModelOnIC |
Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation. |
| chooseSpatialModelOnIC.asrtests |
Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation. |
| convAsremlobj |
Recreates an 'asreml' object so that it is compatible with the currently loaded 'asreml' version. |
| convAsremlobj.asreml |
Recreates an 'asreml' object so that it is compatible with the currently loaded 'asreml' version. |
| convEffectNames2DataFrame |
Converts the effects names for a term stored in the component of an 'asreml' object into a 'data.frame'. |
| convEffectNames2DataFrame.asreml |
Converts the effects names for a term stored in the component of an 'asreml' object into a 'data.frame'. |
| pairdiffsTransform |
Calculates the differences between nominated pairs of predictions stored in an 'alldiffs.object'. |
| pairdiffsTransform.alldiffs |
Calculates the differences between nominated pairs of predictions stored in an 'alldiffs.object'. |
| permute.square |
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. |
| pickLSDstatistics |
Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions. |
| pickLSDstatistics.alldiffs |
Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions. |
| plotLSDerrors |
Plots a map of the errors that occur in using the computed LSD values for pairwise differences between predictions. |
| plotLSDerrors.alldiffs |
Plots a map of the errors that occur in using the computed LSD values for pairwise differences between 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 |
Plots a heat map of computed LSD values for pairwise differences between predictions. |
| plotLSDs.alldiffs |
Plots a heat map of computed LSD values for pairwise differences between predictions. |
| plotLSDs.data.frame |
Plots a heat map of computed LSD-values for pairwise differences between predictions. |
| plotPredictions |
Plots the predictions for a term, possibly with error bars. |
| plotPredictions.data.frame |
Plots the predictions for a term, possibly with error bars. |
| plotPvalues |
Plots a heat map of p-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 |
Plots empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009). |
| plotvariofaces.asreml |
Deprecated Functions in the Package asremlPlus |
| plotVariofaces.data.frame |
Plots empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009). |
| power.transform |
Deprecated Functions in the Package asremlPlus |
| powerTransform |
Performs a combination of a linear and a power transformation on a variable. The transformed variable is stored in the 'data.frame data'. |
| pred.present.asreml |
Deprecated Functions in the Package asremlPlus |
| predictiondiffs.asreml |
Deprecated Functions in the Package asremlPlus |
| predictionplot.asreml |
Deprecated Functions in the Package asremlPlus |
| predictions.frame |
Description of a predictions object |
| predictions.frame-class |
Description of a predictions object |
| predictparallel.asreml |
Deprecated Functions in the Package asremlPlus |
| predictPlus |
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.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 |
Forms the predictions for each of one or more terms and presents them in tables and/or graphs. |
| predictPresent.asreml |
Forms the predictions for each of one or more terms and presents them in tables and/or graphs. |
| print.alldiffs |
Prints the values in an 'alldiffs.object' in a nice format. |
| print.asrtests |
Prints the values in an 'asrtests.object' |
| print.LSDdata |
Prints the components of a list containing data on the LSDs for all pairwise differences of predictions. |
| 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. |
| print.wald.tab |
Prints a data.frame containing a Wald or pseudoanova table. |
| printFormulae |
Prints the formulae from an asreml object. |
| printFormulae.asreml |
Prints the formulae from an asreml object. |
| R2adj |
Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms. |
| R2adj.asreml |
Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms. |
| ratioTransform |
Calculates the ratios of nominated pairs of predictions stored in an 'alldiffs.object'. |
| ratioTransform.alldiffs |
Calculates the ratios of nominated pairs of predictions stored in an 'alldiffs.object'. |
| recalc.wald.tab.asreml |
Deprecated Functions in the Package asremlPlus |
| recalc.wald.tab.asrtests |
Deprecated Functions in the Package asremlPlus |
| recalcLSD |
Adds or recalculates the 'LSD.frame' that is a component of an 'alldiffs.object'. |
| recalcLSD.alldiffs |
Adds or recalculates the 'LSD.frame' that is a component of an 'alldiffs.object'. |
| recalcWaldTab |
Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using 'wald.asreml' |
| recalcWaldTab.asrtests |
Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using 'wald.asreml' |
| redoErrorIntervals |
Adds or replaces the error intervals stored in a prediction component of an 'alldiffs.object'. |
| redoErrorIntervals.alldiffs |
Adds or replaces the error intervals stored in a prediction component of an 'alldiffs.object'. |
| reml.lrt |
Deprecated Functions in the Package asremlPlus |
| reml.lrt.asreml |
Deprecated Functions in the Package asremlPlus |
| REMLRT |
Performs a REML ratio test to compare two models. |
| REMLRT.asreml |
Performs a REML ratio test to compare two models. |
| renewClassify |
Renews the components in an 'alldiffs.object' according to a new classify. |
| renewClassify.alldiffs |
Renews the components in an 'alldiffs.object' according to a new classify. |
| reorderClassify |
Deprecated Functions in the Package asremlPlus |
| reorderClassify.alldiffs |
Deprecated Functions in the Package asremlPlus |
| reparamSigDevn |
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.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'. |
| rmboundary |
Removes any boundary or singular variance components from the fit stored in 'asrtests.obj' and records their removal in an 'asrtests.object'. |
| rmboundary.asreml |
Deprecated Functions in the Package asremlPlus |
| rmboundary.asrtests |
Removes any boundary or singular variance components from the fit stored in 'asrtests.obj' and records their removal in an 'asrtests.object'. |
| setvarianceterms |
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.asreml |
Deprecated Functions in the Package asremlPlus |
| 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. |
| sig.devn.reparam.asreml |
Deprecated Functions in the Package asremlPlus |
| sig.devn.reparam.asrtests |
Deprecated Functions in the Package asremlPlus |
| simulate.asreml |
Produce sets of simulated data from a multivariate normal distribution and save quantities related to the simulated data |
| sort.alldiffs |
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. |
| subset.alldiffs |
Subsets the components in an 'alldiffs.object' according to the supplied condition. |
| subset.list |
Forms a 'list' that contains a subset of the components of the supplied 'list'. |
| testranfix |
Tests for a single fixed or random term in model fitted using 'asreml' and records the result in an 'asrtests.object'. |
| testranfix.asreml |
Deprecated Functions in the Package asremlPlus |
| testranfix.asrtests |
Tests for a single fixed or random term in model fitted using 'asreml' and records the result in an 'asrtests.object'. |
| testrcov.asreml |
Deprecated Functions in the Package asremlPlus |
| testrcov.asrtests |
Deprecated Functions in the Package asremlPlus |
| testresidual |
Fits a new residual formula, tests whether the change is significant and records the result in an 'asrtests.object'. |
| testresidual.asrtests |
Fits a new residual formula, tests whether the change is significant and records the result in an 'asrtests.object'. |
| testswapran |
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.asreml |
Deprecated Functions in the Package asremlPlus |
| 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'. |
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