A B C E F G I L M N O P R S T V W

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

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 |

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

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

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'. |

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

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

exploreLSDs | Explores the computed LSD values for pairwise differences between predictions. |

exploreLSDs.alldiffs | Explores the computed LSD values for pairwise differences between predictions. |

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

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

facRecast | 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.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. |

facRecode | Deprecated Functions in the Package asremlPlus |

facRecode.alldiffs | Deprecated Functions in the Package asremlPlus |

facRename | Renames 'factor's in the 'prediction' component of an 'alldiffs.object'. |

facRename.alldiffs | Renames 'factor's in the 'prediction' component of an 'alldiffs.object'. |

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

getFormulae | Gets the formulae from an asreml object. |

getFormulae.asreml | Gets the formulae from an asreml object. |

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

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

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

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

info.crit | Deprecated Functions in the Package asremlPlus |

info.crit.asreml | Deprecated Functions in the Package asremlPlus |

infoCriteria | Computes AIC and BIC for models. |

infoCriteria.asreml | Computes AIC and BIC for models. |

infoCriteria.list | Computes AIC and BIC for models. |

is.alldiffs | Tests whether an object is of class alldiffs |

is.asrtests | Tests whether an object is of class asrtests |

is.predictions.frame | Tests whether an object is of class predictions.frame |

iterate | Subject the fitted 'asreml.obj' stored in an 'asrtests.object' to further iterations of the fitting process. |

iterate.asrtests | Subject the fitted 'asreml.obj' stored in an 'asrtests.object' to further iterations of the fitting process. |

Ladybird.dat | Data for an experiment to investigate whether ladybirds transfer aphids |

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

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

loadASRemlVersion | Ensures that a specific version of 'asreml' is loaded. |

LSD.frame | Description of an LSD frame |

makeTPPSplineMats | Make the spline basis matrices and data needed to fit Tensor Product P-splines. |

makeTPPSplineMats.data.frame | Make the spline basis matrices and data needed to fit Tensor Product P-splines. |

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

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

newrcov.asrtests | Deprecated Functions in the Package asremlPlus |

num.recode | Recodes the unique values of a vector using the values in a new vector. |

Oats.dat | Data for an experiment to investigate nitrogen response of 3 oats varieties |

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'. |

validAlldiffs | Checks that an object is a valid alldiffs object. |

validAsrtests | Checks that an object is a valid asrtests object. |

validPredictionsFrame | Checks that an object is a valid predictions.frame. |

variofaces | Plots empirical variogram faces, including envelopes, as described by Stefanova, Smith & Cullis (2009). |

variofaces.asreml | Plots empirical variogram faces, including envelopes, as described by Stefanova, Smith & Cullis (2009). |

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 |