addrm.terms.asreml |
Deprecated Functions in the Package asremlPlus |
addrm.terms.asrtests |
Deprecated Functions in the Package asremlPlus |
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 hypthesis 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 |
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. |
asrtests-class |
Description of an asrtests object |
asrtests.object |
Description of an asrtests 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. |
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.predictions.frame |
Prints the values in a 'predictions.frame', with or without title and heading. |
print.wald.tab |
Prints a Wald or pseudoanova table. |
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 component of an 'alldiffs.object'. |
recalcLSD.alldiffs |
Adds or recalculates the LSD 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. |
reorderClassify |
Reorders the components in an 'alldiffs.object' according to a new classify. |
reorderClassify.alldiffs |
Reorders the components in an 'alldiffs.object' according to a new classify. |
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 distribtion and save quantites related to the simulated data |
sort.alldiffs |
Sorts the components in an 'alldiffs.object' according to the predicted values associated with a factor. |
subset.alldiffs |
Subsets the components in an 'alldiffs.object' according to the supplied condition. |
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'. |