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| asreml3Plus-package | Augments the Use of 'ASReml3-R' in Fitting Mixed Models |
| addrm.terms.asreml | Deprecated Functions in Package asreml3Plus |
| addrm.terms.asrtests | Adds or removes the specified set terms from either the fixed or random model and records the change in a data.frame. |
| alldiffs | Forms an object of S3-class 'alldiffs' that stores the predictions for a model fitted using asreml, along with supplied statistics for all pairwise differences. |
| angular | Applies the angular transformation to proportions. |
| angular.mod | Applies the modified angular transformation to a vector of counts. |
| asreml3Plus | Augments the Use of 'ASReml3-R' in Fitting Mixed Models |
| asreml3Plus-deprecated | Deprecated Functions in Package asreml3Plus |
| asrtests | Forms an object of S3-class 'asrtests' that stores a fitted asreml object, a pseudo-anova table for the fixed and a history of changes and hypthesis testing used in obtaining the model. |
| choose.model.asreml | Deprecated Functions in Package asreml3Plus |
| choose.model.asrtests | Determines the set of significant terms taking into account the hierarchy or marginality relations. |
| info.crit | Deprecated Functions in Package asreml3Plus |
| info.crit.asreml | Computes AIC and BIC for a model. |
| newfit.asreml | refits an asreml model with modified model formula using either a call to 'update.asreml' or a direct call to 'asreml'. |
| newrcov.asrtests | Fits a new rcov formula using 'asreml'. |
| num.recode | Recodes the unique values of a vector using the values in a new vector. |
| 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. |
| plotvariofaces.asreml | plot empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009) |
| power.transform | Perform a combination of a linear and power transformation on a variable whose name is given as a character string in 'var.name'. The transformed variable is stored in the 'data.frame data'. |
| pred.present.asreml | This function forms the predictions for each significant term and presents them in tables and/or graphs. |
| predictiondiffs.asreml | Uses information in a supplied alldiffs object to forms all pairwise differences between a set of predictions, the p-values for a test of whether the differences are significantly different from zero, and the minimum, mean and maximum LSD values, provided they are not present in the suppplied alldiffs object. |
| predictionplot.asreml | This function plots the predictions for a term, possibly with error bars. |
| predictparallel.asreml | Uses an asreml object and a wald.tab to form the predictions and associated statistics for a term. It stores the results in an object of class alldifffs and may print the results. It can be used when a numeric vector and a factor that have parallel values both occur in the model and need to be taken into account. |
| print.alldiffs | Prints the values in an 'alldiffs' object in a nice format. |
| print.asrtests | Prints the values in an 'asrtests' object |
| recalc.wald.tab.asreml | Deprecated Functions in Package asreml3Plus |
| recalc.wald.tab.asrtests | Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using 'wald.asreml' |
| reml.lrt | Deprecated Functions in Package asreml3Plus |
| reml.lrt.asreml | Performs REML likelihood ratio test. |
| rmboundary.asreml | Deprecated Functions in Package asreml3Plus |
| rmboundary.asrtests | Removes any boundary or singular variance components from the fit stored in 'asreml.obj' and records their removal in a data.frame. |
| setvarianceterms.asreml | allows the seting of constraints and initial values for terms in the 'random' and 'rcov' arguments of an 'asreml' call, with the resulting call being evaluated. |
| sig.devn.reparam.asreml | Deprecated Functions in Package asreml3Plus |
| sig.devn.reparam.asrtests | This function 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'. |
| simulate.asreml | Produce sets of simulated data from a multivariate normal distribtion and save quantites related to the simulated data |
| testranfix.asreml | Deprecated Functions in Package asreml3Plus |
| testranfix.asrtests | Tests for a single fixed or random term in model fitted using 'asreml' |
| testrcov.asreml | Deprecated Functions in Package asreml3Plus |
| testrcov.asrtests | Fits a new rcov formula using 'asreml' and tests whether the change is significant. |
| testswapran.asreml | Deprecated Functions in Package asreml3Plus |
| testswapran.asrtests | Tests, using a REMLRT, whether the difference between current random model and one in which oldterms are dropped and newterms are added is significant. |
| variofaces.asreml | plot 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 an experiment to investigate 25 varieties of wheat |