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asremlPlus (version 1.10-16)

Augments the Use of 'Asreml' in Fitting Mixed Models

Description

Provides functions that assist in automating the testing of terms in mixed models when 'asreml' is used to fit the models. The package 'asreml' is marketed by 'VSNi' (http://www.vsni.co.uk/) as 'asreml-R' and provides a computationally efficient algorithm for fitting mixed models using Residual Maximum Likelihood. The content falls into the following natural groupings: (i) Data, (ii) Object manipulation functions, (iii) Model modification functions, (iv) Model testing functions, (v) Model diagnostics functions, (vi) Prediction production and presentation functions, (vii) Response transformation functions, and (viii) Miscellaneous functions. A history of the fitting of a sequence of models is kept in a data frame. Procedures are available for choosing models that conform to the hierarchy or marginality principle and for displaying predictions for significant terms in tables and graphs.

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Version

Install

install.packages('asremlPlus')

Monthly Downloads

818

Version

1.10-16

License

GPL (>= 2)

Maintainer

Chris Brien

Last Published

June 6th, 2015

Functions in asremlPlus (1.10-16)

angular

Applies the angular transformation to proportions.
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.
permute.to.zero.lowertri

Permutes a square matrix until all the lower triangular elements are zero.
angular.mod

Applies the modified angular transformation to a vector of counts.
predictionplot.asreml

This function plots the predictions for a term, possibly with error bars.
plotvariofaces.asreml

plot empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009)
pred.present.asreml

This function forms the predictions for each significant term and presents them in tables and/or graphs.
sig.devn.reparam.asreml

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.
testswapran.asreml

Tests, using a REMLRT, whether the difference between current random model and one in which oldterms are dropped and newterms are added is significant.
num.recode

Recodes the unique values of a vector using the values in a new vector.
info.crit.asreml

Computes AIC and BIC for a model.
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.
choose.model.asreml

Determines the set of significant terms taking into account the hierarchy or marginality relations.
rmboundary.asreml

Removes any boundary or singular variance components from the fit stored in asreml.obj and records their removal in a data.frame.
print.alldiffs

Prints the values in an alldiffs object in a nice format.
asremlPlus-package

Augments the use of asreml-R in fitting mixed models
testrcov.asreml

Fits a new rcov formula using asreml and tests whether the change is significant.
Wheat.dat

Data for an experiment to investigate 25 varieties of wheat
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 has parallel values both occur in the model and need to be taken into account.
newfit.asreml

refits an asreml model with modified model formula using either a call to update.asreml or a direct call to asreml.
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.
variofaces.asreml

plot empirical variogram faces, including envelopes, as described by Stefanova, Smith & Cullis (2009)
recalc.wald.tab.asreml

Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using wald.asreml
addrm.terms.asreml

Adds or removes the specified set terms from either the fixed or random model and records the change in a data.frame.
print.asrtests

Prints the values in an asrtests object
reml.lrt.asreml

Performs REML likelihood ratio test.
testranfix.asreml

Tests for a single fixed or random term in model fitted using asreml
permute.square

Permutes the rows and columns of a square matrix.
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.
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.
simulate.asreml

Produce sets of simulated data from a multivariate normal distribtion and save quantites related to the simulated data