Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences
Description of an alldiffs object
Determines the set of significant terms from results stored in a `data...
Using supplied predictions and standard errors of pairwise differences...
Adds or recalculates the backtransforms component of an `alldiffs.obje...
Adds, to a supplied model, a spatial model that accounts for local spa...
Uses information criteria to decide whether to add a spatial model to ...
Adds a row to a test.summary data.frame.
Reorders and/or revises the factor levels using the order of old level...
Applies the modified angular transformation to a vector of counts.
Applies the angular transformation to proportions.
Forms an alldiffs.object from the supplied predictions, along with t...
Forms an asrtests object that stores (i) a fitted asreml object, (ii) ...
Forms a predictions.frame from a data.frame, ensuring that the cor...
Deprecated Functions in the Package asremlPlus
tools:::Rd_package_title("asremlPlus")
The randomly-presented, startup tips.
Permutes the rows and columns of a square matrix.
Description of an asrtests object
Uses the parametric bootstrap to calculate the p-value for a REML rati...
Uses information criteria to decide whether to change an already fitte...
Adds and drops terms from one or both of the fixed or random model, re...
A large data set comprising the end of imaging data from a chick pea e...
Determines and records the set of significant terms using an `asrtests...
Determines the set of significant terms using p-values and records the...
Uses information criteria to choose the best fitting spatial model for...
Recreates an asreml object so that it is compatible with the current...
Converts the effects names for a term stored in the component of an `a...
Forms the estimated variance, random or residual matrix for the observ...
Explores the computed LSD values for pairwise differences between pred...
Combines several factors into one in the components of an `alldiffs.ob...
Renames factors in the prediction component of an `alldiffs.object...
Finds the version of asreml that is loaded and returns the initial cha...
Gets the formulae from an asreml object.
Gets the entry for a test recorded in the test.summary data.frame of a...
Gets the p-value for a test recorded in the test.summary data.frame of...
Computes AIC and BIC for models.
Tests whether an object is of class alldiffs
Tests whether an object is of class asrtests
Tests whether an object is of class predictions.frame
Tests whether an object of class matrix is compound symmetric
Subject the fitted asreml.obj stored in an asrtests.objectto furth...
Permutes a square matrix until all the lower triangular elements are z...
Calculates a linear transformation of the predictions stored in an `al...
Ensures that a specific version of asreml is loaded.
Description of an LSD frame
Make the spline basis matrices and data needed to fit Tensor Product P...
Refits an asreml model with changed arguments by extracting, modifyi...
Recodes the unique values of a vector using the values in a new vector...
Calculates the differences between nominated pairs of predictions stor...
Pick LSDstatistics whose values minimize the number of errors in pairw...
Plots a map of the errors that occur in using the computed LSD values ...
Plots a map of the supplied errors that occur in using the computed LS...
Plots a heat map of computed LSD values for pairwise differences betwe...
Plots a heat map of computed LSD-values for pairwise differences betwe...
Plots the predictions for a term, possibly with error bars.
Plots a heat map of p-values for pairwise differences between predicti...
Plots a heat map of p-values for pairwise differences between predicti...
Plots empirical variogram faces, including envelopes, from supplied re...
Performs a combination of a linear and a power transformation on a var...
Description of a predictions object
Forms the predictions for a term, their pairwise differences and assoc...
Forms the predictions for each of one or more terms and presents them ...
Prints the values in an alldiffs.object in a nice format.
Prints the values in an asrtests.object
Prints the components of a list containing data on the LSDs for all pa...
Prints the values in a predictions.frame, with or without title and ...
Prints a data.frame containing a test.summary.
Prints a data.frame containing a Wald or pseudoanova table.
Prints the formulae from an asreml object.
Calculates the adjusted coefficient of determination for a specified c...
Calculates the ratios of nominated pairs of predictions stored in an `...
Adds or recalculates the LSD.frame that is a component of an `alldif...
Recalculates the denDF, F.inc and P values for a table of Wald test st...
Adds or replaces the error intervals stored in a prediction component ...
Performs a REML ratio test to compare two models.
Renews the components in an alldiffs.object according to a new class...
Reparamterizes each random (deviations) term involving devn.fac to a...
Removes any boundary or singular variance components from the fit stor...
allows the setting of bounds and initial values for terms in the `rand...
Produce sets of simulated data from a multivariate normal distribution...
Sorts the components in an alldiffs.object according to the predicte...
Sorts a predictions.frame according to the predicted values associat...
Subsets the components in an alldiffs.object according to the suppli...
Forms a list that contains a subset of the components of the supplie...
Tests for a single fixed or random term in model fitted using asreml...
Fits a new residual formula, tests whether the change is significant a...
Tests, using a REMLRT, the significance of the difference between the ...
Checks that an object is a valid alldiffs object.
Checks that an object is a valid asrtests object.
Checks that an object is a valid predictions.frame.
Plots empirical variogram faces, including envelopes, as described by ...
Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The 'asreml' package provides a computationally efficient algorithm for fitting a wide range of linear mixed models using Residual Maximum Likelihood. It is a commercial package and a license for it can be purchased from 'VSNi' <https://vsni.co.uk/> as 'asreml-R', who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from <http://chris.brien.name/rpackages/>.