Data for a 1976 experiment to investigate 25 varieties of wheat
Data for an experiment to investigate whether ladybirds transfer aphids
Performs a REML ratio test to compare two models.
Data for an experiment to investigate the quality of water runoff over time
addBacktransforms.alldiffs
Adds or recalculates the backtransforms component of an alldiffs.object.
Data for an experiment to investigate nitrogen response of 3 oats varieties
A large data set comprising the end of imaging data from a chick pea experiment conducted in high-throughput greenhouses
Calculates the adjusted coefficient of determination for a specified combination of fixed and random terms.
Description of an LSD frame
Adds, to a supplied model, a spatial model that accounts for local spatial variation.
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.
Forms an alldiffs.object from the supplied predictions, along with those statistics,
associated with the predictions and their pairwise differences, that have been supplied.
Description of an alldiffs object
addSpatialModelOnIC.asrtests
Uses information criteria to decide whether to add a spatial model to account for local spatial variation.
Adds a row to a test.summary data.frame.
Forms a predictions.frame from a data.frame, ensuring that the correct
columns are present.
Deprecated Functions in the Package asremlPlus
Applies the angular transformation to proportions.
Applies the modified angular transformation to a vector of counts.
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.
Determines the set of significant terms using p-values and records the tests performed in a
data.frame Uses information criteria to decide whether to change an already fitted model.
Determines and records the set of significant terms using an asrtests.object,
taking into account the hierarchy or marginality relations of the terms.
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.asrtests
Uses information criteria to choose the best fitting spatial model for accounting for local spatial variation.
tools:::Rd_package_title("asremlPlus")
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.
The randomly-presented, startup tips.
Combines several factors into one in the components of an alldiffs.object
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.
Description of an asrtests object
Recreates an asreml object so that it is compatible with the currently loaded asreml version.
Uses the parametric bootstrap to calculate the p-value for a REML ratio test to compare two models.
convEffectNames2DataFrame.asreml
Converts the effects names for a term stored in the component of an asreml object into a data.frame Forms the estimated variance, random or residual matrix for the observations
from the variance parameter estimates.
Tests whether an object is of class predictions.frame
Gets the p-value for a test recorded in the test.summary data.frame of an asrtests.object
Computes AIC and BIC for models.
Plots a map of the supplied errors that occur in using the computed LSD values for pairwise differences between predictions.
Gets the formulae from an asreml object.
Plots a heat map of computed LSD values for pairwise differences between predictions.
Plots a heat map of p-values for pairwise differences between predictions.
Subject the fitted asreml.obj stored in an asrtests.object
to further iterations of the fitting process.
Gets the entry for a test recorded in the test.summary data.frame of an asrtests.object
Renames factor prediction component of an
alldiffs.object. Finds the version of asreml that is loaded and returns the initial characters in version.
Plots a heat map of p-values for pairwise differences between predictions.
Renews the components in an alldiffs.object according to a new classify.
Calculates a linear transformation of the predictions stored in an
alldiffs.object.
Explores the computed LSD values for pairwise differences between predictions.
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.
Fits a new residual formula, tests whether the change
is significant and records the result in an asrtests.object.
Ensures that a specific version of asreml is loaded.
pickLSDstatistics.alldiffs
Pick LSDstatistics whose values minimize the number of errors in pairwise comparisons of predictions.
makeTPPSplineMats.data.frame
Make the spline basis matrices and data needed to fit Tensor Product P-splines.
Plots a map of the errors that occur in using the computed LSD values for pairwise differences between predictions.
Permutes the rows and columns of a square matrix.
Refits an asreml model with changed arguments by extracting, modifying
and evaluating its call - an alternate to update.asreml.
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.
Plots a heat map of computed LSD-values for pairwise differences between predictions.
plotPredictions.data.frame
Plots the predictions for a term, possibly with error bars.
plotVariofaces.data.frame
Plots empirical variogram faces, including envelopes, from supplied residuals as
described by Stefanova, Smith & Cullis (2009).
Prints the values in an alldiffs.object in a nice format.
Prints the values in an asrtests.object
Permutes a square matrix until all the lower triangular elements are zero.
Description of a predictions object
Prints the components of a list containing data on the LSDs for all pairwise differences of predictions.
Performs a combination of a linear and a power transformation on a variable. The
transformed variable is stored in the data.frame data.
Prints a data.frame containing a Wald or pseudoanova table.
Prints the formulae from an asreml object.
Produce sets of simulated data from a multivariate normal distribution and save
quantities related to the simulated data
Prints the values in a predictions.frame, with or without title and heading.
Sorts the components in an alldiffs.object according to the predicted values
associated with a factor.
Tests whether an object is of class alldiffs
Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained
using wald.asreml
Tests whether an object is of class asrtests
Recodes the unique values of a vector using the values in a new vector.
pairdiffsTransform.alldiffs
Calculates the differences between nominated pairs of predictions stored in
an alldiffs.object.
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.
redoErrorIntervals.alldiffs
Adds or replaces the error intervals stored in a prediction component
of an alldiffs.object.
Forms a list list Forms the predictions for each of one or more terms and presents
them in tables and/or graphs.
Calculates the ratios of nominated pairs of predictions stored in an alldiffs.object.
Prints a data.frame containing a test.summary.
Tests for a single fixed or random term in model fitted using asreml
and records the result in an asrtests.object.
Checks that an object is a valid alldiffs object.
Sorts a predictions.frame according to the predicted values
associated with a factor.
Checks that an object is a valid asrtests object.
Subsets the components in an alldiffs.object according to the supplied condition.
Checks that an object is a valid predictions.frame.
Plots empirical variogram faces, including envelopes, as described by
Stefanova, Smith & Cullis (2009).
Adds or recalculates the LSD.frame that is a component of an
alldiffs.object.
Removes any boundary or singular variance components from the fit stored in
asrtests.obj and records their removal in an asrtests.object.
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.