alldiffs {asreml3Plus}R Documentation

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.

Description

Creates an object of S3-class alldiffs that consists of a list containing the following components: predictions, differences, p.differences, sed, LSD and backtransforms. Predictions must be supplied to the functions while the others will be set only if they are supplies; those not supplied are set to NULL. It also has attributes response, response.title, term, classify and tdf, which will be set to the values supplied or NULL if none are supplied.

Usage

alldiffs(predictions, differences = NULL, p.differences = NULL, 
         sed = NULL, LSD = NULL, backtransforms = NULL, 
         response = NULL, response.title = NULL, 
         term = NULL, classify = NULL, tdf = NULL)

Arguments

predictions

a data.frame containing the predicted values that is consistent with an object of class asremlPredict such as is stored in the pvals component of the prediction component of the value produced by predict.asreml. That is, in addition to variables classifying the predictions, it will include columns named predicted.value, standard.error and est.status; each row contains a single predicted value. It may also contain columns for the lower and upper confidence limits for the predictions. If LSD is not NULL, the mean LSD will be added as an attribute named meanLSD.

differences

a matrix containing all pairwise differences between the predictions; it should have the same number of rows and columns as there are rows in predictions.

p.differences

a matrix containing p-values for all pairwise differences between the predictions; each p-value is computed as the probability of a t-statistic as large as or larger than the observed difference divided by its standard error. The degrees of freedom of the t distribution for computing it are computed as the denominator degrees of freedom of the F value for the fixed term, if available; otherwise, the degrees of freedom stored in the attribute tdf are used; the matrix should be of the same size as that for differences.

sed

a matrix containing the standard errors of all pairwise differences between the predictions; they are used in computing the p-values.

LSD

a data.frame containing the mean, minimum and maximum LSD for determining the significance of pairwise differences.

backtransforms

a data.frame containing the backtransformed values of the predicted values that is consistent with an object of class asremlPredict such as is stored in the pvals component of the prediction component of the value produced by predict.asreml. That is, in addition to variables classifying the predictions, it will include columns named backtransformed.predictions and est.status; it may also contain columns for the lower and upper confidence limits; each row contains a single predicted value.

response

a character specifying the response variable for the predictions. It is stored as an attribute to the alldiffs object.

response.title

a character specifying the title for the response variable for the predictions. It is stored as an attribute to the alldiffs object.

term

a character string giving the variables that define the term that was fitted using asreml and that corresponds to classify. It is often the same as classify. It is stored as an attribute to the alldiffs object.

classify

a character string giving the variables that define the margins of the multiway table used in the prediction. Multiway tables are specified by forming an interaction type term from the classifying variables, that is, separating the variable names with the : operator. It is stored as an attribute to the alldiffs object.

tdf

an integer specifying the degrees of freedom of the standard error. It is used as the degrees of freedom for the t-distribution on which p-values and confidence intervals are based. It is stored as an attribute to the alldiffs object.

Value

An object of S3-class alldiffs with attributes response, response.title, term, classify and tdf.

See Also

asreml3Plus-package, print.alldiffs, predictparallel.asreml,predictionplot.asreml,
predictiondiffs.asreml, pred.present.asreml

Examples

## Not run: 
  Var.pred <- predict(current.asr, classify="Variety", sed=TRUE)$predictions
  wald.tab <-  current.asrt$wald.tab
  den.df <- wald.tab[match("Variety", rownames(wald.tab)), "denDF"]
  Var.diffs <- alldiffs(predictions = Var.pred$pvals, 
                        sed = Var.pred$sed, 
                        tdf = den.df)
  Var.diffs <- predictiondiffs.asreml(classify = "Variety", 
                                      alldiffs.obj=Var.diffs)
  print.alldiffs(Var.diffs, which="differences")

## End(Not run)

[Package asreml3Plus version 2.0-14 Index]