facRename.alldiffs: Renames 'factor's in the 'prediction' component of an...

In asremlPlus: Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

Renames factors in the prediction component of an alldiffs.object.

Description

Renames factors in the prediction component of an alldiffs.object. These changes are propagated to the other components and attributes of the alldiffs.object.

Usage

## S3 method for class 'alldiffs'
facRename(object, factor.names, newnames,  ...)

Arguments

object	An alldiffs.object.
factor.names	A character containing the names of the factors in the prediction component of object that are to be renamed.
newnames	A character containing the new names of the factors in the prediction component of object.
...	Provision for passing arguments to functions called internally - not used at present.

Value

A modified alldiffs.object.

Author(s)

Chris Brien

See Also

as.alldiffs, allDifferences.data.frame, print.alldiffs, sort.alldiffs,
facCombine.alldiffs, facRecast.alldiffs, renewClassify.alldiffs; fac.recast in package dae.

Examples

  data("Ladybird.dat")
  
  ## Use asreml to get predictions and associated statistics

  ## Not run: 
  m1.asr <- asreml(logitP ~ Host*Cadavers*Ladybird, 
                   random = ~ Run,
                   data = Ladybird.dat)
  current.asrt <- as.asrtests(m1.asr)
  HCL.pred <- asreml::predict.asreml(m1.asr, classify="Host:Cadavers:Ladybird", 
                                     sed=TRUE)
  HCL.preds <- HCL.pred$pvals
  HCL.sed <- HCL.pred$sed
  HCL.vcov <- NULL
  wald.tab <-  current.asrt$wald.tab
  den.df <- wald.tab[match("Host:Cadavers:Ladybird", rownames(wald.tab)), "denDF"]
  
## End(Not run)
  
  ## Use lmeTest and emmmeans to get predictions and associated statistics
  if (requireNamespace("lmerTest", quietly = TRUE) & 
      requireNamespace("emmeans", quietly = TRUE))
  {
    m1.lmer <- lmerTest::lmer(logitP ~ Host*Cadavers*Ladybird + (1|Run),
                              data=Ladybird.dat)
    HCL.emm <- emmeans::emmeans(m1.lmer, specs = ~ Host:Cadavers:Ladybird)
    HCL.preds <- summary(HCL.emm)
    den.df <- min(HCL.preds$df)
    ## Modify HCL.preds to be compatible with a predictions.frame
    HCL.preds <- as.predictions.frame(HCL.preds, predictions = "emmean", 
                                      se = "SE", interval.type = "CI", 
                                      interval.names = c("lower.CL", "upper.CL"))
    HCL.vcov <- vcov(HCL.emm)
    HCL.sed <- NULL
  }
  
  ## Use the predictions obtained with either asreml or lmerTest
  if (exists("HCL.preds"))
  {
    ## Form an all.diffs object
    HCL.diffs <- allDifferences(predictions = HCL.preds, 
                                classify = "Host:Cadavers:Ladybird", 
                                sed = HCL.sed, vcov = HCL.vcov, tdf = den.df)
    
    ## Check the class and validity of the alldiffs object
    is.alldiffs(HCL.diffs)
    validAlldiffs(HCL.diffs)

    ## Rename Cadavers 
    HCL.diffs <- facRename(HCL.diffs, factor.names = "Cadavers", newnames = "Cadaver.nos")
    
    ## Check the validity of HCL.diffs
    validAlldiffs(HCL.diffs)
  }

asremlPlus documentation built on Oct. 27, 2024, 5:06 p.m.