validPredictionsFrame: Checks that an object is a valid predictions.frame.

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

Checks that an object is a valid predictions.frame.

Description

Checks that an object is a predictions.frame of S3-class data.frame that contains the columns predicted.value, standard.error and est.status.

Usage

validPredictionsFrame(object)

Arguments

object

an predictions.frame.

Value

TRUE or a character describing why the object is not a valid predictions.frame.

Author(s)

Chris Brien

See Also

predictions.frame, is.predictions.frame, as.predictions.frame,
validAsrtests, validAlldiffs

Examples

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

  ## Not run: 
  m1.asr <- asreml(Yield ~ Nitrogen*Variety, 
                   random=~Blocks/Wplots,
                   data=Oats.dat)
  current.asrt <- as.asrtests(m1.asr)
  Var.pred <- asreml::predict.asreml(m1.asr, classify="Nitrogen:Variety", 
                                      sed=TRUE)
  if (getASRemlVersionLoaded(nchar = 1) == "3")
    Var.pred <- Var.pred$predictions
  Var.preds <- as.predictions.frame(Var.pred$pvals, se = "std.error", 
                                    est.status = "status")

  
## End(Not run)
  
  ## Use lmerTest and emmmeans to get predictions and associated statistics
  if (requireNamespace("lmerTest", quietly = TRUE) & 
      requireNamespace("emmeans", quietly = TRUE))
  {
    m1.lmer <- lmerTest::lmer(Yield ~ Nitrogen*Variety + (1|Blocks/Wplots),
                              data=Oats.dat)
    Var.emm <- emmeans::emmeans(m1.lmer, specs = ~ Nitrogen:Variety)
    Var.preds <- summary(Var.emm)
    Var.preds <- as.predictions.frame(Var.preds, predictions = "emmean", 
                                      se = "SE", interval.type = "CI", 
                                      interval.names = c("lower.CL", "upper.CL"))
  }

  if (exists("Var.preds"))
  {
    ## Check the class and validity of the predictions.frame
    is.predictions.frame(Var.preds)
    validPredictionsFrame(Var.preds)
  }

asremlPlus documentation built on Nov. 5, 2023, 5:07 p.m.