addBacktransforms.alldiffs {asremlPlus}R Documentation

Adds or recalculates the backtransforms component of an alldiffs.object.

Description

Given an alldiffs.object, adds or recalculate its backtransforms component.

Usage

## S3 method for class 'alldiffs'
addBacktransforms(alldiffs.obj, transform.power = 1, 
                  offset = 0, scale = 1, ...)

Arguments

alldiffs.obj

An alldiffs.object.

transform.power

A numeric specifying the power of a transformation, if one has been applied to the response variable. Unless it is equal to 1, the default, back-transforms of the predictions will be obtained and presented in tables or graphs as appropriate. The back-transformation raises the predictions to the power equal to the reciprocal of transform.power, unless it equals 0 in which case the exponential of the predictions is taken.

offset

A numeric that has been added to each value of the response after any scaling and before applying any power transformation.

scale

A numeric by which each value of the response has been multiplied before adding any offset and applying any power transformation.

...

Provision for passsing arguments to functions called internally - not used at present.

Value

An alldiffs.object with components predictions, vcov, differences, p.differences, sed, LSD and backtransforms.

Author(s)

Chris Brien

See Also

asremlPlus-package, as.alldiffs, sort.alldiffs, subset.alldiffs, print.alldiffs,
renewClassify.alldiffs, redoErrorIntervals.alldiffs, plotPredictions.data.frame,
predictPlus.asreml, predictPresent.asreml

Examples


##Subset WaterRunoff data to reduce time to execute
data(WaterRunoff.dat)
tmp <- subset(WaterRunoff.dat, Date == "05-18" & Benches != "3")

##Use asreml to get predictions and associated statistics

## Not run: 
asreml.options(keep.order = TRUE) #required for asreml-R4 only
current.asr <- asreml(fixed = log.Turbidity ~ Benches + (Sources * (Type + Species)), 
                      random = ~ Benches:MainPlots,
                      keep.order=TRUE, data= tmp)
current.asrt <- as.asrtests(current.asr, NULL, NULL)
TS.diffs <- predictPlus(classify = "Sources:Type", 
                        asreml.obj = current.asr, 
                        wald.tab = current.asrt$wald.tab, 
                        present = c("Sources", "Type", "Species"))

## 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(log.Turbidity ~ Benches + (Sources * (Type + Species)) + 
                              (1|Benches:MainPlots),
                            data=tmp)
  TS.emm <- emmeans::emmeans(m1.lmer, specs = ~ Sources:Species)
  TS.preds <- summary(TS.emm)
  den.df <- min(TS.preds$df, na.rm = TRUE)
  ## Modify TS.preds to be compatible with a predictions.frame
  TS.preds <- as.predictions.frame(TS.preds, predictions = "emmean", 
                                   se = "SE", interval.type = "CI", 
                                   interval.names = c("lower.CL", "upper.CL"))
  
  ## Form an all.diffs object and check its validity
  TS.vcov <- vcov(TS.emm)
  TS.diffs <- allDifferences(predictions = TS.preds, classify = "Sources:Species", 
                             vcov = TS.vcov, tdf = den.df)
  validAlldiffs(TS.diffs)
}  

## Recalculate the back-transforms of the predictions obtained using asreml or lmerTest
if (exists("TS.diffs"))
{
  TS.diffs <- addBacktransforms.alldiffs(TS.diffs, transform.power = 0)
}

[Package asremlPlus version 4.2-32 Index]