asremlPlus (version 4.3-19)

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

Description

Given an alldiffs.object, adds or recalculate its backtransforms component. The values of transform.power, offset, scale from the backtransforms component will be used, unless this component is NULL when the values supplied in the call will be used.

Usage

# S3 method for 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.

The backtransforms component will have the attributes (i) LSDtpe, LSDby and LSDstatistic added from the predictions component and (ii) transform.power, offset, scale.

See Also

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

Examples

# NOT RUN {
##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

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"))


##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
  els <- as.numeric(rownames(TS.preds))
  TS.vcov <- vcov(TS.emm)[els,els]
  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)
}
# }