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

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

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 and transform.function 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 class 'alldiffs'
addBacktransforms(alldiffs.obj, 
                  transform.power = 1, offset = 0, scale = 1, 
                  transform.function =  "identity", ...)

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.
transform.function	A character giving the name of a function that specifies the scale on which the predicted values are defined. This may be the result of a transformation of the data using the function or the use of the function as a link function in the fitting of a generalized linear (mixed) model (GL(M)M). The possible transform.functions are identity, log, inverse, sqrt, logit, probit, and cloglog. The predicted.values and error.intervals, if not StandardError intervals, will be back-transformed using the inverse function of the transform.function. The standard.error column will be set to NA, unless (i) asreml returns columns named transformed.value and approx.se, as well as those called predicted.values and standard.error (such as when a GLM is fitted) and (ii) the values in transformed.value are equal to those obtained by backtransforming the predicted.values using the inverse function of the transform.function. Then, the approx.se values will be saved in the standard.error column of the backtransforms component of the returned alldiffs.obj. Also, the transformed.value and approx.se columns are removed from both the predictions and backtransforms components of the alldiffs.obj. Note that the values that end up in the standard errors column are approximate for the backtransformed values and are not used in calculating error.intervals.
...	Provision for passing 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) LSDtype, LSDby and LSDstatistic added from the predictions component and (ii) transform.power, offset, scale, and link.

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)
}

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