facRecast.alldiffs {asremlPlus} | R Documentation |
Reorders and/or revises the factor levels using the order of old levels in levels.order
and the new labels for the levels given in newlabels
. The values in levels.order
must be unique.
Description
Reorders and revises the levels and labels of a factor
, in the prediction
component of an alldiffs.object
. The values in the
levels.order
vector should be the same as the levels in the existing factor
,
but the order can be changed. To revise the levels, specify the new levels in the
newlabels
vector and these will replace the corresponding value in the
levels.order
vector. The matching
changes are made to the other components and attributes of the alldiffs.object
.
Usage
## S3 method for class 'alldiffs'
facRecast(object, factor, levels.order = NULL, newlabels = NULL, ...)
Arguments
object |
An |
factor |
A |
levels.order |
A |
newlabels |
A |
... |
Further arguments passed to the |
Value
A modified alldiffs.object
.
Author(s)
Chris Brien
See Also
as.alldiffs
, allDifferences.data.frame
,
print.alldiffs
, sort.alldiffs
,
facCombine.alldiffs
, facRename.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)
## Recast the Ladybird and Host factors
HCL.diffs <- facRecast(HCL.diffs, factor = "Ladybird",
newlabels = c("none", "present"))
HCL.diffs <- facRecast(HCL.diffs, factor = "Ladybird",
levels.order = c("present", "none"),
newlabels = c("yes","no"))
HCL.diffs <- facRecast.alldiffs(HCL.diffs, factor = "Host",
levels.order = c("trefoil", "bean"))
## Check the validity of HCL.diffs
validAlldiffs(HCL.diffs)
}