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Hello,
1. The following code (below) and output <varIdentOutput.txt>
illustrate that
argument fixed= in varIdent function is ignored during the execution.
2. File named <RevisedvarIdent.txt> shows how to fix the problem.
The changed line in this file is labeled using comment " # !!! This
line changed".
Thank you
Andrzej Galecki
### Code used for illustration starts here ####
library(nlme)
sessionInfo()
Orth <- subset(Orthodont, Subject %in% c("M01","F01"))
# Argument fixed in varIdent is ignored
vf1.incorrect <- varIdent(form=~1|Sex,fixed=c(Female=0.5))
vf1I <- Initialize(vf1.incorrect, data=Orth)
varWeights(vf1I)
# Tentative varIdent function (revised)
source("C:/temp/RevisedvarIdent.txt")
vf2.correct <- varIdent(form=~1|Sex,fixed=c(Female=0.5))
vf2I <- Initialize(vf2.correct, data=Orth)
coef(vf2I)
varWeights(vf2I)
# rm(varIdent) # Remove tentative varIdent function
### Code ends here ####
--------------000706080709050507050106
Content-Type: text/plain;
name="RevisedvarIdent.txt"
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filename="RevisedvarIdent.txt"
varIdent <-
function (value = numeric(0), form = ~1, fixed = NULL)
{
if (is.null(getGroupsFormula(form))) {
value <- numeric(0)
attr(value, "fixed") <- NULL
}
else {
if ((lv <- length(value)) > 0) {
if (is.null(grpNames <- names(value)) && (lv > 1)) {
stop("Initial values must have group names in varIdent")
}
value <- unlist(value)
if (any(value <= 0)) {
stop("Initial values for \"varIdent\" must be > 0.")
}
value <- log(value)
}
else grpNames <- NULL
attr(value, "groupNames") <- grpNames
if (!is.null(fixed)) { # !!! This line changed
fix <- attr(value, "fixed") <- log(unlist(fixed))
if (is.null(fixNames <- names(fix))) {
stop("Fixed parameters must have names in varIdent")
}
if (!is.null(attr(value, "groupNames"))) {
attr(value, "groupNames") <- c(attr(value, "groupNames"),
fixNames)
}
}
}
attr(value, "formula") <- asOneSidedFormula(form)
class(value) <- c("varIdent", "varFunc")
value
}
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Content-Type: text/plain;
name="varIdentOutput.txt"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline;
filename="varIdentOutput.txt"
> library(nlme)
> sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
other attached packages:
nlme
"3.1-80"
>
> # Argument fixed in varIdent is ignored
> Orth <- subset(Orthodont, Subject %in% c("M01","F01"))
> # Argument fixed in varIdent is ignored
> vf1.incorrect <- varIdent(form=~1|Sex,fixed=c(Female=0.5))
> vf1I <- Initialize(vf1.incorrect, data=Orth)
> varWeights(vf1I)
Male Male Male Male Female Female Female Female
1 1 1 1 1 1 1 1
>
> # Tentative varIdent function (revised)
> source("C:/temp/RevisedvarIdent.txt")
>
> vf2.correct <- varIdent(form=~1|Sex,fixed=c(Female=0.5))
> vf2I <- Initialize(vf2.correct, data=Orth)
> varWeights(vf2I)
Male Male Male Male Female Female Female Female
1 1 1 1 2 2 2 2
> rm(varIdent) # Remove tentative varIdent function
--------------000706080709050507050106--
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