Nothing
###################################################
### code chunk: Chap8init
###################################################
options(width = 65, digits = 5, show.signif.stars = FALSE)
date()
packageVersion("nlmeU")
packageVersion("nlme")
sessionInfo()
data(armd, package = "nlmeU")
## lm1.form was defined in Chapter 4
lm1.form <- formula(visual ~ -1 + visual0 + time.f + treat.f:time.f )
library(nlme)
###################################################
### code chunk: R8.1
###################################################
(val <- c("12wks" = 0.5, "24wks" = 2)) # delta1 = 1, delta2 = 0.5, delta3 = 2
(fix <- c("52wks" = 3)) # delta4 = 3 (fixed)
frm <- formula(~1|time.f) # time.f is a stratifying factor
(vf0 <-
varIdent(value = val, # Var. function object defined...
fixed = fix,
form = frm))
(vf0i <- Initialize(vf0, armd)) # ... and initialized
###################################################
### code chunk: R8.2a
###################################################
coef(vf0i, unconstrained = FALSE, allCoef = TRUE) # All delta coefs
coef(vf0i, unconstrained = FALSE, allCoef = FALSE)# Varying only
###################################################
### code chunk: R8.2b
###################################################
coef(vf0i, unconstrained = TRUE, allCoef = TRUE) # All delta* coefs
coef(vf0i, unconstrained = TRUE, allCoef = FALSE) # Varying (default)
coef(vf0i) <- c(-0.6, 0.7) # New coefs assigned
coef(vf0i, allCoef = TRUE) # All coefs printed
###################################################
### code chunk: R8.3
###################################################
summary(vf0i) # Summary
formula(vf0i) # Variance function formula
getCovariate(vf0i) # Variance covariate
getGroupsFormula(vf0i) # Formula for variance strata
length(stratum <- # Length of stratum indicator
getGroups(vf0i))
unique(stratum) # Unique strata
stratum[1:6] # First six observations
varWeights(vf0i)[3:6] # Variance weights 1/lambdai:(7.8)
logLik(vf0i) # Contribution to the log-likelihood
###### sessionInfo() with packages attached
sessionInfo()
detach(package:nlme)
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