
R Under development (unstable) (2017-11-28 r73785) -- "Unsuffered Consequences"
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> ## tests of fix for PR#9831
> library(nlme)
> val <- c("10"=1.10,"14"=1.14)
> vf <- varIdent(value=val, form=~1|age, fixed=c("12"=1.12))
> vfi <- Initialize(vf,Orthodont)
> vfi
Variance function structure of class varIdent representing
   8   10   14   12 
1.00 1.10 1.14 1.12 
> str(vfi)
 'varIdent' Named num [1:2] 0.0953 0.131
 - attr(*, "names")= chr [1:2] "10" "14"
 - attr(*, "groupNames")= chr [1:4] "8" "10" "14" "12"
 - attr(*, "fixed")= Named num 0.113
  ..- attr(*, "names")= chr "12"
 - attr(*, "formula")=Class 'formula'  language ~1 | age
  .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv> 
 - attr(*, "groups")= chr [1:108] "8" "10" "12" "14" ...
 - attr(*, "whichFix")= logi [1:3] FALSE FALSE TRUE
 - attr(*, "weights")= Named num [1:108] 1 0.909 0.893 0.877 1 ...
  ..- attr(*, "names")= chr [1:108] "8" "10" "12" "14" ...
 - attr(*, "logLik")= num -9.17
> stopifnot(
+     all.equal(coef(vfi), c(0.0953101798043, 0.131028262406)),
+     all.equal(coef(vfi, unconstrained = FALSE, allCoef = TRUE),
+               c("8" = 1, "10" = 1.1, "14" = 1.14, "12" = 1.12)))
> 
> vfiCopy <- vfi        # copy of an initialized object
> length(vfiCopy)             # length is 2
[1] 2
> coef(vfiCopy) <- c(11,12)   # error in 3.1-84
> stopifnot(identical(coef(vfiCopy), c(11,12)))
> 
> ## error in 3.1-84
> (gls. <- gls(distance ~ age, weights = vfi, data=Orthodont))
Generalized least squares fit by REML
  Model: distance ~ age 
  Data: Orthodont 
  Log-restricted-likelihood: -253.4207

Coefficients:
(Intercept)         age 
  16.746600    0.659796 

Variance function:
 Structure: Different standard deviations per stratum
 Formula: ~1 | age 
 Parameter estimates:
       8       10       14       12 
1.000000 0.872009 1.121849 1.120000 
Degrees of freedom: 108 total; 106 residual
Residual standard error: 2.453257 
> 
> proc.time()
   user  system elapsed 
  0.246   0.040   0.272 
