R version 3.2.2 Patched (2015-11-27 r69713) -- "Fire Safety" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## 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) Classes 'varIdent', 'varFunc' atomic [1:2] 0.0953 0.131 ..- attr(*, "groupNames")= chr [1:4] "8" "10" "14" "12" ..- attr(*, "fixed")= Named num 0.113 .. ..- attr(*, "names")= chr "12" ..- attr(*, "formula")=Class 'formula' length 2 ~1 | age .. .. ..- attr(*, ".Environment")= ..- 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 0.488 0.058 0.547