R Under development (unstable) (2023-11-03 r85470 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

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.

> ## test for models containing data-defined bases
> 
> ## ?makepredictcall
> ## ?model.frame
> ## ????
> 
> data(sleepstudy,package="lme4")
> library(splines)
> 
> ## lm0 <- lm(Reaction~ns(Days,2),sleepstudy)
> ## attr(terms(lm0),"predvars")
> ## library(nlme)
> ## lme1 <- lme(Reaction~ns(Days,2),random=~1|Subject,sleepstudy)
> ## attr(terms(lme1),"predvars")  ## no!
> ## attr(lme1$terms,"predvars")   ## yes
> ## detach("package:nlme")
> 
> library(lme4)
Loading required package: Matrix
> fm1 <- lmer(Reaction ~ ns(Days,2) + (1|Subject), sleepstudy)
> fm2 <- lmer(Reaction ~ poly(Days,2) + (1|Subject), sleepstudy)
> fm3 <- lmer(Reaction ~ poly(Days,2,raw=TRUE) + (1|Subject), sleepstudy)
> 
> newdat0 <- data.frame(Days = unique(sleepstudy$Days))
> newdat  <- data.frame(Days = 5:12)
> tmpf <- function(fit) {
+     with(sleepstudy, {
+         plot  (Reaction~Days, xlim=c(0,12))
+         points(Days, predict(fit), col=2)
+     })
+     lines(newdat0$ Days, predict(fit,ReForm=NA,newdata=newdat0), col=4)
+     lines(newdat $ Days, predict(fit,ReForm=NA,newdata=newdat ), col=5)
+ }
> 
> stopifnot(all.equal(predict(fm2,newdat,ReForm=NA),
+                     predict(fm3,newdat,ReForm=NA)))
Warning messages:
1: 'ReForm' is deprecated; use 're.form' instead 
2: 'ReForm' is deprecated; use 're.form' instead 
> 
> ## pictures
> tmpf(fm1)
Warning messages:
1: 'ReForm' is deprecated; use 're.form' instead 
2: 'ReForm' is deprecated; use 're.form' instead 
> tmpf(fm2)
Warning messages:
1: 'ReForm' is deprecated; use 're.form' instead 
2: 'ReForm' is deprecated; use 're.form' instead 
> tmpf(fm3)
Warning messages:
1: 'ReForm' is deprecated; use 're.form' instead 
2: 'ReForm' is deprecated; use 're.form' instead 
> 
> ## test for GLMMs
> set.seed(101)
> d <- data.frame(y=rbinom(10,size=1,prob=0.5),
+                 x=1:10,
+                 f=factor(rep(1:5,each=2)))
> gm1 <- glmer(y ~ poly(x,2) + (1|f), d, family=binomial)
> gm2 <- glmer(y ~ poly(x,2,raw=TRUE) + (1|f), d, family=binomial)
> 
> newdat <- data.frame(x=c(1,4,6))
> stopifnot(all.equal(predict(gm1,newdat,ReForm=NA),
+                     predict(gm2,newdat,ReForm=NA),tolerance=3e-6))
Warning messages:
1: 'ReForm' is deprecated; use 're.form' instead 
2: 'ReForm' is deprecated; use 're.form' instead 
> 
> 
> proc.time()
   user  system elapsed 
   1.53    0.14    1.65