[R] nlme splines model.frame.default error

[Jacob Wegelin]

I want to use a specialized function to compute knots on the fly to pass to splines::bs within a call to nlme::lme.

The specialized function will compute knots from the x-axis variable (the x argument in a call to splines::bs).

The syntax works with lm. But when I try it with lme, the following error is returned:

Error in model.frame.default(formula = ~why + eks + toydat + ID, data = list( :
   invalid type (list) for variable 'toydat'

Below is a simplified example showing the "desired syntax," which returns the error, and a workaround. I am mystified what inherently is wrong with the "desired syntax", since it works fine with stats::lm.

set.seed(5)
library(splines)
library(nlme)
NID<-5
toydat<-data.frame(eks=0:0:((2*NID)-1))
toydat$ID<-factor(rep(LETTERS[1:NID], each=2))
toydat
toydat$why<-with(toydat, as.integer(100*sin((eks / 7 * pi)^2) + rnorm(eks)/10))
customKnotsFn<-function(some)3.5
print(toydat)
print(summary(toydat))
print(customKnotsFn)

# lm has no trouble:

mylm<-lm(why~bs(eks,knots=customKnotsFn(some=toydat$eks)), data=toydat)
print(mylm$call)

#  The "desired syntax" returns an error:

lme(fixed=why~bs(eks,knots=customKnotsFn(some=toydat$eks)),random=~1|ID, data=toydat)

#  Removing the argument from customKnotsFn eliminates the error, but then customKnotsFn is useless for practical purposes:

lme(fixed=why~bs(eks,knots=customKnotsFn()),random=~1|ID, data=toydat)

#  Workaround returns no error:

mylme<- with(toydat, lme(fixed=why~bs(eks,knots=customKnotsFn(some=eks)),random=~1|ID))
print(mylme$call)

Of course, with the workaround the resulting mylme does not know where the data came from.

Why should a workaround be necessary? Is there something inherently misguided about the "desired syntax" (above)?

Thanks for any insight

Jacob Wegelin

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.7.5 (Lion)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] nlme_3.1-120

loaded via a namespace (and not attached):
[1] grid_3.1.3      lattice_0.20-30