On 2015-06-02 Tue 14:20, Jacob Wegelin wrote:
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)
# Here is a perhaps slicker workaround:
mybs <-function(x, df) {
myknots<-customKnotsFn(x)
bs(x, knots=myknots)
}
lme(fixed=why~mybs(eks, df=2), random=~1|ID, data=toydat)
# But why cannot lme handle the "desired syntax"?
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