Dear all,
predict.lme() throws an error when the fixed part consists of only an intercept
and using newdata. See the reproducible example below. I've tracked the error
down to asOneFormula() which returns in this case NULL instead of a formula.
Changing NULL instead of ~1 in that function (see below) solves the problem in
the case of an intercept only model (m1). It does not solve the problem in case
of a model without intercept nor covariates (m2). The package with altered
asOneFormula() passes R CMD check on my machine.
Best regards,
Thierry Onkelinx
library(nlme)
data(Orthodont)
m0 <- lme(distance ~ Sex, random = ~1|Subject, data = Orthodont)
m1 <- lme(distance ~ 1, random = ~1|Subject, data = Orthodont)
m2 <- lme(distance ~ 0, random = ~1|Subject, data = Orthodont)
test.data <- Orthodont
test.data$Fitted <- predict(m0, level = 0)
test.data$Fitted.Newdata <- predict(m0, level = 0, newdata = test.data)
sum(abs(test.data$Fitted - test.data$Fitted.Newdata))
test.data$Fitted <- predict(m0, level = 1)
test.data$Fitted.Newdata <- predict(m0, level = 1, newdata = test.data)
sum(abs(test.data$Fitted - test.data$Fitted.Newdata))
test.data$Fitted <- predict(m1, level = 0)
test.data$Fitted.Newdata <- predict(m1, level = 0, newdata = test.data)
sum(abs(test.data$Fitted - test.data$Fitted.Newdata))
test.data$Fitted <- predict(m1, level = 1)
test.data$Fitted.Newdata <- predict(m1, level = 1, newdata = test.data)
sum(abs(test.data$Fitted - test.data$Fitted.Newdata))
test.data$Fitted <- predict(m2, level = 0)
test.data$Fitted.Newdata <- predict(m2, level = 0, newdata = test.data)
sum(abs(test.data$Fitted - test.data$Fitted.Newdata))
test.data$Fitted <- predict(m2, level = 1)
test.data$Fitted.Newdata <- predict(m2, level = 1, newdata = test.data)
sum(abs(test.data$Fitted - test.data$Fitted.Newdata))
#new version
asOneFormula <-
## Constructs a linear formula with all the variables used in a
## list of formulas, except for the names in omit
function(..., omit = c(".", "pi"))
{
names <- unique(allVarsRec((list(...))))
names <- names[is.na(match(names, omit))]
if (length(names)) {
eval(parse(text = paste("~", paste(names, collapse = "+")))[[1]])
} else {
~ 1 #this was NULL
}
}
sessionInfo()
R Under development (unstable) (2013-08-24 r63687)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Dutch_Belgium.1252 LC_CTYPE=Dutch_Belgium.1252
[3] LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Belgium.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] grid_3.1.0 lattice_0.20-15 tools_3.1.0
* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
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