Dear R-helpers,
I'm running Sweave() on a file. First run:
> Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
9 : echo term verbatim (label=efficiency)
10 : echo term verbatim (label=wear)
11 : echo term verbatim (label=wearX)
12 : echo term verbatim (label=gyd)
Loading required package: crossdes
Loading required package: AlgDesign
Loading required package: gtools
Attaching package: 'gtools'
The following object(s) are masked from package:faraway :
logit
Loading required package: MASS
13 : echo term verbatim (label=2wt)
14 : echo term verbatim (label=ablm)
15 : echo term verbatim (label=abaov)
You can now run LaTeX on '20080331.tex'
There were 42 warnings (use warnings() to see them)
Second run:
> Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
Error: chunk 8 (label=tukey)
Error in parse(text = x) :
unexpected symbol in "yield ~ variety + block + preds(yield+variety
+block+preds.sq)sq"
It failed in:
<<tukey>>=
require(alr3)
tukey.nonadd.test(ov.lm)
@
At that point I ran debug() on the call:
debug(tukey.nonadd.test)
tukey.nonadd.test(ov.lm)
debugging in: tukey.nonadd.test(ov.lm1)
debug: {
envir <- environment(formula(m))
dd <- eval(m$call$data, envir)
subs <- eval(m$call$subset, envir)
wgts <- eval(m$call$weights, envir)
naa <- m$call$na.action
dd <- data.frame(dd, preds.sq = predict(m, dd)^2)
uf <- update.formula(formula(m$terms), ~. + preds.sq)
environment(uf) <- environment(NULL)
mup <- if (is.null(naa))
lm(uf, data = dd, subset = subs, weights = wgts)
else lm(uf, data = dd, subset = subs, weights = wgts, na.action =
naa)
if (mup$rank > m$rank) {
ans <- summary(mup)$coef[, 3:4]
ans <- ans[match("preds.sq", rownames(ans)), ]
ans[2] <- pnorm(-abs(ans[1])) * 2
ans
}
else c(NA, NA)
}
Browse[1]>
debug: envir <- environment(formula(m))
Browse[1]>
debug: dd <- eval(m$call$data, envir)
Browse[1]>
debug: subs <- eval(m$call$subset, envir)
Browse[1]>
debug: wgts <- eval(m$call$weights, envir)
Browse[1]>
debug: naa <- m$call$na.action
Browse[1]>
debug: dd <- data.frame(dd, preds.sq = predict(m, dd)^2)
Browse[1]>
debug: uf <- update.formula(formula(m$terms), ~. + preds.sq)
Browse[1]>
debug: environment(uf) <- environment(NULL)
Browse[1]>
debug: mup <- if (is.null(naa)) lm(uf, data = dd, subset = subs,
weights = wgts) else lm(uf,
data = dd, subset = subs, weights = wgts, na.action = naa)
Browse[1]>
Error in parse(text = x) :
unexpected symbol in "yield ~ variety + preds(yield+variety
+preds.sq)sq"
Advice?
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels: Room 102 Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011 +1-434-982-4729
Lab: B019 +1-434-982-4751
Fax: +1-434-982-4766
WWW: http://www.people.virginia.edu/~mk9y/
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