>>>>> David Winsemius <dwinsemius at comcast.net>
>>>>> on Thu, 3 Sep 2009 22:34:05 -0400 writes:
> I'm having difficulties with plot.locfit.3d, at least I think that
is
> the problem. I have a large dataframe (about 4 MM cases) and was
> hoping to see a non-parametric estimate of the hazard plotted against
> two variables:
>> fit <- locfit(~surv.yr+ ur_protein + ur_creatinine, data=TRdta,
> cens = 1-death, family = "hazard", xlim=c(0,10))
> # it took somewhere between 1 and 2 hours to complete, but it did
> complete and reported no errors or warnings.
>> plot(fit, pv=c("ur_protein", "ur_creatinine"))
> Error in if (from == to) rep.int(from, length.out) else
> as.vector(c(from, :
> missing value where TRUE/FALSE needed
well, either 'from' or 'to' will be NaN or NA ..
[probably because some part of the locfit code was not written
with so many observations in mind .. ]
Why don't you repeat the plot() call
*after* saying
options(error=recover)
and then inspect 'from' and 'to' ?
maybe also
debug(plot.locfit.3d)
plot(.........)
and evaluate stepwisely,
using
ls.str()
to quickly get a picture of the function's local variables?
>> plot(fit, type="persp")
> Error in if (from == to) rep.int(from, length.out) else
> as.vector(c(from, :
> missing value where TRUE/FALSE needed
>> plot(fit, pv=c("ur_protein", "ur_creatinine"),
type="persp",
> xlim=c(0,400), ylim=c(0,400))
> Error in if (from == to) rep.int(from, length.out) else
> as.vector(c(from, :
> missing value where TRUE/FALSE needed
> I am guessing this may be a missing parameter needed by persp() but I
> cannot figure out what to offer.
well, it should give a better error message, if it really needs
another argument .
A reproducible example *would* be very useful here, indeed,
I see you tried .. but still.
Hoping the above helps,
Martin Maechler, ETH Zurich
> My efforts to construct a minimal example are also hitting a dead end:
> # From first of Harrell's cph() examples
>> n <- 1000
>> set.seed(731)
>> age <- 50 + 12*rnorm(n)
>> label(age) <- "Age"
>> sex <- factor(sample(c('Male','Female'), n,
> + rep=TRUE, prob=c(.6, .4)))
>> cens <- 15*runif(n)
>> h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
>> dt <- -log(runif(n))/h
>> label(dt) <- 'Follow-up Time'
>> e <- ifelse(dt <= cens,1,0)
>> dt <- pmin(dt, cens)
>> cfit <- locfit( ~ dt + age + sex, cens=cens, family =
"hazard",
> xlim=c(0, max(dt)) )
> Error in lfproc(x, y, weights = weights, cens = e, base = base, geth =
> geth, :
> NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning message:
> In lfproc(x, y, weights = weights, cens = cens, base = base, geth =
> geth, :
> NAs introduced by coercion
> Running the example on the locfit help page works fine, .... just
> like Loader's book, which I have been trying to follow in chapter
7.
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
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