error in geom_smooth

[Elena]

Hi,

I've had a lot of trouble adding a smooth geom to my scatterplots.
I've searched through the ggplot2 archive for the answer, but unable
to find one, I thought I'd appeal to the infinite wisdom of the
ggplot2 listserv subscribers. I've already tried method = "gam" from
the mgcv library, which is meant for modelling large datasets. My code
is below.

Thanks in advance,
Elena

#first I took a subset of my data, encompassing 10,000 rows
> small <- Fig1A[sample(nrow(Fig1A), 10000),]
> b <- ggplot(data=small, aes(X.val, Y.val)) + scale_x_log10() + scale_y_log10() + geom_point()
> b
#this appears to work great, but then I run into a problem when I try
to add geom_smooth, as implemented on p. 15 of the ggplot2 book when
working with large dataframes
> b + geom_smooth(method = "gam", formula = y ~ s(x, bs = "cs"), se = TRUE, level = 0.99, alpha = 1, span =0.2)
Error in smooth.construct.cr.smooth.spec(object, data, knots) :
NA/NaN/Inf in foreign function call (arg 1)
#the default also doesn't work:
> b + geom_smooth()
Error in smooth.construct.cr.smooth.spec(object, data, knots) :
NA/NaN/Inf in foreign function call (arg 1)
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] foreign_0.8-43 arm_1.4-11 abind_1.3-0
[4] R2WinBUGS_2.1-18 coda_0.14-4 lme4_0.999375-39
[7] Matrix_0.999375-50 lattice_0.19-23 MASS_7.3-12
[10] Hmisc_3.8-3 survival_2.36-5 mgcv_1.7-5
[13] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4
[16] plyr_1.5.2

[Joshua Wiley]

What about precomputing the smooth and just using ggplot2 to draw the line?

Josh

> --
> You received this message because you are subscribed to the ggplot2 mailing list.
> Please provide a reproducible example: http://gist.github.com/270442
>
> To post: email ggp...@googlegroups.com
> To unsubscribe: email ggplot2+u...@googlegroups.com
> More options: http://groups.google.com/group/ggplot2
>

--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/

[Dennis Murphy]

Hi:

It's possible that you have a sparsity of data points in a certain
region (usually on one end or the other of the x-axis) that causes the
smoother to choke. A span of 0.2 may be a bit tight - the default in
loess() is 0.75, for example. You might try increasing the span to 0.3
or 0.4 to see if that helps - it will likely create a smoother curve
than the model with span 0.2.

Untested since no referent data was provided, so caveat emptor...

HTH,
Dennis

On Tue, Jun 7, 2011 at 3:19 PM, Elena <elena....@gmail.com> wrote:

[Joran]

I suspect Dennis may be right, but another thing to check is whether
you have NAs in your data and that you haven't set the NA action to
na.fail or something.