Re: [R] strangeness in Predict() {rms}

Frank E Harrell Jr Wed, 17 Feb 2010 09:28:02 -0800

William Dunlap wrote:

Both plyr and rms contain an object called ".".
In plyr it is a "closure" (the common kind of
function) and in rms is is NA.  If plyr is attached
in front of rms then you get your problem with

Predict().

Bill Dunlap
Spotfire, TIBCO Software

wdunlap tibco.com

I think I should modify rms to not let this happen. Whenever an rmsfunction uses ... as an argument to pass this type of information I canchange list(...) to eval(substitute(list(...)), list(.=NA))

If anyone sees a better approach or a problem with this approach pleaselet me know.


Frank

-----Original Message-----
From: r-help-boun...@r-project.org[mailto:r-help-boun...@r-project.org] On Behalf Ofbill.venab...@csiro.au
Sent: Tuesday, February 16, 2010 4:21 PM
To: dylan.beaude...@gmail.com; r-help@r-project.org
Subject: Re: [R] strangeness in Predict() {rms}
This works without a glitch on my linux system (info below).You might try upgrading your R to 2.10.1, perhaps.
sessionInfo()
R version 2.10.1 (2009-12-14)x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8[5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C[9] LC_ADDRESS=C LC_TELEPHONE=C[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines grid stats graphics grDevices utilsdatasets[8] methods base
other attached packages:
[1] rms_2.1-0 plyr_0.1.9 Design_2.3-0 Hmisc_3.7-0[5] survival_2.35-9
loaded via a namespace (and not attached):
[1] ASOR_0.1 cluster_1.12.1 lattice_0.18-3 tcltk_2.10.1tools_2.10.1
Bill Venables
CSIRO/CMIS Cleveland Laboratories


-----Original Message-----
From: r-help-boun...@r-project.org[mailto:r-help-boun...@r-project.org] On Behalf Of Dylan Beaudette
Sent: Wednesday, 17 February 2010 10:05 AM
To: r-help@r-project.org
Subject: [R] strangeness in Predict() {rms}

Hi,
Running the following example from ?Predict() throws an errorI have neverseen before:
set.seed(1)
x1 <- runif(300)
x2 <- runif(300)
ddist <- datadist(x1,x2); options(datadist='ddist')
y  <- exp(x1+ x2 - 1 + rnorm(300))
f  <- ols(log(y) ~ pol(x1,2) + x2)
p1 <- Predict(f, x1=., conf.type='mean')
Error in paste(nmc[i], "=", if (is.numeric(x)) format(x) elsex, sep = "") :cannot coerce type 'closure' to vector of type 'character'
In addition: Warning message:
In is.na(v) : is.na() applied to non-(list or vector) of type'closure'
Here is the output from sessionInfo()
R version 2.9.0 (2009-04-17)i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
TE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=
en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
NT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grid splines stats graphics grDevices utilsdatasets[8] methods base
other attached packages:
[1] plyr_0.1.9 mgcv_1.5-5 RColorBrewer_1.0-2nlme_3.1-94[5] rms_2.1-0 Hmisc_3.7-0 survival_2.35-6lattice_0.17-25
loaded via a namespace (and not attached):
[1] cluster_1.12.0


Any ideas?
Thanks!

Dylan


--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341

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______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



--
Frank E Harrell Jr   Professor and Chairman        School of Medicine
                     Department of Biostatistics   Vanderbilt University

______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] strangeness in Predict() {rms}

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