Frank E Harrell Jr wrote:
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 rms
function uses ... as an argument to pass this type of information I can
change list(...) to eval(substitute(list(...)), list(.=NA))
If anyone sees a better approach or a problem with this approach please
let me know.
Frank
On second thought I think I will change rms to not require . I will use
this construct for Predict, summary, nomogram:
Predict(fit, age, sex='male') -> default range for age, males
Predict(fit, age=c(10,20,30), sex) -> 3 ages x 2 sexes
I found a way to process the ... arguments without evaluating them, so
that the name of a predictor without a value can trigger the use of the
default values for that variable. I hope to have a new version out
within 2 weeks. The current . (if plyr is not in effect) or NA methods
will still work but will not be recommended.
Note that the workaround to the plyr conflict for now is to use NA in
place of .
Frank
-----Original Message-----
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of
bill.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 utils
datasets [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_2.10.1
tools_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 error I have
never seen 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) else x, 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 utils
datasets [8] methods base
other attached packages:
[1] plyr_0.1.9 mgcv_1.5-5 RColorBrewer_1.0-2
nlme_3.1-94 [5] rms_2.1-0 Hmisc_3.7-0
survival_2.35-6 lattice_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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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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
