On 05/28/2010 05:31 PM, Dylan Beaudette wrote:
On Friday 28 May 2010, Frank E Harrell Jr wrote:
On 05/28/2010 03:49 PM, Dylan Beaudette wrote:
Hi,
I have fit a model using the rms package with the Gls() function.
Is there a way to get the model estimates, std errors, and p-values (i.e.
what you get with print(fit)) into latex format?
I have tried:
f<- Gls(...)
latex(f, file='')
... but I get the following error
Error in replace.substring.wild(s, old, new, test = test, front = front,
: does not handle> 1 * in old
I think that this might have something to do with the fact that I fit the
model with GLS. (?)
Thanks for the quick reply Frank.
What is GLS? I thought you fit the model with Gls. And please follow
the posting guide instead of submitting only parts of lines of code.
Right, that would have been helpful. I didn't want to paste in the enormous
example from the Gls() manual page...
The latex method for a Gls object typesets the mathematical form of the
fitted model formula.
OK. That would have been nice too, but why did I get the above error message?
Lets recreate my data with an example:
# fake data
w<- rnorm(50)
x<- rnorm(50)
y<- rnorm(50)
z<- rnorm(50)
p<- runif(50)
g<- rep(c('a','b'), each=25)
# sprinkle in some NA
w[sample(1:50, 4)]<- NA
# fit data with similar correlation structure
f<- Gls(p ~ y * x * (z + w), na.action='na.omit', cor=corCAR1(form= ~ z | g))
# hmmm.... "Error in terms.default(f) : no terms component"
Thanks for the good example and sorry about the error. I've posted a
fix for Gls. Use the following to override the current version with the
fixed one:
source('http://biostat.mc.vanderbilt.edu/tmp/Gls.s')
I've also changed the default na.action to na.omit. For some reason
model.frame doesn't work with the output of the Hmisc package's more
comprehensive na.delete function when used with Gls.
latex(f, file='')
The attached packages are:
nlme_3.1-96 rms_3.0-0 Hmisc_3.8-0 survival_2.35-8
To get what you want:
w<- nlme:::summary.gls(f)$tTable
w
latex(w, ....)
Got it. Thanks-- this does exactly what I was looking for. I wonder if it
might be worth the effort to include a small snippet on this in the manual
pages...
done
Frank
Cheers,
Dylan
Frank
I am looking for a simple way to get a table of estimated coeficients
without hand-making a table in a text editor for inclusion within a LATEX
document.
Thanks!
--
Frank E Harrell Jr Professor and Chairman School of Medicine
Department of Biostatistics Vanderbilt University
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