[R] latex.rms and models fit with Gls
Frank E Harrell Jr
f.harrell at Vanderbilt.Edu
Sat May 29 05:06:33 CEST 2010
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:
>>> 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
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
>> 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
>>> 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
Frank E Harrell Jr Professor and Chairman School of Medicine
Department of Biostatistics Vanderbilt University
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