[R] Syntax for fit.contrast

David Winsemius dwinsemius at comcast.net
Sun Oct 22 19:20:48 CEST 2017


> On Oct 22, 2017, at 6:04 AM, Sorkin, John <jsorkin at som.umaryland.edu> wrote:
> 
> I have a model (run with glm) that has a factor, type. Type has two levels, "general" and "regional". I am trying to get estimates (and SEs) for the model with type="general" and type ="regional" using fit.contrast

 ?fit.contrast
No documentation for ‘fit.contrast’ in specified packages and libraries:
you could try ‘??fit.contrast’

Perhaps the gmodels function of that name?

> but I can't get the syntax of the coefficients to use in fit.contrast correct. I hope someone can show me how to use fit.contrast, or some other method to get estimate with SEs. (I know I can use the variance co-variance matrix, but I would rather not have to code the linear contrast my self from the coefficients of the matrix)
> 

I'm having trouble understanding what you are trying to extract. There are only 2 levels so there is really only one interesting contrast ("general" vs "regional") , and it's magnitude would be reported by just typing `model`, and it's SE would show up in output of `summary(model)`.

I'm thinking you should pick one of the examples in gmodels::fit.contrast that most resembles your real problem,  post it,  and  and then explain what difficulties you are having with interpretation.

-- 
David.


> Thank  you,
> 
> John
> 
> 
> My model:
> 
> model=glm(events~type,family=poisson(link=log),offset=log(SS),data=data)
> 
> 
> Model details:
> 
>> summary(data$type)
> 
> general regional
>      16       16
> 
>> levels(data$type)
> [1] "general"  "regional"
> 
>> contrasts(data$type)
>         regional
> general         0
> regional        1
> 
> 
> I have tried the following syntax for fit.contrast
> 
> fit.contrast(model,type,c(1,0))
> and get an error:
> Error in `[[<-`(`*tmp*`, varname, value = cmat) :
>  no such index at level 1
> 
> 
>> fit.contrast(model,type,c(0,1),showall=TRUE)
> and get an error:
> Error in `[[<-`(`*tmp*`, varname, value = cmat) :
>  no such index at level 1
> 
> 
> 
>> fit.contrast(model,type,c(1,-1),showall=TRUE)
> and get an error:
> Error in `[[<-`(`*tmp*`, varname, value = cmat) :
>  no such index at level 1
> 
> 
>> fit.contrast(model,type,c(0))
> and get an error:
> Error in make.contrasts(coeff, ncol(coeff)) :
>  Too many contrasts specified. Must be less than the number of factor levels (columns).
> 
>> fit.contrast(model,type,c(1))
> Error in make.contrasts(coeff, ncol(coeff)) :
> and get an error
>  Too many contrasts specified. Must be less than the number of factor levels (columns).
> 
> 
> 
> 
> 
> 
> 
> 
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> 
> 
> 	[[alternative HTML version deleted]]
> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law



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