R help - Mar 2016 - Logistic Regression output baseline (reference) category

Hi,
   I am trying to use the summary from the glm function as a data source. I
am using the call sink(<some file>) then
summary(logisticRegModel)$coefficients then sink().  The independent
variables are categorical and thus there is always a baseline value for
every category that is omitted from the glm output.  I am interested in how
to get the Z column for all of the categorical values.  I don't see any row
for the reference category.  How can I get this Z value in the output?

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The reference category is aliased with the constant term in the
default contr.treatment contrasts.

See ?contr.treatment , ?C, ?contrasts

If you don't know what this means, you should probably consult a local
statistical resource or ask about linear model contrasts at a
statistical help website like stats.stackexchange.com. This list is
for R programming questions.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Mar 15, 2016 at 1:27 PM, Michael Artz <michaeleartz at gmail.com>
wrote:
> Hi,
>    I am trying to use the summary from the glm function as a data source. I
> am using the call sink(<some file>) then
> summary(logisticRegModel)$coefficients then sink().  The independent
> variables are categorical and thus there is always a baseline value for
> every category that is omitted from the glm output.  I am interested in how
> to get the Z column for all of the categorical values.  I don't see any
row
> for the reference category.  How can I get this Z value in the output?
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

> On Mar 15, 2016, at 1:27 PM, Michael Artz <michaeleartz at gmail.com>
wrote:
> 
> Hi,
>   I am trying to use the summary from the glm function as a data source. I
> am using the call sink(<some file>) then
> summary(logisticRegModel)$coefficients then sink().
Since it's a matrix you may need to locate a function that write matrices to
files. I seem to remember that the MASS package has one.
>  The independent
> variables are categorical and thus there is always a baseline value for
> every category that is omitted from the glm output.
Well, it's not really omitted, so much as shared among all variables. For
further reading in the halp pages consult:

?model.matrix
?contrasts
?contr.treatment

But you probably need to supplement that with an introductory text that covers R
regression defaults.
>  I am interested in how
> to get the Z column for all of the categorical values.
The Z column? You meant the "z value" column. Again, since it's a
matrix you need to use column indexing with "["

summary(logisticRegModel)$coefficients[  , "z value"]

Read up on the summary function for glm objects at:

?summary.glm

>  I don't see any row
> for the reference category.
What do you imagine the (Intercept) row to be doing? If you are having
difficulty understanding this (which is not really an R-specific issue) there
are probably already several explanations to similar questions on:

http://stats.stackexchange.com/

 
> 
> How can I get this Z value in the output?
Asked and answered.
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
David Winsemius
Alameda, CA, USA

Hi,
  I have now read an introductory text on regression and I think I do
understand what the intercept is doing.  However, my original question is
still unanswered.  I understand that the intercept term is the constant
that each other term is measured against.  I think baseline is a good word
for it.  However, it does not represent any one of the x variables by
itself.  Is there a way in R, to extrapolate the individual x variable
intercepts from the equation somehow.


On Tue, Mar 15, 2016 at 8:26 PM, David Winsemius <dwinsemius at
comcast.net>
wrote:
>
> > On Mar 15, 2016, at 1:27 PM, Michael Artz <michaeleartz at
gmail.com>
> wrote:
> >
> > Hi,
> >   I am trying to use the summary from the glm function as a data
source.
> I
> > am using the call sink(<some file>) then
> > summary(logisticRegModel)$coefficients then sink().
>
> Since it's a matrix you may need to locate a function that write
matrices
> to files. I seem to remember that the MASS package has one.
>
> >  The independent
> > variables are categorical and thus there is always a baseline value
for
> > every category that is omitted from the glm output.
>
> Well, it's not really omitted, so much as shared among all variables.
For
> further reading in the halp pages consult:
>
> ?model.matrix
> ?contrasts
> ?contr.treatment
>
> But you probably need to supplement that with an introductory text that
> covers R regression defaults.
>
> >  I am interested in how
> > to get the Z column for all of the categorical values.
>
> The Z column? You meant the "z value" column. Again, since
it's a matrix
> you need to use column indexing with "["
>
> summary(logisticRegModel)$coefficients[  , "z value"]
>
> Read up on the summary function for glm objects at:
>
> ?summary.glm
>
>
> >  I don't see any row
> > for the reference category.
>
> What do you imagine the (Intercept) row to be doing? If you are having
> difficulty understanding this (which is not really an R-specific issue)
> there are probably already several explanations to similar questions on:
>
> http://stats.stackexchange.com/
>
>
> >
> > How can I get this Z value in the output?
>
> Asked and answered.
>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
> David Winsemius
> Alameda, CA, USA
>
>
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