Thanks Josh,

This makes sense. The coefficient of one parameter is given in reference to
another parameter. (Aha! The "reference" parameter.)

I'm still a little confused on the standard errors (SEs) and why they change
too? Should I change the reference around until I find the best-looking SEs?
Somehow that doesn't seem right...

 I am trying to eventually make statements like:
"Fish A showed a weak, yet positive, response to HS and the low SE gives us
confidence in this association"
"Fish A showed a weak negative response to SH and the low SE gives us
confidence in this association (though less confidence than for HS)"
"Fish A showed a strong negative response to SS, however the SE is very high
so we cannot say this with high certainty"

Do these sound like an accurate reflection of what the output is saying? (I
know that "low SE" is arguable but...)

So then the SE for HH 923.60 (2nd run) or 0.2781 (1st run)?

Thank you!
Ashley


On Sat, May 28, 2011 at 11:49 PM, Joshua Wiley-2 [via R] <
ml-node+3558477-671379230-241127@n4.nabble.com> wrote:

> Hi Ashley,
>
> It does not look like you have done the wrong thing to me.  The
> results will be different because eacho f the parameter estimates is
> now the change from SS to ___ instead of from HH to ____.  In fact,
> from your first table, you can calculate all the parameters in the
> second.  The intercept for SS as reference is:
>
> (-5.2671) + (-18.2990) = -23.5661
>
> the difference between SH and SS is:
> > (-0.5736) - (-18.2990)
> [1] 17.7254
>
> which is now the parameter estimate for SH in the SS as reference
> model.  You could go on in like fashion for the rest.
>
> HTH,
>
> Josh
>
> On Sat, May 28, 2011 at 4:27 PM, ashley <[hidden email]<http://user/SendEmail.jtp?type=node&node=3558477&i=0>>
> wrote:
>
> > Hello list readers,
> >
> > I am running a set of GLMs on fish spp presence/absence as a function of
> > various habitat characteristics. My response is binomial and I have four
> > predictors, three of which are categorical.
> >
> > So, R takes one of my predictor-variables away to use as the intercept
> (the
> > first one alphabetically). However, I want to know the coefficient and SE
> of
> > this predictor. I tried relevel() and reran the model. Abbreviated
> summary()
> > results for each run are below. The results seem drastically different.
> Have
> > I done the wrong thing?
> >
> > (Below is a result from the model with only one predictor, to save space
> and
> > hassle.)
> >
> > Thanks,
> > Ashley
> >
> > #Default reference level = HH:
> >
> >                                 Estimate Std. Error z value Pr(>|z|)
> > (Intercept)                     -5.2671     0.2781 -18.942   <2e-16 ***
> > raw.table$SubsComboHS    0.8127     0.6438   1.262    0.207
> > raw.table$SubsComboSH  -0.5736     1.0393  -0.552    0.581
> > raw.table$SubsComboSS -18.2990   923.6023  -0.020    0.984
> >
> > #Command used to change reference level:
> >> raw.table$SubsCombo<-relevel(raw.table$SubsCombo, ref="SS")
> >
> > #New reference level = SS:
> >
> >                                   Estimate Std. Error z value Pr(>|z|)
> > (Intercept)                     -23.57     923.60  -0.026    0.980
> > raw.table$SubsComboHH    18.30     923.60   0.020    0.984
> > raw.table$SubsComboHS    19.11     923.60   0.021    0.983
> > raw.table$SubsComboSH    17.73     923.60   0.019    0.985
> >
> >
> >
> > --
> > View this message in context:
> http://r.789695.n4.nabble.com/Relevel-catagorical-variables-in-a-GLM-tp3558181p3558181.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > ______________________________________________
> > [hidden email] <http://user/SendEmail.jtp?type=node&node=3558477&i=1>mailing list
> > 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.
> >
>
>
>
> --
> Joshua Wiley
> Ph.D. Student, Health Psychology
> University of California, Los Angeles
> http://www.joshuawiley.com/
>
> ______________________________________________
> [hidden email] <http://user/SendEmail.jtp?type=node&node=3558477&i=2>mailing list
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>
>
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-- 
**Please note new extension
_____________________________________________

Ashley Knight
Rote Program Assistant
Research Assistant
Institute for Applied Marine Ecology, CSU Monterey Bay
Chapman Science Academic Center (Bldg 53)
100 Campus Center, Seaside, CA 93950

(831) 582-4522
aknight@csumb.edu
http://sep.csumb.edu/ifame
_____________________________________________


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