R help - May 2011 - Relevel() catagorical variables in a GLM

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



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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 <aknight at csumb.edu>
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.
>
> ______________________________________________
> R-help at r-project.org mailing list
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> 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/