[R] interpreting GLM results and plotting fits

[Ista Zahn]

Hi Robert,

On Sun, Jun 30, 2013 at 1:40 AM, Robert Lynch <robert.b.lynch at gmail.com> wrote:
> I am trying to interpret the output of GLM and I am not sure how it is
> treating the factor GENDER with levels G-M and G-F.

Probably using dummy codes (or "treatment contrasts" as useRs refer to
them) unless you've changed the defaults. See

getOption("contrasts")
contr.treatment
contrasts(master1$Gender)

>
> Below is the output of summary(GPA.lm)
>
>
> Call:
> glm(formula = zGPA ~ Units.Bfr.7A * GENDER, data = Master1)
>
> Deviance Residuals:
>     Min       1Q   Median       3Q      Max
> -1.1432  -0.3285  -0.1061   0.2283   1.8286
>
> Coefficients:
>                          Estimate Std. Error t value Pr(>|t|)
> (Intercept)            -2.513e-01  2.238e-02 -11.230  < 2e-16 ***
> Units.Bfr.7A            2.297e-05  2.851e-04   0.081    0.936
> GENDERG-M               3.183e-01  4.536e-02   7.018 2.56e-12 ***
> Units.Bfr.7A:GENDERG-M -3.073e-03  5.975e-04  -5.142 2.82e-07 ***
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> (Dispersion parameter for gaussian family taken to be 0.2432662)
>
>     Null deviance: 1204.2  on 4875  degrees of freedom
> Residual deviance: 1185.2  on 4872  degrees of freedom
>   (106 observations deleted due to missingness)
> AIC: 6950.8
>
> Number of Fisher Scoring iterations: 2
>
>
>
> second I would like to draw two lines w/ confidince intervals on the
> scatter plot.  One for G-M and the other for G-F
>
> I think I am doing this with
> stat_smooth(aes(group=GENDER), method="glm", fullrange=TRUE)
>  but again am not sure quite what is being outputted.

I think this runs separate regressions for each level of group. That's
probably not quite what you want, though it may be close enough. A
better option would be to calculate predicted values and standard
errors from the model. You can do this several ways; here are two of
them:

## Option 1: create a data.frame containing the x values for which you
want predictions, and calculate predicted falues using predict()
m1PredData <- expand.grid(GENDER=levels(Master1$GENDER),
                          Units.Bfr.7A = with(Master1, {
                              seq(min(Units.Bfr.7A),
                                  max(Units.Bfr.7A),
                                  by=1)
                          }))

m1PredData <- cbind(m1PredData,
                    predict(GPA.lm,
                            se.fit=TRUE,
                            newdata=m1PredData))

## Option 2: Use the effects package:

library(effects)
m1Effects <- effect("Units.Bfr.7A:GENDER", GPA.lm, se=TRUE)
plot(m1Effects)


Hope this helps,

Ista
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