# [R] Can't find all levels of categorical predictors in output of zeroinfl()

Petr PIKAL petr.pikal at precheza.cz
Mon Mar 5 08:48:28 CET 2012

```Hi

Far from being an expert in this field I assume the answer is that it is
included in intercept term. It has something to do with contrasts
specification, but its usage is above my modelling knowledge.

You could try to see what

?contrasts

tells you.

Regards
Petr

you can
>
> Hello,
> I’m using zero-inflated Poisson regression via the zeroinfl() function
to
> analyze data on seed-set of plants, but for some reason, I don’t seem to
be
> getting the output for all three levels of my two categorical
predictors.
>
> More about my data and model:
> My response variable is the number of viable seeds (AVInt), and my two
> categorical predictors are elevation (Elev) and Treatment (Treatment).
Elev
> has three levels: 01-Low, 02-Mid, and 03-High; Treatment also has three
> possibilities: B, F, or O.
>
> Because the response variable (AVInt) is zero-inflated and
> Poisson-distributed, I’m using zeroinfl() under the pcsl library as an
> alternative to factorial ANOVA (I’ve also tried the zero-inflated
negative
> binomial).  This is early in my data-analysis, but I will likely
incorporate
> additional categorical and continuous predictors at a later time.
>
> This gives me the following model:
>
> zipclay=zeroinfl(AVInt ~ Elev + Treatment)
>
> So running the model, I have:
> > zipclay=zeroinfl(AVInt ~ Elev + Treatment)
> > summary(zipclay)
>
> Call:
> zeroinfl(formula = AVInt ~ Elev + Treatment)
>
> Pearson residuals:
>     Min      1Q  Median      3Q     Max
> -1.1958 -0.5612 -0.3764  0.2704  5.5130
>
> Count model coefficients (poisson with log link):
>             Estimate Std. Error z value Pr(>|z|)
> (Intercept)  -0.2035     0.3435  -0.592  0.55368
> Elev02-Mid    0.3937     0.1806   2.180  0.02923 *
> Elev03-High   0.1635     0.1792   0.912  0.36159
> TreatmentF    1.0026     0.3305   3.033  0.00242 **
> TreatmentO    0.5915     0.3293   1.796  0.07244 .
>
> Zero-inflation model coefficients (binomial with logit link):
>             Estimate Std. Error z value Pr(>|z|)
> (Intercept)   1.6086     0.5080   3.167  0.00154 **
> Elev02-Mid   -0.3813     0.4345  -0.878  0.38020
> Elev03-High  -0.9512     0.4532  -2.099  0.03584 *
> TreatmentF   -0.9774     0.4690  -2.084  0.03718 *
> TreatmentO   -3.0242     0.6561  -4.609 4.05e-06 ***
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
> Number of iterations in BFGS optimization: 16
> Log-likelihood: -363.2 on 10 Df
>
> So my question is, where did my "Elev01-Low" and "TreatmentB" go??  Why
> aren't they appearing in the output table?
>
> Any insight would be greatly appreciated!
>
> - Jason
>
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Can-t-find-
>
all-levels-of-categorical-predictors-in-output-of-zeroinfl-tp4444214p4444214.html
> Sent from the R help mailing list archive at Nabble.com.
>
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