[R] interpreting the output of a glm with an ordered categorical predictor.

[kmuller]

Greetings.

I'm a Master's student working on an analysis of herbivore damage on plants.
I have a tried running a glm with one categorical predictor (aphid
abundance) and a binomial response (presence/absence of herbivore damage).
My predictor has four categories: high, medium, low, and none. I used the
"ordered" function to sort my categories for a glm.

ah <-
read.csv("http://depot.northwestern.edu/class/2012WI_PBC_435-0_AND_BIOL_SCI_313/muller/herbivoryEdit.csv")
ah1<- ah[ah$date=="110810",] 
ah2<-ah[ah$date=="110904",]

aphidOrder <- ordered(ah2$aphidLevelMax,levels=c("none", "low", "med",
"high"))

ordAph <- glm(chewholebinom~aphidOrder,family=binomial,data=ah2)


When I ran the summary for the glm (output pasted below), I could not tell
which intercept referred to which factor level. My question is, what do .L,
.Q, and .C mean and how can I relate these factors to my original factors
(none, low, med, high)?

Thank you for your help,

Katherine

summary(ordAph)

Call:
glm(formula = chewholebinom ~ aphidOrder, family = binomial, 
    data = ah2)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-1.6512  -0.9817   0.7687   0.7687   1.5353  

Coefficients:
             Estimate Std. Error z value Pr(>|z|)   
(Intercept)  -0.05567    0.25097  -0.222   0.8245   
aphidOrder.L -1.36755    0.49366  -2.770   0.0056 **
aphidOrder.Q  0.36824    0.50195   0.734   0.4632   
aphidOrder.C -0.09840    0.51011  -0.193   0.8470   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 137.99  on 99  degrees of freedom
Residual deviance: 124.05  on 96  degrees of freedom
AIC: 132.05

Number of Fisher Scoring iterations: 4





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