Re: [R] nontabular logistic regression

From: Sundar Dorai-Raj <sundar.dorai-raj_at_pdf.com>
Date: Fri 13 Oct 2006 - 15:28:27 GMT

Jeffrey Stratford said the following on 10/13/2006 9:28 AM:
> Hi. I'm attempting to fit a logistic/binomial model so I can determine
> the influence of landscape on the probability that a box gets used by a
> bird. I've looked at a few sources (MASS text, Dalgaard, Fox and
> google) and the examples are almost always based on tabular predictor
> variables. My data, however are not. I'm not sure if that is the
> source of the problems or not because the one example that includes a
> continuous predictor looks to be coded exactly the same way. Looking at
> the output, I get estimates for each case when I should get a single
> estimate for purbank. Any suggestions?
>
> Many thanks,
>
> Jeff
>
>
> THE DATA: (200 boxes total, used [0 if unoccupied, 1 occupied], the rest
> are landscape variables).
>
> box use purbank purban2 purban1 pgrassk pgrass2 pgrass1 grassdist grasspatchk
> 1 1 0.003813435 0.02684564 0.06896552 0.3282487 0.6845638 0.7586207 0 3.73
> 2 1 0.04429451 0.1610738 0.1724138 0.1534174 0.3825503 0.6551724 0 1.023261
> 3 1 0.04458785 0.06040268 0 0.1628043 0.557047 0.7586207 0 0.9605769
> 4 1 0.06072162 0.2080537 0.06896552 0.01936052 0 0 323.1099 0.2284615
> 5 0 0.6080962 0.6979866 0.6896552 0.03168084 0.1275168 0.2413793 30 0.2627027
> 6 1 0.6060428 0.6107383 0.3448276 0.04077442 0.2885906 0.4482759 30 0.2978571
> 7 1 0.3807568 0.4362416 0.6896552 0.06864183 0.03355705 0 94.86833 0.468
> 8 0 0.3649164 0.3154362 0.4137931 0.06277501 0.1275168 0 120 0.4585714
>
> THE CODE:
>
> box.use<- read.csv("c:\\eabl\\2004\\use_logistic2.csv", header=TRUE)
> attach(box.use)
> box.use <- na.omit(box.use)
> use <- factor(use, levels=0:1)
> levels(use) <- c("unused", "used")
> glm1 <- glm(use ~ purbank, binomial)
>
> THE OUTPUT:
>
> Coefficients:
> Estimate Std. Error z value Pr(>|z|)
> (Intercept) -4.544e-16 1.414e+00 -3.21e-16 1.000
> purbank0 2.157e+01 2.923e+04 0.001 0.999
> purbank0.001173365 2.157e+01 2.067e+04 0.001 0.999
> purbank0.001466706 2.157e+01 2.923e+04 0.001 0.999
> purbank0.001760047 6.429e-16 2.000e+00 3.21e-16 1.000
> purbank0.002346729 2.157e+01 2.923e+04 0.001 0.999
> purbank0.003813435 2.157e+01 2.923e+04 0.001 0.999
> purbank0.004106776 2.157e+01 2.067e+04 0.001 0.999
> purbank0.004693458 2.157e+01 2.067e+04 0.001 0.999
>
>
> ****************************************
> Jeffrey A. Stratford, Ph.D.
> Postdoctoral Associate
> 331 Funchess Hall
> Department of Biological Sciences
> Auburn University
> Auburn, AL 36849
> 334-329-9198
> FAX 334-844-9234
> http://www.auburn.edu/~stratja
>
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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.

That's not what I get:

lines <-
"box,use,purbank,purban2,purban1,pgrassk,pgrass2,pgrass1,grassdist,grasspatchk

1,1,0.003813435,0.02684564,0.06896552,0.3282487,0.6845638,0.7586207,0,3.73
2,1,0.04429451,0.1610738,0.1724138,0.1534174,0.3825503,0.6551724,0,1.023261
3,1,0.04458785,0.06040268,0,0.1628043,0.557047,0.7586207,0,0.9605769
4,1,0.06072162,0.2080537,0.06896552,0.01936052,0,0,323.1099,0.2284615
5,0,0.6080962,0.6979866,0.6896552,0.03168084,0.1275168,0.2413793,30,0.2627027
6,1,0.6060428,0.6107383,0.3448276,0.04077442,0.2885906,0.4482759,30,0.2978571
7,1,0.3807568,0.4362416,0.6896552,0.06864183,0.03355705,0,94.86833,0.468
8,0,0.3649164,0.3154362,0.4137931,0.06277501,0.1275168,0,120,0.4585714"
box.use <- read.csv(textConnection(lines))

box.use <- na.omit(box.use)
box.use$use <- factor(box.use$use, levels=0:1) levels(box.use$use) <- c("unused", "used") (glm1 <- glm(use ~ purbank, binomial, box.use))

You need to check why purbank is being interpreted as a factor in your code.

Also, I removed your use of "attach" because I find it dangerous (especially with no detach). Better to be explicit.

HTH, --sundar



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