[R] nontabular logistic regression

[Sundar Dorai-Raj]

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
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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