Gavin, That worked! I went through and I found a few missing cases where I had "." instead of "NA" - I'm still in SAS mode.
Many thanks! **************************************** 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 **************************************** >>> Gavin Simpson <[EMAIL PROTECTED]> 10/13/06 11:23 AM >>> On Fri, 2006-10-13 at 09:28 -0500, Jeffrey Stratford wrote: > 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 Hi Jeff, using the snippet of data you provided (copy/paste into a text file and read in with read.table) worked fine: box.use <- read.table("~/tmp/tmp.txt", header = TRUE) box.use str(box.use) 'data.frame': 8 obs. of 10 variables: $ box : int 1 2 3 4 5 6 7 8 $ use : int 1 1 1 1 0 1 1 0 $ purbank : num 0.00381 0.04429 0.04459 0.06072 0.60810 ... $ purban2 : num 0.0268 0.1611 0.0604 0.2081 0.6980 ... $ purban1 : num 0.069 0.172 0.000 0.069 0.690 ... $ pgrassk : num 0.3282 0.1534 0.1628 0.0194 0.0317 ... $ pgrass2 : num 0.685 0.383 0.557 0.000 0.128 ... $ pgrass1 : num 0.759 0.655 0.759 0.000 0.241 ... $ grassdist : num 0 0 0 323 30 ... $ grasspatchk: num 3.730 1.023 0.961 0.228 0.263 ... Now I don't like attach, and you just don't need it so I deviate a little now. Replace box.use$use directly and make use of the data argument in glm. Also, your data didn't have any missing data so I'm not sure whether the response or predictor is missing and whether your na.omit is needed or not - I don't use it below. box.use$use <- factor(box.use$use, levels=0:1) levels(box.use$use) <- c("unused", "used") box.use str(box.use) glm1 <- glm(use ~ purbank, data = box.use, family = binomial()) summary(glm1) Call: glm(formula = use ~ purbank, family = binomial(), data = box.use) Deviance Residuals: Min 1Q Median 3Q Max -1.61450 -0.03098 0.31935 0.45888 1.39194 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 3.223 2.225 1.448 0.147 purbank -6.129 4.773 -1.284 0.199 (Dispersion parameter for binomial family taken to be 1) Null deviance: 8.9974 on 7 degrees of freedom Residual deviance: 6.5741 on 6 degrees of freedom AIC: 10.574 Number of Fisher Scoring iterations: 5 I suspect something got messed up in your reading of the data and R thought purbank was a factor or character. Always check your data after reading in, and str() is a your friend here as printed representations are not always what they seem. HTH G > > > 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@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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC & ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/cv/ London, UK. WC1E 6BT. [w] http://www.ucl.ac.uk/~ucfagls/ %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@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.
