Hi. I'm trying to plot the ratio of used versus unused bird houses (coded 1 or 0) versus a continuous environmental gradient (proportion of urban cover [purban2]) that I would like to convert into bins (0 - 0.25, 0.26 - 0.5, 0.51 - 0.75, 0.76 - 1.0) and I'm not having much luck figuring this out. I ran a logistic regression and purban2 ends up driving the probability of a box being occupied so it would be nice to show this relationship. I'm also plotting the fitted values vs. purban2 but that's done. Any suggestions would be appreciated. Many thanks, Jeff Data sample: box use purbank purban2 1 1 0.003813435 0.02684564 2 1 0.04429451 0.1610738 3 1 0.04458785 0.06040268 4 1 0.06072162 0.2080537 5 0 0.6080962 0.6979866 6 1 0.6060428 0.6107383 7 1 0.3807568 0.4362416 8 0 0.3649164 0.3154362 9 0 0.3505427 0.2483221 10 0 0.3476093 0.1409396 11 0 0.3719566 0.3020134 12 1 0.09238011 0.1342282 13 0 0.08616111 0.1073826 14 0 0.07388724 0.04026845 15 1 0.07046477 0.03355705 . . . **************************************** 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 auburn.edu/~stratja
Jeffrey Stratford <stratja <at> auburn.edu> writes:> > I'm trying to plot the ratio of used versus unused bird houses > (coded 1 or 0) versus a continuous environmental gradient (proportion of > urban cover [purban2]) that I would like to convert into bins (0 - > 0.25, 0.26 - 0.5, 0.51 - 0.75, 0.76 - 1.0) and I'm not having much luck > figuring this out. I ran a logistic regression and purban2 ends up > driving the probability of a box being occupied so it would be nice to > show this relationship. I'm also plotting the fitted values vs. purban2 > but that's done.Check the example under predict.glm. It does not use binning, though. --- Code below added because gmane complains about too much quoted text. ## example from Venables and Ripley (2002, pp. 190-2.) ldose <- rep(0:5, 2) numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16) sex <- factor(rep(c("M", "F"), c(6, 6))) SF <- cbind(numdead, numalive=20-numdead) budworm.lg <- glm(SF ~ sex*ldose, family=binomial) summary(budworm.lg) Dieter
Jeffrey, not sure what you mean by showing the relationship between the prob and purban2, but something like this could work: library(gtools) #inverse logit fl <- function(x,beta){inv.logit(beta[1]+beta[2]*x)} # for beta fill in your intercept and the coefficient of purban2 flb<-function(x,beta=c(-0.09,3.65)){fl(x,beta)} # plot over the range of purban2 by: plot(flb,0,1) hth, Ingmar On 10/19/06 12:24 AM, "Jeffrey Stratford" <stratja at auburn.edu> wrote:> Hi. I'm trying to plot the ratio of used versus unused bird houses > (coded 1 or 0) versus a continuous environmental gradient (proportion of > urban cover [purban2]) that I would like to convert into bins (0 - > 0.25, 0.26 - 0.5, 0.51 - 0.75, 0.76 - 1.0) and I'm not having much luck > figuring this out. I ran a logistic regression and purban2 ends up > driving the probability of a box being occupied so it would be nice to > show this relationship. I'm also plotting the fitted values vs. purban2 > but that's done. Any suggestions would be appreciated. > > Many thanks, > > Jeff > > > Data sample: > > box use purbank purban2 > 1 1 0.003813435 0.02684564 > 2 1 0.04429451 0.1610738 > 3 1 0.04458785 0.06040268 > 4 1 0.06072162 0.2080537 > 5 0 0.6080962 0.6979866 > 6 1 0.6060428 0.6107383 > 7 1 0.3807568 0.4362416 > 8 0 0.3649164 0.3154362 > 9 0 0.3505427 0.2483221 > 10 0 0.3476093 0.1409396 > 11 0 0.3719566 0.3020134 > 12 1 0.09238011 0.1342282 > 13 0 0.08616111 0.1073826 > 14 0 0.07388724 0.04026845 > 15 1 0.07046477 0.03355705 > . > . > . > > > **************************************** > 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 > auburn.edu/~stratja > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands users.fmg.uva.nl/ivisser tel: +31-20-5256735
I suggest you look at the functions cut and tapply. for instance: breaks = 0:40 / 40 bucket <- cut(purban2, breaks) used.c = tapply(used, bucket, sum) unused.c = tapply(1 - used, bucket, sum) used.c[is.na(used.c)] = 0 unused.c[is.na(unused.c)] = 0 plot(breaks[-length(breaks)], used.c / unused.c) -Alex Brown On 18 Oct 2006, at 23:24, Jeffrey Stratford wrote:> Hi. I'm trying to plot the ratio of used versus unused bird houses > (coded 1 or 0) versus a continuous environmental gradient > (proportion of > urban cover [purban2]) that I would like to convert into bins (0 - > 0.25, 0.26 - 0.5, 0.51 - 0.75, 0.76 - 1.0) and I'm not having much > luck > figuring this out. I ran a logistic regression and purban2 ends up > driving the probability of a box being occupied so it would be nice to > show this relationship. I'm also plotting the fitted values vs. > purban2 > but that's done. Any suggestions would be appreciated. > > Many thanks, > > Jeff > > > Data sample: > > box use purbank purban2 > 1 1 0.003813435 0.02684564 > 2 1 0.04429451 0.1610738 > 3 1 0.04458785 0.06040268 > 4 1 0.06072162 0.2080537 > 5 0 0.6080962 0.6979866 > 6 1 0.6060428 0.6107383 > 7 1 0.3807568 0.4362416 > 8 0 0.3649164 0.3154362 > 9 0 0.3505427 0.2483221 > 10 0 0.3476093 0.1409396 > 11 0 0.3719566 0.3020134 > 12 1 0.09238011 0.1342282 > 13 0 0.08616111 0.1073826 > 14 0 0.07388724 0.04026845 > 15 1 0.07046477 0.03355705 > . > . > . > > > **************************************** > 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 > auburn.edu/~stratja > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.