Re: [R] creating bins for a plot
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 __ 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.
Re: [R] creating bins for a plot
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 [EMAIL PROTECTED] 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
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.
--
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15, 1018 WB Amsterdam
The Netherlands
http://users.fmg.uva.nl/ivisser/
tel: +31-20-5256735
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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.
Re: [R] creating bins for a plot
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 100 0.3476093 0.1409396 110 0.3719566 0.3020134 121 0.09238011 0.1342282 130 0.08616111 0.1073826 140 0.07388724 0.04026845 151 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 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. __ 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.
[R] creating bins for a plot
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 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.
