Re: [R] Plot binomial regression line

From: Achim Zeileis <Achim.Zeileis_at_uibk.ac.at>
Date: Thu, 26 May 2011 12:05:09 +0200 (CEST)

On Thu, 26 May 2011, Jörgen Svan wrote:

> Dear all,
>
> I am quite new with R and I have a problem with plotting a binomial
> regression line in a plot.
>
> This is what I type in:
>> model<-glm(Para~Size,binomial)
>> par(mfrow=c(1,1))
>> xv<-seq(3.2,4.5,0.01)
>> yv<-predict(model,list(area=xv),type="response")
>> plot(Size,Para)
>> lines(xv,yv)
>
> The error message that I get is:
>
>> Error in xy.coords(x, y) : 'x' and 'y' lengths differ

I assume that setting "area" is not correct.

> My txt-file is attached. Could someone please help me to find out what I
> did wrong.

For a plain scatterplot you could do this:

## read data (and code Para as factor)
d <- read.table("PerBinom.txt", header = TRUE) d$Para <- factor(d$Para)

## model fit and predicted probabilies

m <- glm(Para ~ Size, data = d, family = binomial)
s <- seq(3.2, 4.5, by = 0.1)
p <- predict(m, data.frame(Size = s), type = "response")

## scatterplot
plot(as.numeric(Para) - 1 ~ Size, data = d) lines(p ~ s, col = 4)

A similar display can be obtained easily with the "effects" package:

library("effects")
plot(allEffects(m), ask = FALSE, rescale = FALSE)

which also works if there is more than one regressor. See http://www.jstatsoft.org/v08/i15/ and http://www.jstatsoft.org/v32/i01/ for more details about the "effects" package.

Finally, you could also use exploratory displays, e.g., a spinogram or a a conditional density plot:

cdplot(Para ~ Size, data = d, ylevels = 2:1) plot(Para ~ Size, data = d, ylevels = 2:1) plot(Para ~ Size, data = d, ylevels = 2:1, breaks = quantile(Size))

Adding a regression line to the latter is not completely straightforward due to the rescaled x axis. You could do something like this:

lines(sapply(s, function(x) mean(d$Size <= x)), p, col = 4)

hth,
Z

> Thank you on beforehand,
> Jörgen
>



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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. Received on Thu 26 May 2011 - 10:10:17 GMT

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