R devel - Feb 2009 - plot.lm: "Cook's distance" label can overplot point labels

The following code demonstrates an annoyance with plot.lm():

library(DAAGxtras)
x11(width=3.75, height=4)
nihills.lm <- lm(log(time) ~ log(dist) + log(climb), data = nihills)
plot(nihills.lm, which=5)

OR try the following
xy <- data.frame(x=c(3,1:5), y=c(-2, 1:5))
plot(lm(y ~ x, data=xy), which=5)

The "Cook's distance" text overplots the label for the point with
the
smallest residual.  This is an issue when the size of the plot is much  
less than the default, and the pointsize is not reduced proportionately.


I suggest the following:
       xx <- hii
       xx[xx >= 1] <- NA
## Insert new code
       fracht <- (1.25*par()$cin[2])/par()$pin[2]
       ylim[1] <- ylim[1] - diff(ylim)*max(0, fracht-0.04)
## End insert new code
       plot(xx, rsp, xlim = c(0, max(xx, na.rm = TRUE)),
            ylim = ylim, main = main, xlab = "Leverage",
            ylab = ylab5, type = "n", ...)

Then, about 15 lines further down, replace
         legend("bottomleft", legend = "Cook's
distance",
                lty = 2, col = 2, bty = "n")

by
         legend("bottomleft", legend = "Cook's
distance",
                lty = 2, col = 2, bty = "n", y.intersp=0.5)

If this second change is not made, then one wants fracht <- (1.5*par() 
$cin[2])/par()$pin[2]
I prefer the "Cook's distance" text to be a bit closer to the
x-axis,
as it separates it more clearly from any point labels.

John Maindonald             email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.

Dear John,

It occurs to me that the title above the graph, "Residuals vs.
Leverage," is
entirely redundant since the x-axis is labelled "Leverage" and the
y-axis
"Studentized residuals." Why not use the title above the graph for
"Cook's
distance countours"?

Regards,
 John
> -----Original Message-----
> From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at
r-project.org]
On
> Behalf Of John Maindonald
> Sent: February-17-09 5:54 PM
> To: r-devel at r-project.org
> Cc: Martin Maechler
> Subject: [Rd] plot.lm: "Cook's distance" label can overplot
point labels
> 
> The following code demonstrates an annoyance with plot.lm():
> 
> library(DAAGxtras)
> x11(width=3.75, height=4)
> nihills.lm <- lm(log(time) ~ log(dist) + log(climb), data = nihills)
> plot(nihills.lm, which=5)
> 
> OR try the following
> xy <- data.frame(x=c(3,1:5), y=c(-2, 1:5))
> plot(lm(y ~ x, data=xy), which=5)
> 
> The "Cook's distance" text overplots the label for the point
with the
> smallest residual.  This is an issue when the size of the plot is much
> less than the default, and the pointsize is not reduced proportionately.
> 
> 
> I suggest the following:
>        xx <- hii
>        xx[xx >= 1] <- NA
> ## Insert new code
>        fracht <- (1.25*par()$cin[2])/par()$pin[2]
>        ylim[1] <- ylim[1] - diff(ylim)*max(0, fracht-0.04)
> ## End insert new code
>        plot(xx, rsp, xlim = c(0, max(xx, na.rm = TRUE)),
>             ylim = ylim, main = main, xlab = "Leverage",
>             ylab = ylab5, type = "n", ...)
> 
> Then, about 15 lines further down, replace
>          legend("bottomleft", legend = "Cook's
distance",
>                 lty = 2, col = 2, bty = "n")
> 
> by
>          legend("bottomleft", legend = "Cook's
distance",
>                 lty = 2, col = 2, bty = "n", y.intersp=0.5)
> 
> If this second change is not made, then one wants fracht <- (1.5*par()
> $cin[2])/par()$pin[2]
> I prefer the "Cook's distance" text to be a bit closer to the
x-axis,
> as it separates it more clearly from any point labels.
> 
> John Maindonald             email: john.maindonald at anu.edu.au
> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
> Centre for Mathematics & Its Applications, Room 1194,
> John Dedman Mathematical Sciences Building (Building 27)
> Australian National University, Canberra ACT 0200.
> 
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