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plot with a regression line(s)

4 messages · Sam Steingold, michael.weylandt at gmail.com (R. Michael Weylandt, David Winsemius +1 more

#
I am sure a common need is to plot a scatterplot with some fitted
line(s) and maybe save to a file.
I have this:

plot.glm <- function (x, y, file = NULL, xlab = deparse(substitute(x)),
                      ylab = deparse(substitute(y)), main = NULL) {
  m <- glm(y ~ x)
  if (!is.null(file))
    pdf(file = file)
  plot(x, y, xlab = xlab, ylab = ylab, main = main)
  lines(x, y = m$fitted.values, col = "green")
  if (!is.null(file))
    dev.off()
  print(m)
}

is there a better/easier/more general way?
I'm not sure what your definition of easier would be, but there are some style things you might want to be aware of:

I) the name is likely to hit up against the S3 generic plot() when applied to a glm object. This might lead to strange bugs at some point. 
II) you can test !is.null once and use on.exit() to delay the clean-up call to dev.off()
III) I'm not sure about glm objects but abline() applied to an lm object automatically plots a best fit line saving you a line or so of code. 
IV) You probably don't want to print() m at the end: the REPL will print it automatically in interactive top level calls and it will be rather noisy if you start wrapping this in other calls. 

Hope this helps,
Michael
On Apr 4, 2012, at 11:13 AM, Sam Steingold <sds at gnu.org> wrote:

            
#
On Apr 4, 2012, at 11:30 AM, R. Michael Weylandt <michael.weylandt at gmail.com
> wrote:

            
If you offer a regression object to abline's 'reg' parameter and that  
object has a coef() method you might get a result. But if the link  
function of the regression is not matched to the plot's scale (as  
might happen with a logistic or poisson fit) then results may not be  
as expected. Most people will probably want to use `predict(reg- 
object, newdata= ...., type = "response")` with .
David Winsemius, MD
West Hartford, CT
#
There is no guarantee that x is sorted in ascending order for a glm (or any other model), so lines(x, fitted()) can give very spiny results. Even if sorted, non-linear fits with large gaps in x will not give smooth lines.

Better to use something along the lines of the budworm example in the glm help page, which uses predict() on a new sequence.
If you want something a bit more general, you can use either range(x) to get the new sequence limits or  par("usr")[1:2]  to gets the current plot x limits.


S Ellison
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