[R] (-1 as index) OR (envelope for QQ)

[Prof Brian D Ripley]

On Thu, 24 Feb 2000, Dan E. Kelley wrote:

> I'm new to R (and to S) and am wondering about code from pages 72 and
> 83 of MASS (Venables+Ripley, 3rd edition), to draw an envelope on a QQ
> plot.  Copying from the book, I've got:
> 
>   #... code whose gist is "a.fit <-  nls(..."
>   num.points <- length(resid(a.fit))
>   qqnorm(residuals(a.fit))     # illustrate data-model residuals
>   qqline(residuals(a.fit))
>   samp <- cbind(residuals(a.fit), matrix(rnorm(num.points*19),num.points,19))
>   samp <- apply(scale(samp), 2, sort)
>   rs <- samp[,1] 
>   xs <- qqnorm(rs, plot=FALSE)$x
>   env <- t(apply(samp[,-1], 1, range))  ###########################3
>   xyul <- par("usr")
>   smidge <- min(diff(c(xyul[1], xs, xyul[2])))/2
>   segments(xs-smidge,env[,1], xs+smidge, env[,1])
>   segments(xs-smidge,env[,2], xs+smidge, env[,2])
> 
> where I've marked a confusing line with ########.  From what I gather
> (from section 2.1, or page 5, of "R complements to MASS" by VR),
> indexing is different in R than in S.  It's not clear to me whether
> this R-to-S difference is giving me problems.  I'm such a newbie that
> I'm not entirely sure what the 'samp[,-1]' is supposed to be doing.
> (Confession: I'm such a newbie that I've spent much of the day typing
> "?apply" and then "?par" etc, working through the program to try to
> figure it out!)

You can look in the R scripts (in the MASS package in the VR bundle) to see
fully tested R versions of the code.  That works, although you left out a
line (starting matplot).

samp[, -1] drops the first column (pp.39-40), so the marked line applies
range to the remaining columns.

That code applies to a variable, not residuals, which may or may not
matter depending on your model complexity.

> In any case, my worry is visible in the QQ plot attached.  Why do I
> have get so few "ledges" from the segments() calls?  It's not clear to
> me how the scale of the data-model deviations come into this problem.
> 
> Q: should I first be standardizing the residuals from the data-model
> comparison?  I would have guessed that something in this 'QQ envelope'
> would be doing that.  

Yes, the `scale' function is already normalizing for you.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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