Lattice: Add abline to Single Value qqmath() Plot

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org] On Behalf Of Rich Shepard
Sent: Tuesday, May 15, 2012 12:31 PM
To: r-help at r-project.org
Subject: [R] Lattice: Add abline to Single Value qqmath() Plot

   The data are not normally distributed when untransformed and I'm
trying
various transformations to see if any would be appropriate to use. The
lattice book (fig. 3.10) shows a 2-sample Q-Q plot with an abline but
the
code for the figure does not include the line.

   I'd appreciate a pointer to a reference on how to add an abline to a
one-sample qqmath() plot in lattice.

Rich

Take a look at section 3.3.6 qqmath
http://www.his.sunderland.ac.uk/~cs0her/Statistics/UsingLatticeGraphicsInR.h
tm

You need to create a panel function. See sections 2.5.2 and 2.5.3 in the
second chapter of the Lattice book
(http://dsarkar.fhcrc.org/lattice/book/chapter2.pdf) available on Deepayan
Sarkar's webpage.

This is a simple example modified from the example in the lattice package
manual:

qqmath(~ rnorm(100),
 panel = function(x, ...) {
   panel.qqmathline(x, ...)
   panel.qqmath(x, ...)
 })

qqmath(~ rnorm(100),
 panel = function(x, ...) {
   panel.qqmathline(x, ...)
   panel.qqmath(x, ...)
 })

source('metals.R')

On Tue, 15 May 2012, David L Carlson wrote:

David,

?I have 130 plots to produce (30 chemicals un-transformed and three
transformations). The R console insists that I retype each of the 6 lines
(adding a prepanel.qqmathline line) each time. Makes more sense to put all
the commands in a script that I can run within R using "source('metals.R')".

?However, R appears to not see that the first line does not terminate the
command and the following lines are continuations. The source is,

pdf('ag_norm.pdf')
qqmath(~ Ag | factor(basin), data = surfchem.cast, main = 'Silver
(Untransformed'),

Error in source("metals.R") : metals.R:4:83: unexpected ','

3: pdf('ag_norm.pdf')
4: qqmath(~ Ag | factor(basin), data = surfchem.cast, main = 'Silver
(Untransformed'),

with a caret under the last ')'.

?What syntax error did I commit in the call to qqmath() above?

Rich

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Apologies in advance if I misinterpret " R console insists that I retype
..." but actually makes more sense (than sourcing a script) to use the
group argument (see the last example in ?qqmath) as in 4 groups in each of
30 panels, or allow.multiple=T, outer=T if you really want separate panels
for each transformation. Also can use layout=c(1,1,120) if you need each
in a separate page - or say c(3,2,20) for 20 pages of 6 panels each, etc.
Regarding your script, there is a syntax error:

pdf('ag_norm.pdf') qqmath(~ Ag | factor(basin), data = surfchem.cast,
main = 'Silver (Untransformed'),

Right here the " ' " is on the wrong side of " ) " causing the error:

Apologies in advance if I misinterpret " R console insists that I retype
..." but actually makes more sense (than sourcing a script) to use the
group argument (see the last example in ?qqmath) as in 4 groups in each of
30 panels, or allow.multiple=T, outer=T if you really want separate panels
for each transformation. Also can use layout=c(1,1,120) if you need each
in a separate page - or say c(3,2,20) for 20 pages of 6 panels each, etc.
Regarding your script, there is a syntax error: