[Rd] bug in plot.table(..., log='y')?

[John Fox]

Dear Martin and Bill,

If I understand correctly, the basicPowerAxis() or bcPowerAxis() (for 
Box-Cox transformations) in the car package do what you describe, 
treating log (to any base) as a "0th" power and making provision for a 
"start," such as 1. There are also functions for two families of 
power-like transformations (Hawkins-Weisberg and Yeo-Johnson) that 
handle 0 and negative values naturally.

I hope this helps,
  John

On 2022-05-31 6:13 a.m., Martin Maechler wrote:
>>>>>> Bill Dunlap
>>>>>>      on Mon, 30 May 2022 09:38:45 -0700 writes:
> 
>      > Martin wrote
> 
>      > If you have a table with  0  counts  and think you'd prefer
>      > log="y" --- something I strongly agree is often a good idea,
>      > giving much more useful plots ---
> 
>      > I'd consider in this case using the good old
>      > log( 1+   y )
>      > or log( eps+ y )  trick.
> 
> 
>      > One could also sqrt(y), which helps stabilize the variances of count data.
> 
> Definitely,  thank you, Bill!
> 
> What I mean above (and I think you understood, but probably not
> many other readers because I was too terse),
> was of course to use   log="y"  with the "+ eps" trick,
> i.e., {in a general situation}
> 
>        plot(x, y+eps, log="y")
> 
> so the labels show numbers on the y+eps scale, and for smallish
> eps, this is visually the same as y-scale - unless you are close to y=0.
> 
> 
>      > Making nicely spaced and labelled tick marks for these transformations can
>      > be a pain.  Perhaps some package already does this.
> 
>      > -Bill
> 
> Not used yet, but from documentation, Stahel's 'plgraphics'
> package (see bottom below),  does allow "arbitrary" transformation.
> 
> For the specific case of table() {or xtable()} results with true counts,
> I agree it would be nice to have something like  'sqrt="y"' or
> just 'sqrt=TRUE' which would "show" sqrt(<count>) but label the
> axis non-equidistantly with counts.
> 
> A bit like
> 
>     y <- sort(rlnorm(333, 3))
>     plot(qnorm(ppoints(y)), y, log="y", yaxt="n")
>     sfsmisc::eaxis(2, sub=1)
> 
> does for log-transformed.
> 
> The simple traditional-graphics    plot(*, log="y") is often
> good enough, but I like to see from the ticks that there was a
> transformation.
> 
> Martin
> 
>      > On Mon, May 30, 2022 at 3:41 AM Martin Maechler <maechler using stat.math.ethz.ch>
>      > wrote:
> 
>      >> >>>>> Spencer Graves
>      >> >>>>>     on Sat, 28 May 2022 11:41:49 -0500 writes:
>      >>
>      >> > On 5/28/22 11:23 AM, Duncan Murdoch wrote:
>      >> >> On 28/05/2022 11:33 a.m., Spencer Graves wrote:
>      >> >>> Dear R Developers:
>      >> >>>
>      >> >>>
>      >> >>>       Consider the following example:
>      >> >>>
>      >> >>>
>      >> >>> (tstTable <- table(rep(1:3, 3:1))) plot(tstTable)
>      >> >>> plot(tstTable, log='y')
>      >> >>>
>      >> >>>
>      >> >>>       "plot(tstTable)" works as expected.
>      >> >>> "plot(tstTable, log='y')" gives a warning:
>      >> >>>
>      >> >>>
>      >> >>> Warning message: In plot.window(...) :     nonfinite
>      >> >>> axis=2 limits [GScale(-inf,0.477121,..); log=TRUE] --
>      >> >>> corrected now
>      >> >>>
>      >> >>>
>      >> >>>       AND the plot has a y axis scale running from
>      >> >>> 1e-307 to 1e+13.
>      >> >>>
>      >> >>>
>      >> >>>       This is with R 4.2.0 (R Console and the current
>      >> >>> RStudio) under macOS 11.6.6.
>      >> >>>
>      >> >>>
>      >> >>>       "plot(as.numeric(names(tstTable),
>      >> >>> as.numeric(tstTable), log='y'))" works as expected ;-)
>      >> >>>
>      >> >>>
>      >> >>>       Comments?        Thanks for your valuable work in
>      >> >>> making it easier for people everywhere to do quality
>      >> >>> statistics.
>      >> >>
>      >> >> The help page ?plot.table says that ylim defaults to c(0,
>      >> >> max(x)), i.e.  c(0,3) in your example.  If you're asking
>      >> >> to plot that on a log scale, there are bound to be
>      >> >> problems.
>      >> >>
>      >> >> If you specify ylim, e.g. as c(min(tstTable),
>      >> >> max(tstTable)), things are fine in your example; they
>      >> >> won't be in examples where the min is zero.
>      >> >>
>      >> >> Duncan Murdoch
>      >>
>      >> >     Thanks.  I looked at the help file but didn't read it
>      >> > carefully enough.
>      >>
>      >> >     Spencer
>      >>
>      >> If you have a table with  0  counts  and think you'd prefer
>      >> log="y" --- something I strongly agree is often a good idea,
>      >> giving much more useful plots ---
>      >>
>      >> I'd consider in this case using the good old
>      >> log( 1+   y )
>      >> or log( eps+ y )  trick.
>      >>
>      >> My colleague Werner Stahel has spent quite a bit of effort in
>      >> order to make such "log-transformed plots in case of {zero etc}"
>      >> plot even smarter and convenient...
>      >> and has put this (and many more related ideas of doing smart and
>      >> robust good data analysis) in his package 'plgraphics'
>      >> (on R-forge, but still not on CRAN unfortunately).
>      >> With many thanks to Ian Howson, still nicely available also here:
>      >>
>      >> https://rdrr.io/rforge/plgraphics/
>      >>
>      >> His generalized  log(1 + y)   is  plgraphics::logst(),
>      >> documented on the rdrr mirror here
>      >> https://rdrr.io/rforge/plgraphics/man/logst.html
>      >>
>      >> Martin
> 
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-- 
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/