R devel - May 2022 - bug in plot.table(..., log='y')?

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

>>>>> 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