R devel - Aug 2016 - "plot.ts" doesn't respect the value of "pch" (+ blocked from Bugzilla signups)

I did a search on Bugzilla for "plot.ts" and didn't find anything
on
this issue. I tried to sign up for Bugzilla to report it, but my e-mail 
address didn't pass your "syntax checking" for a legal e-mail
address.

The bug is easily reproducible on my machine as follows:

## start

# generate some data
y <- arima.sim(list(), 150)

# this will definitely dispatch to a ".ts" method
class(y)[1] == 'ts'

# compare and note that `cex = 0.5` has no effect
plot(y, type = 'b', pch = 16)
plot(y, type = 'b', pch = 16, cex = 0.5)

# it works if `y` is coerced back to a regular vector
plot(as.numeric(y), type = 'b', pch = 16, cex = 0.5)

# another way to see the issue
plot.ts(y, type = 'b', pch = 16, cex = 0.5)
plot.default(y, type = 'b', pch = 16, cex = 0.5)

## end

Skimming through source code for `plot.ts`, it seems like the `cex` 
argument is being "eaten" by a `...` somewhere without being properly 
passed to `plot.default`.

The output of `R.version` is:
platform       x86_64-apple-darwin15.5.0
arch           x86_64
os             darwin15.5.0
system         x86_64, darwin15.5.0
status
major          3
minor          3.1
year           2016
month          06
day            21
svn rev        70800
language       R
version.string R version 3.3.1 (2016-06-21)
nickname       Bug in Your Hair

Greg

> On Aug 24, 2016, at 5:59 PM, Gregory Werbin <greg.werbin at
libertymail.net> wrote:
> 
> I did a search on Bugzilla for "plot.ts" and didn't find
anything on this issue. I tried to sign up for Bugzilla to report it, but my
e-mail address didn't pass your "syntax checking" for a legal
e-mail address.
> 
> The bug is easily reproducible on my machine as follows:
> 
> ## start
> 
> # generate some data
> y <- arima.sim(list(), 150)
> 
> # this will definitely dispatch to a ".ts" method
> class(y)[1] == 'ts'
> 
> # compare and note that `cex = 0.5` has no effect
> plot(y, type = 'b', pch = 16)
> plot(y, type = 'b', pch = 16, cex = 0.5)
> 
> # it works if `y` is coerced back to a regular vector
> plot(as.numeric(y), type = 'b', pch = 16, cex = 0.5)
> 
> # another way to see the issue
> plot.ts(y, type = 'b', pch = 16, cex = 0.5)
> plot.default(y, type = 'b', pch = 16, cex = 0.5)
> 
> ## end
> 
> Skimming through source code for `plot.ts`, it seems like the `cex`
argument is being "eaten" by a `...` somewhere without being properly
passed to `plot.default`.
'...' does not "eat" parameters, it passes them on.

Looking at the very top of the body we see this in the definition of the
internal `plotts` function:

        cex = par("cex"), lty = par("lty"), lwd =
par("lwd"),
        axes = TRUE, frame.plot = axes, ann = par("ann"), cex.lab =
par("cex.lab"),
        col.lab = par("col.lab"), font.lab =
par("font.lab"),
        cex.axis = par("cex.axis"), col.axis =
par("col.axis"),

And at the end of the body we se the call to plotts (including the
"dots")

So I would suggest using par-settings.


par(cex=0.5)
plot(y, type = 'b', pch = 16)


(Question seems more appropriate for r-help.)

-- 
David.
> 
> The output of `R.version` is:
> platform       x86_64-apple-darwin15.5.0
> arch           x86_64
> os             darwin15.5.0
> system         x86_64, darwin15.5.0
> status
> major          3
> minor          3.1
> year           2016
> month          06
> day            21
> svn rev        70800
> language       R
> version.string R version 3.3.1 (2016-06-21)
> nickname       Bug in Your Hair
> 
> Greg
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
David Winsemius
Alameda, CA, USA

>>>>> David Winsemius <dwinsemius at comcast.net>
>>>>>     on Thu, 25 Aug 2016 00:00:04 -0700 writes:
    >> On Aug 24, 2016, at 5:59 PM, Gregory Werbin <greg.werbin at
libertymail.net> wrote:
    >> 
    >> I did a search on Bugzilla for "plot.ts" and didn't
find anything on this issue. I tried to sign up for Bugzilla to report it, but
my e-mail address didn't pass your "syntax checking" for a legal
e-mail address.

If you read (and you should :-)
   https://www.r-project.org/bugs.html
you will see the reason for the "syntax checking".
We currently need manual white listing (of e-mail addresses),
because we had months of "spam" bug reports and then complete
spam explosion aka "bug site devastation" action.

I have added your e-mail (above) to be valid / legal...
Please "subscribe", because we will not keep that changed string for
so long.

[ Actually, I'd tend to say that for short term, we are now
  looking for volunteers for "bugzilla moderation".... ]


    >> 
    >> The bug is easily reproducible on my machine as follows:
    >> 
    >> ## start
    >> 
    >> # generate some data
    >> y <- arima.sim(list(), 150)
    >> 
    >> # this will definitely dispatch to a ".ts" method
    >> class(y)[1] == 'ts'
    >> 
    >> # compare and note that `cex = 0.5` has no effect
    >> plot(y, type = 'b', pch = 16)
    >> plot(y, type = 'b', pch = 16, cex = 0.5)
    >> 
    >> # it works if `y` is coerced back to a regular vector
    >> plot(as.numeric(y), type = 'b', pch = 16, cex = 0.5)
    >> 
    >> # another way to see the issue
    >> plot.ts(y, type = 'b', pch = 16, cex = 0.5)
    >> plot.default(y, type = 'b', pch = 16, cex = 0.5)
    >> 
    >> ## end
    >> 
    >> Skimming through source code for `plot.ts`, it seems like the `cex`
argument is being "eaten" by a `...` somewhere without being properly
passed to `plot.default`.

    > '...' does not "eat" parameters, it passes them on.

    > Looking at the very top of the body we see this in the definition of
the internal `plotts` function:

    > cex = par("cex"), lty = par("lty"), lwd =
par("lwd"),
    > axes = TRUE, frame.plot = axes, ann = par("ann"), cex.lab =
par("cex.lab"),
    > col.lab = par("col.lab"), font.lab =
par("font.lab"),
    > cex.axis = par("cex.axis"), col.axis =
par("col.axis"),

    > And at the end of the body we se the call to plotts (including the
"dots")

    > So I would suggest using par-settings.

    > par(cex=0.5)
    > plot(y, type = 'b', pch = 16)

as a workaround, yes, thank you David!

    > (Question seems more appropriate for r-help.)

Still, I would tend to think that it was reasonable feature
request to ask for  plot.ts() to be improved there,  and then
R-devel or the R-bugzilla would be ok, too.

Martin Maechler, ETH Zurich


    > -- 
    > David.
    >> 
    >> The output of `R.version` is:
    >> platform       x86_64-apple-darwin15.5.0
    >> arch           x86_64
    >> os             darwin15.5.0
    >> system         x86_64, darwin15.5.0
    >> status
    >> major          3
    >> minor          3.1
    >> year           2016
    >> month          06
    >> day            21
    >> svn rev        70800
    >> language       R
    >> version.string R version 3.3.1 (2016-06-21)
    >> nickname       Bug in Your Hair
    >> 
    >> Greg
    >> 
    >> ______________________________________________
    >> R-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel

    > David Winsemius
    > Alameda, CA, USA

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

I've had a chance to read the source more thoroughly. The chain of 
events is as follows:

1. Local function `plotts()` is defined with argument `cex` that 
defaults to `par("cex")`
2. `...` is passed to `plotts()`. If "cex" is an element in `...`, 
inside `plotts()` the variable `cex` is assigned thereby (overriding the 
default arg). Importantly, this means that the element "cex" is
captured
and _removed_ from `...`. `...` is eventually passed to `plot.window()`.
3.
   - In the univariate case (NCOL(x) == 1): When `lines.default()` is 
called to actually plot the data 
(https://github.com/wch/r-source/blob/trunk/src/library/stats/R/ts.R#L588 
and 
https://github.com/wch/r-source/blob/trunk/src/library/stats/R/ts.R#L597 
for reference), `cex` is not included in the call.
   - In the bivariate case (NCOL(x) > 1): Because "cex" was
captured and
removed from `...`, it is not passed to `plot.default` when it is called 
(https://github.com/wch/r-source/blob/trunk/src/library/stats/R/ts.R#L548).

It turns out that the "eating" is not being done by `...` but by the 
signature of `plotts`.

The documentation currently reads:
> ...: additional graphical arguments, see 'plot',
'plot.default' and
> 'par'.
This, to me, suggests parity with the 'plot' function in how the 
arguments in '...' are handled. Therefore either the code is wrong or 
the documentation is incomplete and misleading.

I filed this is as a bug because it's undocumented, and inconsistent 
with how other arguments typically passed through `plot.default` are 
handled.

I'll be happy to do the patch myself -- I just need to know which thing 
to patch (the source or the docs).


Greg


On 2016-08-25 03:00, David Winsemius wrote:
>> On Aug 24, 2016, at 5:59 PM, Gregory Werbin 
>> <greg.werbin at libertymail.net> wrote:
>> 
>> I did a search on Bugzilla for "plot.ts" and didn't find
anything on
>> this issue. I tried to sign up for Bugzilla to report it, but my 
>> e-mail address didn't pass your "syntax checking" for a
legal e-mail
>> address.
>> 
>> The bug is easily reproducible on my machine as follows:
>> 
>> ## start
>> 
>> # generate some data
>> y <- arima.sim(list(), 150)
>> 
>> # this will definitely dispatch to a ".ts" method
>> class(y)[1] == 'ts'
>> 
>> # compare and note that `cex = 0.5` has no effect
>> plot(y, type = 'b', pch = 16)
>> plot(y, type = 'b', pch = 16, cex = 0.5)
>> 
>> # it works if `y` is coerced back to a regular vector
>> plot(as.numeric(y), type = 'b', pch = 16, cex = 0.5)
>> 
>> # another way to see the issue
>> plot.ts(y, type = 'b', pch = 16, cex = 0.5)
>> plot.default(y, type = 'b', pch = 16, cex = 0.5)
>> 
>> ## end
>> 
>> Skimming through source code for `plot.ts`, it seems like the `cex` 
>> argument is being "eaten" by a `...` somewhere without being
properly
>> passed to `plot.default`.
> 
> '...' does not "eat" parameters, it passes them on.
> 
> Looking at the very top of the body we see this in the definition of 
> the internal `plotts` function:
> 
> cex = par("cex"), lty = par("lty"), lwd =
par("lwd"),
> axes = TRUE, frame.plot = axes, ann = par("ann"), cex.lab = 
> par("cex.lab"),
> col.lab = par("col.lab"), font.lab = par("font.lab"),
> cex.axis = par("cex.axis"), col.axis = par("col.axis"),
> 
> And at the end of the body we se the call to plotts (including the 
> "dots")
> 
> So I would suggest using par-settings.
> 
> par(cex=0.5)
> plot(y, type = 'b', pch = 16)
> 
> (Question seems more appropriate for r-help.)
> 
> --
> David.
> 
>> The output of `R.version` is:
>> platform       x86_64-apple-darwin15.5.0
>> arch           x86_64
>> os             darwin15.5.0
>> system         x86_64, darwin15.5.0
>> status
>> major          3
>> minor          3.1
>> year           2016
>> month          06
>> day            21
>> svn rev        70800
>> language       R
>> version.string R version 3.3.1 (2016-06-21)
>> nickname       Bug in Your Hair
>> 
>> Greg
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> David Winsemius
> Alameda, CA, USA