[R] Unintended behaviour (possibly bugs)
Alexey Shipunov
d@cty|orh|z@ @end|ng |rom gm@||@com
Fri Jul 3 05:40:13 CEST 2020
Martin,
Yes, I should have test it earlier. Thank you for the response!
With best wishes,
Alexey
чт, 2 июл. 2020 г. в 22:30, Martin Maechler <maechler using stat.math.ethz.ch>:
>
> >>>>> Alexey Shipunov
> >>>>> on Wed, 1 Jul 2020 23:58:04 +0900 writes:
>
> > Dear colleagues,
> > There is a new problem with dotchart(), and it is very simple to reproduce.
>
> > Just run example(dotchart).
>
> > On R versions < 4, group labels ("Urban Female" and so on) were
> > visible. Now they are not visible.
>
> > If in the dotchart() code, we replace the string
>
> > ===
>
> > goffset <- (max(linch + offset, ginch, na.rm = TRUE) + 1/16)/lheight
>
> > ===
>
> > with the string
>
> > ===
>
> > goffset <- (max(linch + 0.2, ginch, na.rm = TRUE) + 1/16)/lheight
>
> > ===
>
> > everything start to be OK. Probably, the reason that in the code,
> > there is another "offset" object and they clash. So if we replace this
> > part of code
>
> > ===
>
> > offset <- cumsum(c(0, diff(as.numeric(groups)) != 0))
> > y <- seq_len(n) + 2 * offset
>
> > ===
>
> > with
>
> > ===
>
> > offset1 <- cumsum(c(0, diff(as.numeric(groups)) != 0))
> > y <- seq_len(n) + 2 * offset1
>
> > ===
>
> > everything will be well again.
>
> Thank you.
>
> I'll have a look *again*, and cautiously consider the above.
> Indeed your second patch seems the correct one, distinguishing the
> two different offsets that where conflated.
> I will commit to R-devel and also to "R 4.0.2 patched" (but note
> that no quick R 4.0.3 has been planned).
>
> Note (Alexey knows, almost everbody else probably not):
> This has come from another dotchart(* , ylab=.) glitch which
> Alexey had reported in February and I had fixed early
> March... evidently not fixed quite correctly... and yes, I'm
> embarrased.
> However I did mention here to have fixed it, on March 12
> (--> https://stat.ethz.ch/pipermail/r-help/2020-March/465921.html )
>
> It would have been really great if people would test such
> changes, as they were in all pre-releases (R 4.0.0 alpha, beta,
> RC), easily available ... and we could have fixed this even
> before R 4.0.0 was released more than a month later than my
> e-mail above...
>
> Martin
>
>
> > With best wishes,
> > Alexey Shipunov
>
> > пт, 13 мар. 2020 г. в 18:56, Alexey Shipunov <dactylorhiza using gmail.com>:
> >>
> >> Dear Martin,
> >>
> >> Great news, thanks!
> >>
> >> If you wish, please also consider my initial note about help(hist),
> >> this is definitely worrying new R users.
> >>
> >> With best wishes,
> >>
> >> Alexey
> >>
> >> пт, 13 мар. 2020 г. в 02:16, Martin Maechler <maechler using stat.math.ethz.ch>:
> >> >
> >> > >>>>> Alexey Shipunov
> >> > >>>>> on Tue, 18 Feb 2020 14:34:48 +0900 writes:
> >> >
> >> > > Thank you for the detailed explanation. I tend to agree. However, this
> >> > > behavior is relatively easy to remediate:
> >> >
> >> > > This is the piece of the current code:
> >> >
> >> > > ===
> >> > > if (!(is.null(labels) && is.null(glabels))) {
> >> > > nmai <- par("mai")
> >> > > nmai[2L] <- nmai[4L] + max(linch + goffset, ginch) + 0.1
> >> > > par(mai = nmai)
> >> > > }
> >> > > ===
> >> >
> >> > > This is my proposal:
> >> >
> >> > > ===
> >> > > yinch <- if (!is.null(ylab)) 0.4 else 0
> >> > > if (!(is.null(labels) && is.null(glabels))) {
> >> > > nmai <- par("mai")
> >> > > nm.2 <- nmai[4L] + max(if(is.null(ylab)) 0 else 0.4) + linch + goffset, ginch) + 0.1
> >> > > if (nmai[2L] < nm.2)
> >> > > nmai[2L] <- nm.2
> >> > > par(mai = nmai)
> >> > > }
> >> > > ===
> >> >
> >> > > Then margins and y-axis labels start to work normally. I wonder if
> >> > > this (or similar) is possible to introduce into the code?
> >> >
> >> > > Alexey
> >> >
> >> > Well, I had looked at this back then (~Feb 18), and now had a
> >> > considerable longer look.
> >> >
> >> > Your suggestion makes sense, but then it needs even more work
> >> > to ensure that the 'ylab' y-axis label will be placed properly.
> >> >
> >> > Of course, Deepayan (author of grid-based 'lattice') is right
> >> > that dotchart()s implementation is pretty hackish ... but then
> >> > still.
> >> >
> >> > I have (+-) fixed this in the sources of "R-devel" the
> >> > development version of R (which should become R 4.0.0 on April
> >> > 24 as was announced today).
> >> >
> >> > Now, things like this (extended) example work nicely :
> >> >
> >> > op <- par(xaxs = "i") # 0 -- 100\%
> >> > dotchart(t(VADeaths), xlim = c(0,100), bg = "skyblue",
> >> > main = "Death Rates in Virginia - 1940", xlab = "rate [ % ]",
> >> > ylab = "Grouping: Age x Urbanity . Gender")
> >> > par(op)
> >> >
> >> >
> >> > Thank you, Alexey, for your report and bug fix suggestion!
> >> >
> >> > Best regards,
> >> >
> >> > Martin Maechler
> >> > ETH Zurich and R Core team
> >> >
> >> >
> >> >
> >> > > ........... 17:37, Deepayan Sarkar <deepayan.sarkar using gmail.com>:
> >> > >>
> >> > >> On Mon, Feb 17, 2020 at 10:24 AM Rui Barradas <ruipbarradas using sapo.pt> wrot=
> >> > > e:
> >> > >> >
> >> > >> > Hello,
> >> > >> >
> >> > >> > Yes, this is definitely a bug.
> >> > >>
> >> > >> I would argue that the only bug here is that the documentation doesn't
> >> > >> say that 'ylab' may not behave as expected.
> >> > >>
> >> > >> dotchart() is mainly designed for 2-way tables (see the VADeaths
> >> > >> example), but it's implementation is really pretty hackish because it
> >> > >> has to work within the limited traditional graphics framework. The
> >> > >> main problem is that dot plots want to put horizontal y-axis labels
> >> > >> (usually derived from factor levels), which are often longer than the
> >> > >> default margins, so the margins are modified. Unfortunately they are
> >> > >> only re-set on exit, and so the ylab that is plotted inside dotchart()
> >> > >> may be clipped. Traditionally, Cleveland dot plots don't have a y-axis
> >> > >> label; it's assumed that the factor levels are sufficient (and for
> >> > >> 2-way tables, there would be two variables, so there is no sensible
> >> > >> default).
> >> > >>
> >> > >> I doubt that dotchart() is worth fixing (except to maybe disallow
> >> > >> ylab). If you want flexibility, use modern grid-based alternatives
> >> > >> such as lattice::dotplot() or ggplot2.
> >> > >>
> >> > >> -Deepayan
> >> > >>
> >> > >> > Even the matrix plot is puzzling, with a "1" as top row sort-of-label
> >> > >> > but no grid line. I'm trying to follow the source code of dotchart but
> >> > >> > am yet to understand exactly what it does to decide the margins setting=
> >> > > s.
> >> > >> >
> >> > >> > if (!(is.null(labels) && is.null(glabels))) {
> >> > >> > nmai <- par("mai")
> >> > >> > nmai[2L] <- nmai[4L] + max(linch + goffset, ginch) +
> >> > >> > 0.1
> >> > >> > par(mai = nmai)
> >> > >> > }
> >> > >> >
> >> > >> > This should be moved to r-devel?
> >> > >> >
> >> > >> > Rui Barradas
> >> > >> >
> >> > >> > 03:33 de 17/02/20, Alexey Shipunov escreveu:
> >> > >> > > John and Rui, thanks!
> >> > >> > >
> >> > >> > > However, if we use the proper object, the problem still persists:
> >> > >> > >
> >> > >> > > dotchart(c("3"=1, "2"=2, "1"=3), ylab="Ylab") # ylab is invisible
> >> > >> > > dotchart(c("aa"=1, "b"=2, "cc"=3), ylab="Ylab") # ylab is partly visible (!!!)
> >> > >> > > dotchart(c("aaa"=1, "bbb"=2, "ccc"=3), ylab="Ylab") # ylab is well visible
> >> > >> > >
> >> > >> > > If the object is matrix, ylab is visible:
> >> > >> > >
> >> > >> > > dotchart(matrix(1:3, dimnames=list(c("aa","bb","cc"), NULL)), ylab="Ylab")
> >> > >> > >
> >> > >> > > But the ?dotchart explicitly says that "x: either a vector or matrix
> >> > >> > > of numeric values" and then "labels: a vector of labels for each
> >> > >> > > point. For vectors the default is to use "names(x) = ...".
> >> > >> > >
> >> > >> > > So this is likely a bug. Do you agree?
> >> > >> > >
> >> > >> > > Alexey
> >> > >> > >
> >> > >> > > ..... 01:55, Rui Barradas <ruipbarradas using sapo.pt>:
> >> > >> > >>
> >> > >> > >> Hello,
> >> > >> > >>
> >> > >> > >> I believe you are wrong, the error is not in dotchart, it's in your
> >> > >> > >> code. You assume that to plot an object of class "table" is the same as
> >> > >> > >> to plot an object of class "numeric".
> >> > >> > >>
> >> > >> > >> Inline.
> >> > >> > >>
> >> > >> > >> =C3=80s 12:21 de 16/02/20, Alexey Shipunov escreveu:
> >> > >> > >>> Dear list,
> >> > >> > >>>
> >> > >> > >>> I have been advised to share these with R-help instead of filling the
> >> > >> > >>> bug report:
> >> > >> > >>>
> >> > >> > >>> 1) dotchart() does not allow to see the left axis title ('ylab') and
> >> > >> > >>> cannot change the left margin (outer margin 2) of the plot
> >> > >> > >>>
> >> > >> > >>> The code:
> >> > >> > >>>
> >> > >> > >>> aa <- table(c(1, 1, 1, 2, 2, 3))
> >> > >> > >>> dotchart(aa, ylab="Ylab") # does not show 'ylab'
> >> > >> > >>
> >> > >> > >> You are right, it does *not* show 'ylab' but the user is warned.
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> aa <- table(c(1, 1, 1, 2, 2, 3))
> >> > >> > >> dotchart(aa, ylab = "Ylab") # does show 'ylab'
> >> > >> > >> #Warning message:
> >> > >> > >> #In dotchart(aa, ylab = "Ylab") :
> >> > >> > >> # 'x' is neither a vector nor a matrix: using as.numeric(x)
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> My code:
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> (mar <- par("mar")) # new R session
> >> > >> > >> #[1] 5.1 4.1 4.1 2.1 # the left margin is 4.1
> >> > >> > >>
> >> > >> > >> aa <- as.numeric(table(c(1, 1, 1, 2, 2, 3)))
> >> > >> > >>
> >> > >> > >> dotchart(aa, ylab = "Ylab") # It does show 'ylab'
> >> > >> > >> old.par <- par(mar = mar + c(0, 5, 0, 0))
> >> > >> > >> par("mar")
> >> > >> > >> #[1] 5.1 9.1 4.1 2.1
> >> > >> > >>
> >> > >> > >> dotchart(aa, ylab = "Ylab") # The left margin is now 9.1, much bigger
> >> > >> > >>
> >> > >> > >> par(old.par) # It does change the left margin
> >> > >> > >> dotchart(aa, ylab = "Ylab") # but only when a new graph is plotted.
> >> > >> > >>
> >> > >> > >>
> >> > >> > >>
> >> > >> > >>> old.par <- par(mar=c(1, 10, 1, 1)) ; dotchart(aa, ylab="Ylab") ;
> >> > >> > >>> par(old.par) # does not change left margin
> >> > >> > >>>
> >> > >> > >>> Possible solution:
> >> > >> > >>>
> >> > >> > >>> I researched the problem and think that the dotchart() code will need
> >> > >> > >>> few corrections. If there is an interest, I can post it here; or you
> >> > >> > >>> can look at the code of shipunov::Dotchart1() function.
> >> > >> > >>>
> >> > >> > >>> 2) example(hist) includes two "wrong" and "extreme" examples which
> >> > >> > >>> slow down and even crash R on some systems; this make it unsuitable
> >> > >> > >>> for demonstration in the class and strikes beginners in R who just
> >> > >> > >>> want to understand how hist() works. Actually, I did it last week (I
> >> > >> > >>> was not aware of these examples), and in the class two computers hang,
> >> > >> > >>> and many others were extremely slow.
> >> > >> > >>>
> >> > >> > >>> The code:
> >> > >> > >>>
> >> > >> > >>> example(hist)
> >> > >> > >>>
> >> > >> > >>> Possible solution:
> >> > >> > >>>
> >> > >> > >>> If R maintainers will enclose parts of "hist" example in \dontrun{},
> >> > >> > >>> this will allow to see the code but in the same time will not strike
> >> > >> > >>> beginners in R who just
> >> > >> > >>> want to understand how hist() works. They will still be possible to
> >> > >> > >>> run with example(..., run.dontrun=TRUE).
> >> > >> > >>
> >> > >> > >> Agree, it's annoying. Sometimes there's a Warning section after the
> >> > >> > >> Details section. Maybe such a section could get users' attention to
> >> > >> > >> those examples? At least it wouldn't hurt...
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> Hope this helps,
> >> > >> > >>
> >> > >> > >> Rui Barradas
> >> > >> > >>
> >> > >> > >>>
> >> > >> > >>> With best wishes,
> >> > >> > >>>
> >> > >> > >>> Alexey Shipunov
> >> > >> > >>> ______________________________________________
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