[R] Unintended behaviour (possibly bugs)
Alexey Shipunov
d@cty|orh|z@ @end|ng |rom gm@||@com
Fri Mar 13 10:56:15 CET 2020
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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