From gmbecker at ucdavis.edu  Wed Feb 21 16:11:44 2018
From: gmbecker at ucdavis.edu (Gabriel Becker)
Date: Wed, 21 Feb 2018 07:11:44 -0800
Subject: [Rd] 
 Duplicate column names created by base::merge() when by.x has
 the same name as a column in y
In-Reply-To: <CADwqtCPTRPfz8xuAiCQ0ccnDc8rbaSdGjTBCcxM=Ef2MEzvj1w@mail.gmail.com>
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Message-ID: <CADwqtCP84q+JyYUGQ_DSBz9eAVCwTfoz6jt_r_8xiAT5HVnYGQ@mail.gmail.com>

Hi all,

For the record this approach isnt 100% backwards compatible, because
names(mergeddf) will e incompatibly different. Thatx why i claimed
bakcwards compatable-ish

That said its still worth considering imho because of the reasons stated
(and honestly one particular simple reading of the docs might suggest that
this was thr intended behavior all along). Im not a member of Rcore through
so i cant do said considering myself.

Best,
~G

On Feb 20, 2018 7:15 PM, <frederik at ofb.net> wrote:

Hi Scott,

I tried the new patch and can confirm that it has the advertised
behavior on a couple of test cases. I think it makes sense to apply
it, because any existing code which refers to a second duplicate
data.frame column by name is already broken, while if the reference is
by numerical index then changing the column name shouldn't break it.

I don't know if you need to update the documentation as part of your
patch, or if whoever applies it would be happy to do that. Somebody
from R core want to weigh in on this?

I attach a file with the test example from your original email as well
as a second test case I added with two "by" columns.

Thanks,

Frederick

On Wed, Feb 21, 2018 at 10:06:21AM +1100, Scott Ritchie wrote:
> Hi Frederick,
>
> It looks like I didn't overwrite the patch.diff file after the last edits.
> Here's the correct patch (attached and copied below):
>
> Index: src/library/base/R/merge.R
> ===================================================================
> --- src/library/base/R/merge.R (revision 74280)
> +++ src/library/base/R/merge.R (working copy)
> @@ -157,6 +157,14 @@
>          }
>
>          if(has.common.nms) names(y) <- nm.y
> +        ## If by.x %in% names(y) then duplicate column names still arise,
> +        ## apply suffixes to just y - this keeps backwards compatibility
> +        ## when referring to by.x in the resulting data.frame
> +        dupe.keyx <- intersect(nm.by, names(y))
> +        if(length(dupe.keyx)) {
> +          if(nzchar(suffixes[2L]))
> +            names(y)[match(dupe.keyx, names(y), 0L)] <- paste(dupe.keyx,
> suffixes[2L], sep="")
> +        }
>          nm <- c(names(x), names(y))
>          if(any(d <- duplicated(nm)))
>              if(sum(d) > 1L)
>
> Best,
>
> Scott
>
> On 21 February 2018 at 08:23, <frederik at ofb.net> wrote:
>
> > Hi Scott,
> >
> > I think that's a good idea and I tried your patch on my copy of the
> > repository. But it looks to me like the recent patch is identical to
> > the previous one, can you confirm this?
> >
> > Frederick
> >
> > On Mon, Feb 19, 2018 at 07:19:32AM +1100, Scott Ritchie wrote:
> > > Thanks Gabriel,
> > >
> > > I think your suggested approach is 100% backwards compatible
> > >
> > > Currently in the case of duplicate column names only the first can be
> > > indexed by its name. This will always be the column appearing in by.x,
> > > meaning the column in y with the same name cannot be accessed.
Appending
> > > ".y" (suffixes[2L]) to this column means it can now be accessed, while
> > > keeping the current behaviour of making the key columns always
accessible
> > > by using the names provided to by.x.
> > >
> > > I've attached a new patch that has this behaviour.
> > >
> > > Best,
> > >
> > > Scott
> > >
> > > On 19 February 2018 at 05:08, Gabriel Becker <gmbecker at ucdavis.edu>
> > wrote:
> > >
> > > > It seems like there is a way that is backwards compatible-ish in the
> > sense
> > > > mentioned and still has the (arguably, but a good argument I think)
> > better
> > > > behavior:
> > > >
> > > > if by.x is 'name', (AND by.y is not also 'name'), then x's 'name'
> > column
> > > > is called name and y's 'name' column (not used int he merge) is
> > changed to
> > > > name.y.
> > > >
> > > > Now of course this would still change output, but it would change
it to
> > > > something I think would be better, while retaining the 'merge
columns
> > > > retain their exact names' mechanic as documented.
> > > >
> > > > ~G
> > > >
> > > > On Sat, Feb 17, 2018 at 6:50 PM, Scott Ritchie <
s.ritchie73 at gmail.com>
> > > > wrote:
> > > >
> > > >> Thanks Duncan and Frederick,
> > > >>
> > > >> I suspected as much - there doesn't appear to be any reason why
> > conflicts
> > > >> between by.x and names(y) shouldn't and cannot be checked, but I
can
> > see
> > > >> how this might be more trouble than its worth given it potentially
may
> > > >> break downstream packages (i.e. any cases where this occurs but
they
> > > >> expect
> > > >> the name of the key column(s) to remain the same).
> > > >>
> > > >> Best,
> > > >>
> > > >> Scott
> > > >>
> > > >> On 18 February 2018 at 11:48, Duncan Murdoch <
> > murdoch.duncan at gmail.com>
> > > >> wrote:
> > > >>
> > > >> > On 17/02/2018 6:36 PM, frederik at ofb.net wrote:
> > > >> >
> > > >> >> Hi Scott,
> > > >> >>
> > > >> >> Thanks for the patch. I'm not really involved in R development;
it
> > > >> >> will be up to someone in the R core team to apply it. I would
> > hazard
> > > >> >> to say that even if correct (I haven't checked), it will not be
> > > >> >> applied because the change might break existing code. For
example
> > it
> > > >> >> seems like reasonable code might easily assume that a column
with
> > the
> > > >> >> same name as "by.x" exists in the output of 'merge'. That's
just my
> > > >> >> best guess... I don't participate on here often.
> > > >> >>
> > > >> >
> > > >> >
> > > >> > I think you're right.  If I were still a member of R Core, I
would
> > want
> > > >> to
> > > >> > test this against all packages on CRAN and Bioconductor, and
since
> > that
> > > >> > test takes a couple of days to run on my laptop, I'd probably
never
> > get
> > > >> > around to it.
> > > >> >
> > > >> > There are lots of cases where "I would have done that
differently",
> > but
> > > >> > most of them are far too much trouble to change now that R is
more
> > than
> > > >> 20
> > > >> > years old.  And in many cases it will turn out that the way R
does
> > it
> > > >> > actually does make more sense than the way I would have done it.
> > > >> >
> > > >> > Duncan Murdoch
> > > >> >
> > > >> >
> > > >> >
> > > >> >> Cheers,
> > > >> >>
> > > >> >> Frederick
> > > >> >>
> > > >> >> On Sat, Feb 17, 2018 at 04:42:21PM +1100, Scott Ritchie wrote:
> > > >> >>
> > > >> >>> The attached patch.diff will make merge.data.frame() append the
> > > >> suffixes
> > > >> >>> to
> > > >> >>> columns with common names between by.x and names(y).
> > > >> >>>
> > > >> >>> Best,
> > > >> >>>
> > > >> >>> Scott Ritchie
> > > >> >>>
> > > >> >>> On 17 February 2018 at 11:15, Scott Ritchie <
> > s.ritchie73 at gmail.com>
> > > >> >>> wrote:
> > > >> >>>
> > > >> >>> Hi Frederick,
> > > >> >>>>
> > > >> >>>> I would expect that any duplicate names in the resulting
> > data.frame
> > > >> >>>> would
> > > >> >>>> have the suffixes appended to them, regardless of whether or
not
> > they
> > > >> >>>> are
> > > >> >>>> used as the join key. So in my example I would expect
"names.x"
> > and
> > > >> >>>> "names.y" to indicate their source data.frame.
> > > >> >>>>
> > > >> >>>> While careful reading of the documentation reveals this is not
> > the
> > > >> >>>> case, I
> > > >> >>>> would argue the intent of the suffixes functionality should
> > equally
> > > >> be
> > > >> >>>> applied to this type of case.
> > > >> >>>>
> > > >> >>>> If you agree this would be useful, I'm happy to write a patch
for
> > > >> >>>> merge.data.frame that will add suffixes in this case - I
intend
> > to do
> > > >> >>>> the
> > > >> >>>> same for merge.data.table in the data.table package where I
> > initially
> > > >> >>>> encountered the edge case.
> > > >> >>>>
> > > >> >>>> Best,
> > > >> >>>>
> > > >> >>>> Scott
> > > >> >>>>
> > > >> >>>> On 17 February 2018 at 03:53, <frederik at ofb.net> wrote:
> > > >> >>>>
> > > >> >>>> Hi Scott,
> > > >> >>>>>
> > > >> >>>>> It seems like reasonable behavior to me. What result would
you
> > > >> expect?
> > > >> >>>>> That the second "name" should be called "name.y"?
> > > >> >>>>>
> > > >> >>>>> The "merge" documentation says:
> > > >> >>>>>
> > > >> >>>>>      If the columns in the data frames not used in merging
have
> > any
> > > >> >>>>>      common names, these have ?suffixes? (?".x"? and ?".y"?
by
> > > >> default)
> > > >> >>>>>      appended to try to make the names of the result unique.
> > > >> >>>>>
> > > >> >>>>> Since the first "name" column was used in merging, leaving
both
> > > >> >>>>> without a suffix seems consistent with the documentation...
> > > >> >>>>>
> > > >> >>>>> Frederick
> > > >> >>>>>
> > > >> >>>>> On Fri, Feb 16, 2018 at 09:08:29AM +1100, Scott Ritchie
wrote:
> > > >> >>>>>
> > > >> >>>>>> Hi,
> > > >> >>>>>>
> > > >> >>>>>> I was unable to find a bug report for this with a cursory
> > search,
> > > >> but
> > > >> >>>>>>
> > > >> >>>>> would
> > > >> >>>>>
> > > >> >>>>>> like clarification if this is intended or unavoidable
> > behaviour:
> > > >> >>>>>>
> > > >> >>>>>> ```{r}
> > > >> >>>>>> # Create example data.frames
> > > >> >>>>>> parents <- data.frame(name=c("Sarah", "Max", "Qin", "Lex"),
> > > >> >>>>>>                        sex=c("F", "M", "F", "M"),
> > > >> >>>>>>                        age=c(41, 43, 36, 51))
> > > >> >>>>>> children <- data.frame(parent=c("Sarah", "Max", "Qin"),
> > > >> >>>>>>                         name=c("Oliver", "Sebastian",
> > "Kai-lee"),
> > > >> >>>>>>                         sex=c("M", "M", "F"),
> > > >> >>>>>>                         age=c(5,8,7))
> > > >> >>>>>>
> > > >> >>>>>> # Merge() creates a duplicated "name" column:
> > > >> >>>>>> merge(parents, children, by.x = "name", by.y = "parent")
> > > >> >>>>>> ```
> > > >> >>>>>>
> > > >> >>>>>> Output:
> > > >> >>>>>> ```
> > > >> >>>>>>     name sex.x age.x      name sex.y age.y
> > > >> >>>>>> 1   Max     M    43 Sebastian     M     8
> > > >> >>>>>> 2   Qin     F    36   Kai-lee     F     7
> > > >> >>>>>> 3 Sarah     F    41    Oliver     M     5
> > > >> >>>>>> Warning message:
> > > >> >>>>>> In merge.data.frame(parents, children, by.x = "name", by.y =
> > > >> >>>>>> "parent") :
> > > >> >>>>>>    column name ?name? is duplicated in the result
> > > >> >>>>>> ```
> > > >> >>>>>>
> > > >> >>>>>> Kind Regards,
> > > >> >>>>>>
> > > >> >>>>>> Scott Ritchie
> > > >> >>>>>>
> > > >> >>>>>>        [[alternative HTML version deleted]]
> > > >> >>>>>>
> > > >> >>>>>> ______________________________________________
> > > >> >>>>>> R-devel at r-project.org mailing list
> > > >> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> > > >> >>>>>>
> > > >> >>>>>>
> > > >> >>>>>
> > > >> >>>>
> > > >> >>>>
> > > >> >> Index: src/library/base/R/merge.R
> > > >> >>> ============================================================
> > =======
> > > >> >>> --- src/library/base/R/merge.R  (revision 74264)
> > > >> >>> +++ src/library/base/R/merge.R  (working copy)
> > > >> >>> @@ -157,6 +157,15 @@
> > > >> >>>           }
> > > >> >>>             if(has.common.nms) names(y) <- nm.y
> > > >> >>> +        ## If by.x %in% names(y) then duplicate column names
> > still
> > > >> >>> arise,
> > > >> >>> +        ## apply suffixes to these
> > > >> >>> +        dupe.keyx <- intersect(nm.by, names(y))
> > > >> >>> +        if(length(dupe.keyx)) {
> > > >> >>> +          if(nzchar(suffixes[1L]))
> > > >> >>> +            names(x)[match(dupe.keyx, names(x), 0L)] <-
> > > >> >>> paste(dupe.keyx, suffixes[1L], sep="")
> > > >> >>> +          if(nzchar(suffixes[2L]))
> > > >> >>> +            names(y)[match(dupe.keyx, names(y), 0L)] <-
> > > >> >>> paste(dupe.keyx, suffixes[2L], sep="")
> > > >> >>> +        }
> > > >> >>>           nm <- c(names(x), names(y))
> > > >> >>>           if(any(d <- duplicated(nm)))
> > > >> >>>               if(sum(d) > 1L)
> > > >> >>>
> > > >> >>
> > > >> >> ______________________________________________
> > > >> >> R-devel at r-project.org mailing list
> > > >> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> > > >> >>
> > > >> >>
> > > >> >
> > > >>
> > > >>         [[alternative HTML version deleted]]
> > > >>
> > > >> ______________________________________________
> > > >> R-devel at r-project.org mailing list
> > > >> https://stat.ethz.ch/mailman/listinfo/r-devel
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > Gabriel Becker, PhD
> > > > Scientist (Bioinformatics)
> > > > Genentech Research
> > > >
> >
> > > Index: src/library/base/R/merge.R
> > > ===================================================================
> > > --- src/library/base/R/merge.R        (revision 74264)
> > > +++ src/library/base/R/merge.R        (working copy)
> > > @@ -157,6 +157,15 @@
> > >          }
> > >
> > >          if(has.common.nms) names(y) <- nm.y
> > > +        ## If by.x %in% names(y) then duplicate column names still
> > arise,
> > > +        ## apply suffixes to these
> > > +        dupe.keyx <- intersect(nm.by, names(y))
> > > +        if(length(dupe.keyx)) {
> > > +          if(nzchar(suffixes[1L]))
> > > +            names(x)[match(dupe.keyx, names(x), 0L)] <-
> > paste(dupe.keyx, suffixes[1L], sep="")
> > > +          if(nzchar(suffixes[2L]))
> > > +            names(y)[match(dupe.keyx, names(y), 0L)] <-
> > paste(dupe.keyx, suffixes[2L], sep="")
> > > +        }
> > >          nm <- c(names(x), names(y))
> > >          if(any(d <- duplicated(nm)))
> > >              if(sum(d) > 1L)
> >
> > > ______________________________________________
> > > R-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >

> Index: src/library/base/R/merge.R
> ===================================================================
> --- src/library/base/R/merge.R        (revision 74280)
> +++ src/library/base/R/merge.R        (working copy)
> @@ -157,6 +157,14 @@
>          }
>
>          if(has.common.nms) names(y) <- nm.y
> +        ## If by.x %in% names(y) then duplicate column names still arise,
> +        ## apply suffixes to just y - this keeps backwards compatibility
> +        ## when referring to by.x in the resulting data.frame
> +        dupe.keyx <- intersect(nm.by, names(y))
> +        if(length(dupe.keyx)) {
> +          if(nzchar(suffixes[2L]))
> +            names(y)[match(dupe.keyx, names(y), 0L)] <- paste(dupe.keyx,
suffixes[2L], sep="")
> +        }
>          nm <- c(names(x), names(y))
>          if(any(d <- duplicated(nm)))
>              if(sum(d) > 1L)

	[[alternative HTML version deleted]]



[Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y
Gabriel Becker