From s.ritchie73 at gmail.com  Fri Feb 23 02:32:41 2018
From: s.ritchie73 at gmail.com (Scott Ritchie)
Date: Fri, 23 Feb 2018 12:32:41 +1100
Subject: [Rd] 
 Duplicate column names created by base::merge() when by.x has
 the same name as a column in y
In-Reply-To: <23182.43548.14172.267191@stat.math.ethz.ch>
References: <20180216165344.GB32564@ofb.net>
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Message-ID: <CAO1VBV1-DtKPUvWLgPywsQ71aibr__OZ0vWUp3_dbpvisE8+Zw@mail.gmail.com>

Thanks Martin!

Can you clarify the functionality of the 'no.dups' argument so I can change
my patch to `data.table:::merge.data.table` accordingly?

- When `no.dups=TRUE` will the suffix to the by.x column name? Or will it
take the functionality of the second functionality where only the column in
y has the suffix added?
- When `no.dups=FALSE` will the output be the same as it currently (no
suffix added to either column)? Or will add the suffix to the column in y?

Best,

Scott

On 22 February 2018 at 22:31, Martin Maechler <maechler at stat.math.ethz.ch>
wrote:

> >>>>> Gabriel Becker <gmbecker at ucdavis.edu>
> >>>>>     on Wed, 21 Feb 2018 07:11:44 -0800 writes:
>
>     > 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
>
> exactly.
>
>     > 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.
>
> I agree with Scott, Frederik and you that this changes seems
> worth considering.
> As Duncan Murdoch has mentioned, this alone may not be
> sufficient.
>
> In addition to your proposed patch (which I have simplified, not
> using intersection() but working with underlying  match()
> directly), it is little work to introduce an extra argument, I'm
> calling  'no.dups = TRUE'  which when set to false would mirror
> current R's behavior... and documenting it, then also documents the
> new behavior (to some extent).
>
> My plan is to commit it soonish ;-)
> Martin
>
>     > 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]]
>
>     > ______________________________________________
>     > R-devel at r-project.org mailing list
>     > https://stat.ethz.ch/mailman/listinfo/r-devel
>

	[[alternative HTML version deleted]]



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