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Scott Ritchie

2018-Feb-20 23:06 UTC

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

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
>
>
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frederik at ofb.net

2018-Feb-21 03:15 UTC

head link

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

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)

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Gabriel Becker

2018-Feb-21 15:11 UTC

head link

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

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]]

Martin Maechler

2018-Feb-22 11:31 UTC

head link

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

>>>>> 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

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