[R] rbind of multiple data frames by column name, when each data frames can contain different columns

Avi Gross @v|gro@@ @end|ng |rom ver|zon@net
Fri Jun 3 20:51:15 CEST 2022


Complexity has all kinds of costs and tradeoffs. In one sense you are doing a conceptual merge between related but not identical database tables albeit from a set of .CSV files.

You do have some  conceptually direct ways using base R or packages like dplyr that  possibly do it in a more complex way outside your view. Hypothetically, you could even work sideways and open a connection to a database and store the contents of each .CSV files into a relational table and then issue some SQL commands asking to do the merge and read them back but that would be weird and overkill as R has similar abilities.

But underneath the covers, as shown by the longer code, the R functionality has to determine what field/column names are common between pairs of data.frames and fill any missing ones with NA and so on, perhaps faster than the code being shown and perhaps not. Much depends on the code used and how general it is as it is often weighted down by lots of additional functionality you are not using, and whether it has big chunks being used that were rewritten in C or C++ or other libraries from FORTRAN ...

But unless the amount of data gets huge and it takes too much time or memory, I would opt for the conceptually simpler method of using merge() or the full_join() in dplyr, or as pointed out, other techniques by changing the formats. I can think of other ways such as getting the combined column names from all the files, then adding missing ones to each data.frame full of NA as needed, then reordering the columns so they all are identical, and finally vertically combining all the resulting rows. Again note the internal methods used by any merge method (including in SQL) may simply automate tasks.

The more complex methods shown strike me as a tad painful to read, let alone to modify when your needs change. Just because some people can program all kinds of things in low-level languages like assembler, that does not justify spending months on what can be done in days or even minutes using pre-built and pre-tested methods layered one upon another.

If there is already an acceptable function that already accepts a list of such overlapping data.frames, then other than HW problems, that might be even better. It looks fairly easy to construct such a function based on the discussion so I wonder if some package already has one.


-----Original Message-----
From: CALUM POLWART <polc1410 using gmail.com>
To: Bert Gunter <bgunter.4567 using gmail.com>
Cc: r-help using R-project.org <r-help using r-project.org>; Stefano Sofia <stefano.sofia using regione.marche.it>
Sent: Fri, Jun 3, 2022 3:48 am
Subject: Re: [R] rbind of multiple data frames by column name, when each data frames can contain different columns

Bert! It sounds like you are warming to the the tidyverse! ;-)

I completed agree with your analysis this data would be best served long as
you have shown.

If the OP was going to use tidy to manipulate it, they can do the same with
tidyr::pivot_ functions (pivot_longer and pivot_wider). The result will be
the same - but understanding how it happened may be easier!

On Thu, 2 Jun 2022, 21:04 Bert Gunter, <bgunter.4567 using gmail.com> wrote:

> Well, it seems better to me to put all the data frames in long format and
> then rbind them instead of the other way round, which results in the piles
> of NA's you see. I note also, FWIW, that this accords with the so-called
> "tidy" format that many advocate these days. You can always subset (rows)
> and choose by station, date, etc. as needed, of course from the long
> format.
>
> Because of the regularity of your data frames, it is easy to do this. Here
> is a little base R function that "reforms" each data frame (I suspect Rui
> may well provide a more elegant version, though):
>
>
> reform<- function(dat){
>    nm <- names(dat)
>    stanums <- unique(gsub("[^[:digit:]]","", nm[-1])) ## station numbers
> present
>    z <- do.call(rbind, lapply(stanums,
>      \(i)
>      structure(dat[,grep(i, nm, fixed = TRUE)],
>                names = c("Hs", "Hn", "flag"))))
>    data.frame(POSIX =rep(dat[,1], length(stanums)),
>              Station = rep(stanums, e = nrow(dat)),
>              z)
> }
>
> e.g.
> > reform(df2)
>        POSIX Station Hs Hn flag
> 1  2001-12-01      1 50 20    0
> 2  2001-12-02      1 60 20    0
> 3  2001-12-03      1 70 20    0
> 4  2001-12-04      1 NA NA  NA
> 5  2001-12-05      1 NA NA  NA
> 6  2001-12-01      3 20  0    0
> 7  2001-12-02      3 20  0    0
> 8  2001-12-03      3 30 10    0
> 9  2001-12-04      3 30  0    1
> 10 2001-12-05      3  0  5    0
>
> A call to rbind() of the following form then gives you all your data in
> long form(you may wish to use some shortcuts to form the list of frames):
>
> > do.call(rbind, lapply(list(df1, df2, df3), reform))
>        POSIX Station Hs Hn flag
> 1  2000-12-01      1 30 10    0
> 2  2000-12-02      1 40 20    0
> 3  2000-12-03      1 50 10    0
> 4  2000-12-04      1 NA NA  NA
> 5  2000-12-05      1 55  5    0
> 6  2000-12-01      2 20  0    0
> 7  2000-12-02      2 20  0    0
> 8  2000-12-03      2 30 10    0
> 9  2000-12-04      2 30  0    1
> 10 2000-12-05      2  0  5    0
> 11 2001-12-01      1 50 20    0
> 12 2001-12-02      1 60 20    0
> 13 2001-12-03      1 70 20    0
> 14 2001-12-04      1 NA NA  NA
> 15 2001-12-05      1 NA NA  NA
> 16 2001-12-01      3 20  0    0
> 17 2001-12-02      3 20  0    0
> 18 2001-12-03      3 30 10    0
> 19 2001-12-04      3 30  0    1
> 20 2001-12-05      3  0  5    0
> 21 2002-12-01      2 50 20    0
> 22 2002-12-02      2 60 20    0
> 23 2002-12-03      2 70 20    0
> 24 2002-12-04      2 NA NA  NA
> 25 2002-12-05      2 NA NA  NA
> 26 2002-12-01      3 20  0    0
> 27 2002-12-02      3 20  0    0
> 28 2002-12-03      3 30 10    0
> 29 2002-12-04      3 30  0    1
> 30 2002-12-05      3  0  5    0
>
>
> Cheers,
> Bert Gunter
>
>
>
>
> On Wed, Jun 1, 2022 at 11:13 PM Stefano Sofia <
> stefano.sofia using regione.marche.it> wrote:
>
> > Dear R-list users,
> >
> > for each winter season from 2000 to 2022 I have a data frame collecting
> > for different weather stations snowpack height (Hs), snowfall in the last
> > 24h (Hn) and a validation flag.
> >
> > Suppose I have these three following data frames
> >
> >
> > df1 <- data.frame(data_POSIX=seq(as.POSIXct("2000-12-01",
> > format="%Y-%m-%d", tz="Etc/GMT-1"), as.POSIXct("2000-12-05",
> > format="%Y-%m-%d", tz="Etc/GMT-1"), by="1 days"), Station1_Hs = c(30, 40,
> > 50, NA, 55), Station1_Hn = c(10, 20, 10, NA, 5), Station1_flag = c(0, 0,
> 0,
> > NA, 0), Station2_Hs = c(20, 20, 30, 30, 0), Station2_Hn = c(0, 0, 10, 0,
> > 5), Station2_flag = c(0, 0, 0, 1, 0))
> >
> >
> > df2 <- data.frame(data_POSIX=seq(as.POSIXct("2001-12-01",
> > format="%Y-%m-%d", tz="Etc/GMT-1"), as.POSIXct("2001-12-05",
> > format="%Y-%m-%d", tz="Etc/GMT-1"), by="1 days"), Station1_Hs = c(50, 60,
> > 70, NA, NA), Station1_Hn = c(20, 20, 20, NA, NA), Station1_flag = c(0, 0,
> > 0, NA, NA), Station3_Hs = c(20, 20, 30, 30, 0), Station3_Hn = c(0, 0, 10,
> > 0, 5), Station3_flag = c(0, 0, 0, 1, 0))
> >
> >
> > df3 <- data.frame(data_POSIX=seq(as.POSIXct("2002-12-01",
> > format="%Y-%m-%d", tz="Etc/GMT-1"), as.POSIXct("2002-12-05",
> > format="%Y-%m-%d", tz="Etc/GMT-1"), by="1 days"), Station2_Hs = c(50, 60,
> > 70, NA, NA), Station2_Hn = c(20, 20, 20, NA, NA), Station2_flag = c(0, 0,
> > 0, NA, NA), Station3_Hs = c(20, 20, 30, 30, 0), Station3_Hn = c(0, 0, 10,
> > 0, 5), Station3_flag = c(0, 0, 0, 1, 0))
> >
> >
> > As you can see, each data frame can have different stations loaded.
> >
> > I would need to call rbind matching data frames by column name (i.e. by
> > station name), keeping in mind that the number of stations loaded in each
> > data frame may differ. The result should be
> >
> > data_POSIX Station1_Hs Station1_Hn Station1_flag Station2_Hs Station2_Hn
> > Station2_flag Station3_Hs Station3_Hn Station3_flag
> > 2000-12-01 30 10 0 20 0 0 NA NA NA
> > 2000-12-02 40 20 0 20 0 0 NA NA NA
> > 2000-12-03 50 10 0 30 10 0 NA NA NA
> > 2000-12-04 NA NA NA 30 0 0 NA NA NA
> > 2000-12-05 55 5 0 0 5 0 NA NA NA
> > 2001-12-01 50 20 0 NA NA NA 20 0 0
> > 2001-12-02 60 20 0 NA NA NA 20 0 0
> > 2001-12-03 70 20 0 NA NA NA 30 10 0
> > 2001-12-04 NA NA NA NA NA NA 30 0 1
> > 2001-12-05 NA NA NA NA NA NA 0 5 0
> > 2002-12-01 NA NA NA 50 20 0 20 0 0
> > 2002-12-02 NA NA NA 60 20 0 20 0 0
> > 2002-12-03 NA NA NA 70 20 0 30 10 0
> > 2002-12-04 NA NA NA NA NA NA 30 0 1
> > 2002-12-05 NA NA NA NA NA NA 0 5 0
> >
> > I tried this code
> >
> > df_list <- list(df1, df2, df3)
> > allNms <- unique(unlist(lapply(df_list, names)))
> > do.call(rbind, c(lapply(df_list, function(x) data.frame(c(x,
> > sapply(setdiff(allNms, names(x)), function(y) NA)))),
> make.row.names=FALSE))
> >
> > but I get this error:
> > Error in (function (..., row.names = NULL, check.rows = FALSE,
> check.names
> > = TRUE,  :
> >  arguments imply differing number of rows
> >
> > Could someone please help me?
> >
> >
> > Thank you for your attention
> >
> > Stefano
> >
> >
> >          (oo)
> > --oOO--( )--OOo--------------------------------------
> > Stefano Sofia PhD
> > Civil Protection - Marche Region - Italy
> > Meteo Section
> > Snow Section
> > Via del Colle Ameno 5
> > 60126 Torrette di Ancona, Ancona (AN)
> > Uff: +39 071 806 7743
> > E-mail: stefano.sofia using regione.marche.it
> > ---Oo---------oO----------------------------------------
> >
> > ________________________________
> >
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