sum multiple csv files

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sum multiple csv files

Alejandra Lopez-Galan
Hi, I am pretty new to R and I would apreciatte very much your help to
solve my problem. I have 40 csv files that have the same structure, and I
want to merge them into a single data frame.

I already have load and combined all the cvs files into a large list, and I
created two

filenames <- list.files('data',full.names=TRUE)

All_data <- lapply(filenames,function(i){
  ###read cvs files and add the row and column names to each data frame###
  read.csv(i, header=FALSE, sep = "", col.names = col_names, row.names =
row_names)
 })

However I would like to sum the rows of cvs files to get a single data
frame (each cvs file has 47 rows and colunms, so the final data frame
should have the same). I could only do it one by one data data frame, but I
was wondering if anyone could give an idea of how to write a function for
this.

Thanks,
Alejandra

        [[alternative HTML version deleted]]

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Re: sum multiple csv files

Jérémie Juste
Alejandra Lopez-Galan <[hidden email]> writes:
Hello,

I'm not sure to fully answer you question but I'll give it a try. I'll
use the library "data.table" as I forgot how to do it in base R. If you
don't have it you will have to install it by doing

> install.packages(data.table,repos ="http://cran.us.r-project.org")

let's say you have this list of data.frame

> lapply(1:2,function(x) data.frame(B=letters[1:10],A=rnorm(10)))

## [[1]]
##     B          A
##  1 a  1.8276026
##  2 b  0.2870562
##  3 c -0.6304431
##  4 d  0.3066375
##  5 e  0.3274438
##  6 f  0.3370640
##  7 g -1.6660051
##  8 h -0.3736336
##  9 i  0.1494459
## 10 j -1.0036616

## [[2]]
##     B          A
##  1 a -1.1488812
##  2 b -0.4423796
##  3 c -0.2690834
##  4 d -1.1390742
##  5 e  0.7142574
##  6 f  0.3316523
##  7 g  0.3187546
##  8 h  0.1099996
##  9 i  0.3972000
## 10 j  0.4749161

and want to sum the A column for each data.frame then you can use the
following:

# Assign the list to the variable aa
aa <- lapply(1:2,function(x) data.table(B=letters[1:10],A=rnorm(10)))

then:
> >lapply(aa,function(x) data.table(x)[,sum(A)])

## [[1]]
## [1] 6.533179

## [[2]]
## [1] 2.075677


Notice that I converted the each data.frame to a data.table and then sum
the column A.

If you want to bind the resutls together you can do
do.call(rbind,lapply(aa,function(x) data.table(x)[,sum(A)]))

          [,1]
[1,] -9.377476
[2,] -3.853971

HTH,

Best Regards,

Jeremie







> Hi, I am pretty new to R and I would apreciatte very much your help to
> solve my problem. I have 40 csv files that have the same structure, and I
> want to merge them into a single data frame.
>
> I already have load and combined all the cvs files into a large list, and I
> created two
>
> filenames <- list.files('data',full.names=TRUE)
>
> All_data <- lapply(filenames,function(i){
>   ###read cvs files and add the row and column names to each data frame###
>   read.csv(i, header=FALSE, sep = "", col.names = col_names, row.names =
> row_names)
>  })
>
> However I would like to sum the rows of cvs files to get a single data
> frame (each cvs file has 47 rows and colunms, so the final data frame
> should have the same). I could only do it one by one data data frame, but I
> was wondering if anyone could give an idea of how to write a function for
> this.
>
> Thanks,
> Alejandra
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: sum multiple csv files

PIKAL Petr
In reply to this post by Alejandra Lopez-Galan
Hi

see in line

> -----Original Message-----
> From: R-help [mailto:[hidden email]] On Behalf Of Alejandra
> Lopez-Galan
> Sent: Monday, January 15, 2018 10:29 AM
> To: [hidden email]
> Subject: [R] sum multiple csv files
>
> Hi, I am pretty new to R and I would apreciatte very much your help to solve
> my problem. I have 40 csv files that have the same structure, and I want to
> merge them into a single data frame.
>
> I already have load and combined all the cvs files into a large list, and I created
> two
>
> filenames <- list.files('data',full.names=TRUE)
>
> All_data <- lapply(filenames,function(i){
>   ###read cvs files and add the row and column names to each data frame###
>   read.csv(i, header=FALSE, sep = "", col.names = col_names, row.names =
> row_names)
>  })
>
> However I would like to sum the rows of cvs files to get a single data frame
> (each cvs file has 47 rows and colunms, so the final data frame should have the
> same). I could only do it one by one data data frame, but I was wondering if

And here I am rather lost. The only possible solution (to me) is to sum all values in first row of file 1, 2, 3, ...

In that case probably the easiest way is to change list to array

aaa<-array(unlist(All_data), dim=c(47,47, 40))
result <- apply(aaa,1:2,sum)

Example:

lll <- structure(list(A = structure(list(V1 = 1:3, V2 = 4:6, V3 = 7:9,
    V4 = 10:12), .Names = c("V1", "V2", "V3", "V4"), row.names = c(NA,
-3L), class = "data.frame"), B = structure(list(V1 = 1:3, V2 = 4:6,
    V3 = 7:9, V4 = 10:12), .Names = c("V1", "V2", "V3", "V4"), row.names = c(NA,
-3L), class = "data.frame")), .Names = c("A", "B"))

> aaa<-array(unlist(lll), dim=c(3,4,2))
> aaa
, , 1

     [,1] [,2] [,3] [,4]
[1,]    1    4    7   10
[2,]    2    5    8   11
[3,]    3    6    9   12

, , 2

     [,1] [,2] [,3] [,4]
[1,]    1    4    7   10
[2,]    2    5    8   11
[3,]    3    6    9   12

> apply(aaa,1:2,sum)
     [,1] [,2] [,3] [,4]
[1,]    2    8   14   20
[2,]    4   10   16   22
[3,]    6   12   18   24

Cheers
Petr

> anyone could give an idea of how to write a function for this.
>
> Thanks,
> Alejandra
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: sum multiple csv files

Jeff Newmiller
In reply to this post by Alejandra Lopez-Galan
Your message seems unclear, and as evidence the respondents are giving various answers. You should provide a small sample of input and output data as it would look in R to avoid this kind of thrashing about. See [1][2][3] for guidance. Note that you also really need to figure out how to make sure your email program sends plain text, because HTML formatting WILL be stripped by the mailing list (read the Posting Guide) and that process often garbles it.

My own possibly-confused reading of your question ("each cvs file has 47 rows and colunms, so the final data frame should have the same") is that you do not yet understand the difference between matrices and data frames ([4]), and you want to perform matrix (element-wise) addition. This would require that you convert the data frames read in by read.csv into matrices before adding them:

All_data <- lapply(filenames
,function(i){
###read cvs files and add the row and column names to each data frame
###
 as.matrix( read.csv(i, header=FALSE, sep = "", col.names = col_names, row.names = row_names)
})

result <- Reduce( `+`, All_data )

This will fail if any of the values in your csv files are non-numeric, but dealing with that would require us to know specifics about your files or intent that you have omitted. (The dput function is indispensable for clarifying such issues [1][2].)
---

[1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

[2] http://adv-r.had.co.nz/Reproducibility.html

[3] https://cran.r-project.org/web/packages/reprex/index.html (read the vignette)

[4] see "Introduction to R" (part of the R documentation)

--
Sent from my phone. Please excuse my brevity.

On January 15, 2018 1:29:05 AM PST, Alejandra Lopez-Galan <[hidden email]> wrote:

>Hi, I am pretty new to R and I would apreciatte very much your help to
>solve my problem. I have 40 csv files that have the same structure, and
>I
>want to merge them into a single data frame.
>
>I already have load and combined all the cvs files into a large list,
>and I
>created two
>
>filenames <- list.files('data',full.names=TRUE)
>
>All_data <- lapply(filenames,function(i){
>###read cvs files and add the row and column names to each data
>frame###
> read.csv(i, header=FALSE, sep = "", col.names = col_names, row.names =
>row_names)
> })
>
>However I would like to sum the rows of cvs files to get a single data
>frame (each cvs file has 47 rows and colunms, so the final data frame
>should have the same). I could only do it one by one data data frame,
>but I
>was wondering if anyone could give an idea of how to write a function
>for
>this.
>
>Thanks,
>Alejandra
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: sum multiple csv files

Alejandra Lopez-Galan
Hi all,

Thanks for your help and sorry for the confusion. Also Thanks Jeff,
your solution worked well, I was trying to perform matrix
(element-wise) addition as you mentioned, but I didn't know how to
formulate my question. Thanks for the references, they also help me to
understand more.

Cheers,
Alejandra



On Tue, Jan 16, 2018 at 2:35 AM, Jeff Newmiller
<[hidden email]> wrote:

> Your message seems unclear, and as evidence the respondents are giving various answers. You should provide a small sample of input and output data as it would look in R to avoid this kind of thrashing about. See [1][2][3] for guidance. Note that you also really need to figure out how to make sure your email program sends plain text, because HTML formatting WILL be stripped by the mailing list (read the Posting Guide) and that process often garbles it.
>
> My own possibly-confused reading of your question ("each cvs file has 47 rows and colunms, so the final data frame should have the same") is that you do not yet understand the difference between matrices and data frames ([4]), and you want to perform matrix (element-wise) addition. This would require that you convert the data frames read in by read.csv into matrices before adding them:
>
> All_data <- lapply(filenames
> ,function(i){
> ###read cvs files and add the row and column names to each data frame
> ###
>  as.matrix( read.csv(i, header=FALSE, sep = "", col.names = col_names, row.names = row_names)
> })
>
> result <- Reduce( `+`, All_data )
>
> This will fail if any of the values in your csv files are non-numeric, but dealing with that would require us to know specifics about your files or intent that you have omitted. (The dput function is indispensable for clarifying such issues [1][2].)
> ---
>
> [1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
>
> [2] http://adv-r.had.co.nz/Reproducibility.html
>
> [3] https://cran.r-project.org/web/packages/reprex/index.html (read the vignette)
>
> [4] see "Introduction to R" (part of the R documentation)
>
> --
> Sent from my phone. Please excuse my brevity.
>
> On January 15, 2018 1:29:05 AM PST, Alejandra Lopez-Galan <[hidden email]> wrote:
>>Hi, I am pretty new to R and I would apreciatte very much your help to
>>solve my problem. I have 40 csv files that have the same structure, and
>>I
>>want to merge them into a single data frame.
>>
>>I already have load and combined all the cvs files into a large list,
>>and I
>>created two
>>
>>filenames <- list.files('data',full.names=TRUE)
>>
>>All_data <- lapply(filenames,function(i){
>>###read cvs files and add the row and column names to each data
>>frame###
>> read.csv(i, header=FALSE, sep = "", col.names = col_names, row.names =
>>row_names)
>> })
>>
>>However I would like to sum the rows of cvs files to get a single data
>>frame (each cvs file has 47 rows and colunms, so the final data frame
>>should have the same). I could only do it one by one data data frame,
>>but I
>>was wondering if anyone could give an idea of how to write a function
>>for
>>this.
>>
>>Thanks,
>>Alejandra
>>
>>       [[alternative HTML version deleted]]
>>
>>______________________________________________
>>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide
>>http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.