Unexpected behaviour of write.csv - read.csv

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Hi

Assuming the following:
x <- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame':	10 obs. of  2 variables:
 $ a: int  1 2 3 4 5 6 7 8 9 10
 $ b: num  0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2 <- read.csv("x.csv")
str(x2)
'data.frame':	10 obs. of  3 variables:
 $ X: int  1 2 3 4 5 6 7 8 9 10
 $ a: int  1 2 3 4 5 6 7 8 9 10
 $ b: num  0.692 0.325 0.634 0.16 0.873 ...

Using the two functions write.csv and read.csv, I would assume, that the
resulting data.frame x2 be identical with x, but it has an additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?

And if this is not compliant with csv files, shouldn't the function
read.csv convert the first column into the row names?

Cheers,

Rainer

- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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Hash: SHA1

Hi

Assuming the following:

x<- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame':	10 obs. of  2 variables:
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2<- read.csv("x.csv")
str(x2)
'data.frame':	10 obs. of  3 variables:
  $ X: int  1 2 3 4 5 6 7 8 9 10
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...

Using the two functions write.csv and read.csv, I would assume, that the
resulting data.frame x2 be identical with x, but it has an additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?
I don't think so.  The CSV format is an export format which holds less 
information than a dataframe.  By exporting the dataframe to CSV and 
importing the result, you are discarding information and you should 
expect to get something different.

If you want to save a dataframe to disk and read it back unchanged, you 
should use save() and load().

Duncan Murdoch
And if this is not compliant with csv files, shouldn't the function
read.csv convert the first column into the row names?

Cheers,

Rainer

- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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=d5aG
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______________________________________________
R-help at r-project.org mailing list
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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On 11-01-13 6:26 AM, Rainer M Krug wrote:
Hi

Assuming the following:

x<- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame':    10 obs. of  2 variables:
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2<- read.csv("x.csv")
str(x2)
'data.frame':    10 obs. of  3 variables:
  $ X: int  1 2 3 4 5 6 7 8 9 10
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...

Using the two functions write.csv and read.csv, I would assume, that the
resulting data.frame x2 be identical with x, but it has an additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?

I don't think so.  The CSV format is an export format which holds less
information than a dataframe.  By exporting the dataframe to CSV and
importing the result, you are discarding information and you should
expect to get something different.
OK - I can follow this logic - and I think I can accept it.

If you want to save a dataframe to disk and read it back unchanged, you
should use save() and load().
And now my question from a previous thread (write.table equivalent for
lists?) comes up again:

using save() and load() definitely works, but it is highly unsave - as
it even keeps the names of the object, more then one can be saved, I can
not easily assign the saved object to a new name, I have problems using
the saved object if I have forgotten what the variable name was.

So I would like to expand my previous question: what are the proper
functions to store R objects? One could argue that all write...
functions are export functions - therefore keeping the data, but not
necessarily column names, rownames, attributes, ...

So what can I really do to save an R object for later usage in R?

Rainer

Duncan Murdoch

And if this is not compliant with csv files, shouldn't the function
read.csv convert the first column into the row names?

Cheers,

Rainer

______________________________________________
R-help at r-project.org mailing list
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.

- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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Hi,

I thought this was already clear from the replies to your previous post:
- save/load
- saveObject/loadObject from R.utils
- dput/dget (I don't remember who proposed it sorry)

There might be more possibilities, but that should do what you're 
looking for. And you should already know how each of them work and 
therefore the pros and cons.

HTH,
Ivan

Le 1/13/2011 15:08, Rainer M Krug a ?crit :
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Hash: SHA1

On 01/13/2011 02:56 PM, Duncan Murdoch wrote:
On 11-01-13 6:26 AM, Rainer M Krug wrote:
Hi

Assuming the following:

x<- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame':    10 obs. of  2 variables:
   $ a: int  1 2 3 4 5 6 7 8 9 10
   $ b: num  0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2<- read.csv("x.csv")
str(x2)
'data.frame':    10 obs. of  3 variables:
   $ X: int  1 2 3 4 5 6 7 8 9 10
   $ a: int  1 2 3 4 5 6 7 8 9 10
   $ b: num  0.692 0.325 0.634 0.16 0.873 ...
Using the two functions write.csv and read.csv, I would assume, that the
resulting data.frame x2 be identical with x, but it has an additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?

I don't think so.  The CSV format is an export format which holds less
information than a dataframe.  By exporting the dataframe to CSV and
importing the result, you are discarding information and you should
expect to get something different.
OK - I can follow this logic - and I think I can accept it.

If you want to save a dataframe to disk and read it back unchanged, you
should use save() and load().
And now my question from a previous thread (write.table equivalent for
lists?) comes up again:

using save() and load() definitely works, but it is highly unsave - as
it even keeps the names of the object, more then one can be saved, I can
not easily assign the saved object to a new name, I have problems using
the saved object if I have forgotten what the variable name was.

So I would like to expand my previous question: what are the proper
functions to store R objects? One could argue that all write...
functions are export functions - therefore keeping the data, but not
necessarily column names, rownames, attributes, ...

So what can I really do to save an R object for later usage in R?

Rainer

Duncan Murdoch
And if this is not compliant with csv files, shouldn't the function
read.csv convert the first column into the row names?

Cheers,

Rainer

______________________________________________
R-help at r-project.org mailing list
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.

- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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=xfWD
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______________________________________________
R-help at r-project.org mailing list
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.

Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. S?ugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calandra at uni-hamburg.de

**********
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php
-----Original Message-----
From: r-help-bounces at r-project.org 
[mailto:r-help-bounces at r-project.org] On Behalf Of Ivan Calandra
Sent: Thursday, January 13, 2011 6:44 AM
To: r-help at r-project.org
Subject: Re: [R] Unexpected behaviour of write.csv - read.csv

Hi,

I thought this was already clear from the replies to your 
previous post:
- save/load
- saveObject/loadObject from R.utils
- dput/dget (I don't remember who proposed it sorry)
Add serialize()/unserialize() from base.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
There might be more possibilities, but that should do what you're 
looking for. And you should already know how each of them work and 
therefore the pros and cons.

HTH,
Ivan

Le 1/13/2011 15:08, Rainer M Krug a ?crit :
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On 01/13/2011 02:56 PM, Duncan Murdoch wrote:
On 11-01-13 6:26 AM, Rainer M Krug wrote:
Hi

Assuming the following:

x<- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame':    10 obs. of  2 variables:
   $ a: int  1 2 3 4 5 6 7 8 9 10
   $ b: num  0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2<- read.csv("x.csv")
str(x2)
'data.frame':    10 obs. of  3 variables:
   $ X: int  1 2 3 4 5 6 7 8 9 10
   $ a: int  1 2 3 4 5 6 7 8 9 10
   $ b: num  0.692 0.325 0.634 0.16 0.873 ...
Using the two functions write.csv and read.csv, I would 
assume, that the
resulting data.frame x2 be identical with x, but it has an 
additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, 
but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?

I don't think so.  The CSV format is an export format 
which holds less
information than a dataframe.  By exporting the dataframe 
to CSV and
importing the result, you are discarding information and 
you should
expect to get something different.
OK - I can follow this logic - and I think I can accept it.

If you want to save a dataframe to disk and read it back 
unchanged, you
should use save() and load().
And now my question from a previous thread (write.table 
equivalent for
lists?) comes up again:

using save() and load() definitely works, but it is highly 
unsave - as
it even keeps the names of the object, more then one can be 
saved, I can
not easily assign the saved object to a new name, I have 
problems using
the saved object if I have forgotten what the variable name was.

So I would like to expand my previous question: what are the proper
functions to store R objects? One could argue that all write...
functions are export functions - therefore keeping the data, but not
necessarily column names, rownames, attributes, ...

So what can I really do to save an R object for later usage in R?

Rainer

Duncan Murdoch
And if this is not compliant with csv files, shouldn't the function
read.csv convert the first column into the row names?

Cheers,

Rainer

______________________________________________
R-help at r-project.org mailing list
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.

- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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=xfWD
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______________________________________________
R-help at r-project.org mailing list
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.

-- 
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. S?ugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calandra at uni-hamburg.de

**********
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php

______________________________________________
R-help at r-project.org mailing list
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.

On 11-01-13 6:26 AM, Rainer M Krug wrote:
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Hash: SHA1

Hi

Assuming the following:

x<- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame':	10 obs. of  2 variables:
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2<- read.csv("x.csv")
str(x2)
'data.frame':	10 obs. of  3 variables:
  $ X: int  1 2 3 4 5 6 7 8 9 10
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...

Using the two functions write.csv and read.csv, I would assume, that the
resulting data.frame x2 be identical with x, but it has an additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?
I don't think so.  The CSV format is an export format which holds less 
information than a dataframe.  By exporting the dataframe to CSV and 
importing the result, you are discarding information and you should expect to 
get something different.
You need to read it with read.csv("x.csv", row.names=1)

Nothing in the csv format lets R know that the first column is the row 
names (in the format used by read.table, having a header that is one 
column short does).  Now R could guess that a .csv file with an empty 
string for the first column name is meant to be the row names, but 
that would be merely a guess based on one (barely documented for 
spreadsheets) convention.
If you want to save a dataframe to disk and read it back unchanged, you 
should use save() and load().
Or one of the other serialization options such as serialize() and 
.saveRDS().  R's own admin uses .saveRDS() for such purposes.
Duncan Murdoch

And if this is not compliant with csv files, shouldn't the function
read.csv convert the first column into the row names?

Cheers,

Rainer

- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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______________________________________________
R-help at r-project.org mailing list
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.

______________________________________________
R-help at r-project.org mailing list
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.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
On Thu, Jan 13, 2011 at 1:06 PM, Prof Brian Ripley
On Thu, 13 Jan 2011, Duncan Murdoch wrote:

On 11-01-13 6:26 AM, Rainer M Krug wrote:
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Hash: SHA1

Hi

Assuming the following:

x<- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame': ? 10 obs. of ?2 variables:
?$ a: int ?1 2 3 4 5 6 7 8 9 10
?$ b: num ?0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2<- read.csv("x.csv")
str(x2)
'data.frame': ? 10 obs. of ?3 variables:
?$ X: int ?1 2 3 4 5 6 7 8 9 10
?$ a: int ?1 2 3 4 5 6 7 8 9 10
?$ b: num ?0.692 0.325 0.634 0.16 0.873 ...

Using the two functions write.csv and read.csv, I would assume, that the
resulting data.frame x2 be identical with x, but it has an additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?
I don't think so. ?The CSV format is an export format which holds less
information than a dataframe. ?By exporting the dataframe to CSV and
importing the result, you are discarding information and you should expect
to get something different.
You need to read it with read.csv("x.csv", row.names=1)

Nothing in the csv format lets R know that the first column is the row names
(in the format used by read.table, having a header that is one column short
does). ?Now R could guess that a .csv file with an empty string for the
first column name is meant to be the row names, but that would be merely a
guess based on one (barely documented for spreadsheets) convention.
read.csv / read.table already use heuristics to determine the column
types so adding this to the heuristic seems not to be a departure from
the established philosophy.
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
Another option to consider is instead of save/load to use save/attach.  You save the data, but then instead of loading it back into the global environment you use the attach function to attach it in a new environment (position 2 on the search list by default).  It will be attached with the same name as it had when you saved it, but it will not overwrite something by the same name in the global environment.  You can still use it as it is, or assign it to a new name in the global environment.  When you are through using it you can then detach it.
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Rainer M Krug
> Sent: Thursday, January 13, 2011 7:09 AM
> To: Duncan Murdoch
> Cc: R-help
> Subject: Re: [R] Unexpected behaviour of write.csv - read.csv
> 
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On 01/13/2011 02:56 PM, Duncan Murdoch wrote:
> > On 11-01-13 6:26 AM, Rainer M Krug wrote:
> > Hi
> >
> > Assuming the following:
> >
> >>>> x<- data.frame(a=1:10, b=runif(10))
> >>>> str(x)
> > 'data.frame':    10 obs. of  2 variables:
> >   $ a: int  1 2 3 4 5 6 7 8 9 10
> >   $ b: num  0.692 0.325 0.634 0.16 0.873 ...
> >>>> write.csv(x, "x.csv")
> >>>> x2<- read.csv("x.csv")
> >>>> str(x2)
> > 'data.frame':    10 obs. of  3 variables:
> >   $ X: int  1 2 3 4 5 6 7 8 9 10
> >   $ a: int  1 2 3 4 5 6 7 8 9 10
> >   $ b: num  0.692 0.325 0.634 0.16 0.873 ...
> >>>>
> >
> > Using the two functions write.csv and read.csv, I would assume, that
> the
> > resulting data.frame x2 be identical with x, but it has an additional
> > column X, which contains the row names of x.
> >
> > I know read.table and write.table which work as expected, but I would
> > like to use a csv for data exchange reasons.
> >
> > I know that I can use
> > write.csv(x, "x.csv", row.names=FALSE)
> >
> > and it would work, but shouldn't that be the default behaviour?
> >
> >> I don't think so.  The CSV format is an export format which holds
> less
> >> information than a dataframe.  By exporting the dataframe to CSV and
> >> importing the result, you are discarding information and you should
> >> expect to get something different.
> 
> OK - I can follow this logic - and I think I can accept it.
> 
> >
> >> If you want to save a dataframe to disk and read it back unchanged,
> you
> >> should use save() and load().
> 
> And now my question from a previous thread (write.table equivalent for
> lists?) comes up again:
> 
> using save() and load() definitely works, but it is highly unsave - as
> it even keeps the names of the object, more then one can be saved, I
> can
> not easily assign the saved object to a new name, I have problems using
> the saved object if I have forgotten what the variable name was.
> 
> So I would like to expand my previous question: what are the proper
> functions to store R objects? One could argue that all write...
> functions are export functions - therefore keeping the data, but not
> necessarily column names, rownames, attributes, ...
> 
> So what can I really do to save an R object for later usage in R?
> 
> Rainer
> 
> >
> >> Duncan Murdoch
> >
> >
> > And if this is not compliant with csv files, shouldn't the function
> > read.csv convert the first column into the row names?
> >
> > Cheers,
> >
> > Rainer
> >
> >>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
> 
> - --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
> 
> Centre of Excellence for Invasion Biology
> Natural Sciences Building
> Office Suite 2039
> Stellenbosch University
> Main Campus, Merriman Avenue
> Stellenbosch
> South Africa
> 
> Tel:        +33 - (0)9 53 10 27 44
> Cell:       +27 - (0)8 39 47 90 42
> Fax (SA):   +27 - (0)8 65 16 27 82
> Fax (D) :   +49 - (0)3 21 21 25 22 44
> Fax (FR):   +33 - (0)9 58 10 27 44
> email:      Rainer at krugs.de
> 
> Skype:      RMkrug
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> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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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On Thu, 13 Jan 2011, Duncan Murdoch wrote:

On 11-01-13 6:26 AM, Rainer M Krug wrote:
Hi

Assuming the following:

x<- data.frame(a=1:10, b=runif(10))
str(x)
'data.frame':    10 obs. of  2 variables:
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...
write.csv(x, "x.csv")
x2<- read.csv("x.csv")
str(x2)
'data.frame':    10 obs. of  3 variables:
  $ X: int  1 2 3 4 5 6 7 8 9 10
  $ a: int  1 2 3 4 5 6 7 8 9 10
  $ b: num  0.692 0.325 0.634 0.16 0.873 ...

Using the two functions write.csv and read.csv, I would assume, that the
resulting data.frame x2 be identical with x, but it has an additional
column X, which contains the row names of x.

I know read.table and write.table which work as expected, but I would
like to use a csv for data exchange reasons.

I know that I can use
write.csv(x, "x.csv", row.names=FALSE)

and it would work, but shouldn't that be the default behaviour?
I don't think so.  The CSV format is an export format which holds less
information than a dataframe.  By exporting the dataframe to CSV and
importing the result, you are discarding information and you should
expect to get something different.

You need to read it with read.csv("x.csv", row.names=1)
Thanks - that makes sense.

Nothing in the csv format lets R know that the first column is the row
names (in the format used by read.table, having a header that is one
column short does).  Now R could guess that a .csv file with an empty
string for the first column name is meant to be the row names, but that
would be merely a guess based on one (barely documented for
spreadsheets) convention.
OK - accepted - assuming things which are only barely documented is the
first step towards incompatibilities - and that is the last thing would
like to have.

Just for clarification, it might be useful to state this in the help
page - or did I miss it there? - as this is an important point and
difference between write.table and write.csv.

If you want to save a dataframe to disk and read it back unchanged,
you should use save() and load().

Or one of the other serialization options such as serialize() and
.saveRDS().  R's own admin uses .saveRDS() for such purposes.
They look exactly like what I was looking for, but it says in the help page:

####################################
Details:
     Since these are internal, the file format is subject to change
     without notice.  The current format is that of ?serialize?,
     compressed as if by ?gzip? if ?compress = FALSE?.
####################################

This sounds frightening - unless, that the existing version is kept and
can be used even if the default version changes.

Cheers,

Rainer

Duncan Murdoch

And if this is not compliant with csv files, shouldn't the function
read.csv convert the first column into the row names?

Cheers,

Rainer

______________________________________________
R-help at r-project.org mailing list
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.

- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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