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Kevin Thorpe

2018-Jul-09 14:42 UTC

[R] Using write.csv as a connection for read.csv

Hi.

I have some data frames I created previously that seem to not be working
correctly anymore. I *think* the problem is that some of the variables in the
data frame are of a type called labelled. There are other attributes in the data
frame as well. I thought that the easiest way to fix this was to convert to, say
a csv and re-load.

I tried something like read.csv(write.csv(df,row.names=FALSE)) but got the error

  Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
  'file' must be a character string or connection

I guess there must be a way to send the output of write.csv to a connection that
read.csv can use but I was mystified by the help page on connections, at least I
could not determine how to achieve my desired result.

I realize I could write to a file and read it back in, but that feels klunky
somehow. Maybe my approach to convert my data to strip the "weird"
stuff is wrong-headed and I would accept alternative strategies.

I would like a more general solution to fix this because I expect to encounter
it some more. For those wondering how I found myself in such a mess, the data
frames were initially imported from SAS data sets through the haven package. I
then did some standard manipulation and added some additional labels with the
upData() function from Hmisc (both packages have been updated since initial
creation of the data frames).

Thanks,

Kevin
 
--
 Kevin E. Thorpe
 Head of Biostatistics,? Applied Health Research Centre (AHRC)
 Li Ka Shing Knowledge Institute of St. Michael's
 Assistant Professor, Dalla Lana School of Public Health
 University of Toronto
 email: kevin.thorpe at utoronto.ca? Tel: 416.864.5776? Fax: 416.864.3016

William Poling, Ph.D., MPH

2018-Jul-09 14:50 UTC

head link

[R] Using write.csv as a connection for read.csv

Hi Kevin.
Maybe?
setwd("C:/RPractice")

write_csv(yourfile, path = "yourfile.csv")
yourfile <- read.csv("yourfile.csv")
HTH
WHP
    On Monday, July 9, 2018, 10:42:24 AM EDT, Kevin Thorpe <kevin.thorpe at
utoronto.ca> wrote:
 
 Hi.

I have some data frames I created previously that seem to not be working
correctly anymore. I *think* the problem is that some of the variables in the
data frame are of a type called labelled. There are other attributes in the data
frame as well. I thought that the easiest way to fix this was to convert to, say
a csv and re-load.

I tried something like read.csv(write.csv(df,row.names=FALSE)) but got the error

? Error in read.table(file = file, header = header, sep = sep, quote = quote,? :
? 'file' must be a character string or connection

I guess there must be a way to send the output of write.csv to a connection that
read.csv can use but I was mystified by the help page on connections, at least I
could not determine how to achieve my desired result.

I realize I could write to a file and read it back in, but that feels klunky
somehow. Maybe my approach to convert my data to strip the "weird"
stuff is wrong-headed and I would accept alternative strategies.

I would like a more general solution to fix this because I expect to encounter
it some more. For those wondering how I found myself in such a mess, the data
frames were initially imported from SAS data sets through the haven package. I
then did some standard manipulation and added some additional labels with the
upData() function from Hmisc (both packages have been updated since initial
creation of the data frames).

Thanks,

Kevin
 
--
 Kevin E. Thorpe
 Head of Biostatistics,? Applied Health Research Centre (AHRC)
 Li Ka Shing Knowledge Institute of St. Michael's
 Assistant Professor, Dalla Lana School of Public Health
 University of Toronto
 email: kevin.thorpe at utoronto.ca? Tel: 416.864.5776? Fax: 416.864.3016
 
? ? 
______________________________________________
R-help at r-project.org 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.  
	[[alternative HTML version deleted]]

Eric Berger

2018-Jul-09 14:51 UTC

head link

[R] Using write.csv as a connection for read.csv

Hi Kevin,
It's good that you provided the background to the problem.
Rather than asking this list to "debug" your proposed solution, I
think you
would be better off showing some of the "corrupted" data frame and ask
for
suggestions how to deal with it.
(Suggestions may or may not match your initial attempt.)
Can you output a piece of your suspect data frame via the dput() function
and post to the list?

Best,
Eric


On Mon, Jul 9, 2018 at 5:42 PM, Kevin Thorpe <kevin.thorpe at utoronto.ca>
wrote:
> Hi.
>
> I have some data frames I created previously that seem to not be working
> correctly anymore. I *think* the problem is that some of the variables in
> the data frame are of a type called labelled. There are other attributes in
> the data frame as well. I thought that the easiest way to fix this was to
> convert to, say a csv and re-load.
>
> I tried something like read.csv(write.csv(df,row.names=FALSE)) but got
> the error
>
>   Error in read.table(file = file, header = header, sep = sep, quote >
quote,  :
>   'file' must be a character string or connection
>
> I guess there must be a way to send the output of write.csv to a
> connection that read.csv can use but I was mystified by the help page on
> connections, at least I could not determine how to achieve my desired
> result.
>
> I realize I could write to a file and read it back in, but that feels
> klunky somehow. Maybe my approach to convert my data to strip the
"weird"
> stuff is wrong-headed and I would accept alternative strategies.
>
> I would like a more general solution to fix this because I expect to
> encounter it some more. For those wondering how I found myself in such a
> mess, the data frames were initially imported from SAS data sets through
> the haven package. I then did some standard manipulation and added some
> additional labels with the upData() function from Hmisc (both packages have
> been updated since initial creation of the data frames).
>
> Thanks,
>
> Kevin
>
> --
>  Kevin E. Thorpe
>  Head of Biostatistics,  Applied Health Research Centre (AHRC)
>  Li Ka Shing Knowledge Institute of St. Michael's
>  Assistant Professor, Dalla Lana School of Public Health
>  University of Toronto
>  email: kevin.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>
>
> ______________________________________________
> R-help at r-project.org 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.
>
	[[alternative HTML version deleted]]

Kevin Thorpe

2018-Jul-09 15:17 UTC

head link

[R] Using write.csv as a connection for read.csv

Although your suggestion to provide the data is excellent and one I typically
agree with, they data are currently unpublished and so should not be publicly
available. I have tried to make a reproducible example in the past (when similar
looking things happened), but was unable to. Maybe I'll try a small subset
and see if that works.


Kevin


--
Kevin E. Thorpe
Head of Biostatistics,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael's
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

________________________________
From: Eric Berger <ericjberger at gmail.com>
Sent: Monday, July 9, 2018 10:51:38 AM
To: Kevin Thorpe
Cc: R Help Mailing List
Subject: Re: [R] Using write.csv as a connection for read.csv

Hi Kevin,
It's good that you provided the background to the problem.
Rather than asking this list to "debug" your proposed solution, I
think you would be better off showing some of the "corrupted" data
frame and ask for suggestions how to deal with it.
(Suggestions may or may not match your initial attempt.)
Can you output a piece of your suspect data frame via the dput() function and
post to the list?

Best,
Eric


On Mon, Jul 9, 2018 at 5:42 PM, Kevin Thorpe <kevin.thorpe at
utoronto.ca<mailto:kevin.thorpe at utoronto.ca>> wrote:
Hi.

I have some data frames I created previously that seem to not be working
correctly anymore. I *think* the problem is that some of the variables in the
data frame are of a type called labelled. There are other attributes in the data
frame as well. I thought that the easiest way to fix this was to convert to, say
a csv and re-load.

I tried something like read.csv(write.csv(df,row.names=FALSE)) but got the error

  Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
  'file' must be a character string or connection

I guess there must be a way to send the output of write.csv to a connection that
read.csv can use but I was mystified by the help page on connections, at least I
could not determine how to achieve my desired result.

I realize I could write to a file and read it back in, but that feels klunky
somehow. Maybe my approach to convert my data to strip the "weird"
stuff is wrong-headed and I would accept alternative strategies.

I would like a more general solution to fix this because I expect to encounter
it some more. For those wondering how I found myself in such a mess, the data
frames were initially imported from SAS data sets through the haven package. I
then did some standard manipulation and added some additional labels with the
upData() function from Hmisc (both packages have been updated since initial
creation of the data frames).

Thanks,

Kevin

--
 Kevin E. Thorpe
 Head of Biostatistics,  Applied Health Research Centre (AHRC)
 Li Ka Shing Knowledge Institute of St. Michael's
 Assistant Professor, Dalla Lana School of Public Health
 University of Toronto
 email: kevin.thorpe at utoronto.ca<mailto:kevin.thorpe at utoronto.ca> 
Tel: 416.864.5776  Fax: 416.864.3016


______________________________________________
R-help at r-project.org<mailto:R-help at r-project.org> 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.


	[[alternative HTML version deleted]]

William Dunlap

2018-Jul-09 16:07 UTC

head link

[R] Using write.csv as a connection for read.csv

>I tried something like read.csv(write.csv(df,row.names=FALSE)) but got
the error>
>  Error in read.table(file = file, header = header, sep = sep, quote quote, 
:
>  'file' must be a character string or connection
To diagnose this without reading the help(write.csv) look at the return
value of write.csv:
  > df <- data.frame(Col1=1:3, Col2=LETTERS[24:26])
  > tmp <- write.csv(df, row.names=FALSE)
  "Col1","Col2"
  1,"X"
  2,"Y"
  3,"Z"
  > tmp
  NULL

read.csv complains about reading from NULL:
  > read.csv(NULL)
  Error in read.table(file = file, header = header, sep = sep, quote quote,  :
    'file' must be a character string or connection




Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Mon, Jul 9, 2018 at 7:42 AM, Kevin Thorpe <kevin.thorpe at utoronto.ca>
wrote:
> Hi.
>
> I have some data frames I created previously that seem to not be working
> correctly anymore. I *think* the problem is that some of the variables in
> the data frame are of a type called labelled. There are other attributes in
> the data frame as well. I thought that the easiest way to fix this was to
> convert to, say a csv and re-load.
>
> I tried something like read.csv(write.csv(df,row.names=FALSE)) but got
> the error
>
>   Error in read.table(file = file, header = header, sep = sep, quote >
quote,  :
>   'file' must be a character string or connection
>
> I guess there must be a way to send the output of write.csv to a
> connection that read.csv can use but I was mystified by the help page on
> connections, at least I could not determine how to achieve my desired
> result.
>
> I realize I could write to a file and read it back in, but that feels
> klunky somehow. Maybe my approach to convert my data to strip the
"weird"
> stuff is wrong-headed and I would accept alternative strategies.
>
> I would like a more general solution to fix this because I expect to
> encounter it some more. For those wondering how I found myself in such a
> mess, the data frames were initially imported from SAS data sets through
> the haven package. I then did some standard manipulation and added some
> additional labels with the upData() function from Hmisc (both packages have
> been updated since initial creation of the data frames).
>
> Thanks,
>
> Kevin
>
> --
>  Kevin E. Thorpe
>  Head of Biostatistics,  Applied Health Research Centre (AHRC)
>  Li Ka Shing Knowledge Institute of St. Michael's
>  Assistant Professor, Dalla Lana School of Public Health
>  University of Toronto
>  email: kevin.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>
>
> ______________________________________________
> R-help at r-project.org 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.
>
	[[alternative HTML version deleted]]

Jeff Newmiller

2018-Jul-09 17:01 UTC

head link

[R] Using write.csv as a connection for read.csv

TL;DR: If you want to do this, go ahead and use a temporary file or text
connection.

Others have pointed out that write.csv returns NULL rather than a file
connection, but I haven't seen comments on your impulse to avoid the use of
files.

*nix operating systems are admirably efficient with multitasking... such that
shells can efficiently run multiple programs connected by pipes, pausing the
producers to pause if they get ahead of the consumers and resuming them if the
consumers run out of data, thus minimizing the amount of temporary disk space
usage.

R does not presume this to be among the fundamental capabilities of the
operating system, rather assuming single tasking capability by default. This
means that even if you do connect write.csv to a pipe then it will run to
completion before read.csv gets a chance to process any of the data. MSDOS used
to simulate command line program chaining by writing all the data to a temporary
file before running the consumer program. R is similar... and like MSDOS there
is little reason to avoid temporary files in R.

set.seed( 42 )
DF <- data.frame( X=1:100, Y=rnorm( 100 ) )
frame <- tempfile()
write.csv( DF, file=fname, row.names=FALSE )
DF2 <- read.csv( file=fname )
all.equal( DF$X, DF2$X ) && all.equal( DF$Y, DF2$Y )
unlink( fname )

On July 9, 2018 7:42:00 AM PDT, Kevin Thorpe <kevin.thorpe at utoronto.ca>
wrote:>Hi.
>
>I have some data frames I created previously that seem to not be
>working correctly anymore. I *think* the problem is that some of the
>variables in the data frame are of a type called labelled. There are
>other attributes in the data frame as well. I thought that the easiest
>way to fix this was to convert to, say a csv and re-load.
>
>I tried something like read.csv(write.csv(df,row.names=FALSE)) but got
>the error
>
>Error in read.table(file = file, header = header, sep = sep, quote
>quote,  :
>  'file' must be a character string or connection
>
>I guess there must be a way to send the output of write.csv to a
>connection that read.csv can use but I was mystified by the help page
>on connections, at least I could not determine how to achieve my
>desired result.
>
>I realize I could write to a file and read it back in, but that feels
>klunky somehow. Maybe my approach to convert my data to strip the
>"weird" stuff is wrong-headed and I would accept alternative
>strategies.
>
>I would like a more general solution to fix this because I expect to
>encounter it some more. For those wondering how I found myself in such
>a mess, the data frames were initially imported from SAS data sets
>through the haven package. I then did some standard manipulation and
>added some additional labels with the upData() function from Hmisc
>(both packages have been updated since initial creation of the data
>frames).
>
>Thanks,
>
>Kevin
> 
>--
> Kevin E. Thorpe
> Head of Biostatistics,? Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: kevin.thorpe at utoronto.ca? Tel: 416.864.5776? Fax: 416.864.3016
> 
>     
>______________________________________________
>R-help at r-project.org 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.
-- 
Sent from my phone. Please excuse my brevity.

Kevin Thorpe

2018-Jul-09 17:14 UTC

head link

[R] Using write.csv as a connection for read.csv

Thanks Jeff and all others.

I will need to use the tempfile route I guess (I'm running in a Linux OS)
for the time-being.

After I re-loaded the data frames that were broken before and they seemed fine,
after using them for awhile they broke again.

I am trying to build my analysis with rmarkdown and tools. I have not been able
to determine (yet) exactly what set of interactions are "breaking"
things. I certainly don't expect the list to debug everything I'm doing.

The only thing is can say is that there appears to be some weird interaction
between SAS data sets imported by haven and other packages. Note that I
encountered (I think) related issues with an imported data set when I tried
working with it in the tidyverse.

Maybe I'm getting too old to learn new stuff. :-)

Sorry I am not being much help with my own problem. I just have not been able to
determine where things break. If can come up with a reproducible example that
reliably breaks, I'll post it.

Kevin

--
 Kevin E. Thorpe
 Head of Biostatistics,? Applied Health Research Centre (AHRC)
 Li Ka Shing Knowledge Institute of St. Michael's
 Assistant Professor, Dalla Lana School of Public Health
 University of Toronto
 email: kevin.thorpe at utoronto.ca? Tel: 416.864.5776? Fax: 416.864.3016

From: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
Sent: Monday, July 9, 2018 1:01 PM
To: r-help at r-project.org; Kevin Thorpe; R Help Mailing List
Subject: Re: [R] Using write.csv as a connection for read.csv
? 

TL;DR: If you want to do this, go ahead and use a temporary file or text
connection.

Others have pointed out that write.csv returns NULL rather than a file
connection, but I haven't seen comments on your impulse to avoid the use of
files.

*nix operating systems are admirably efficient with multitasking... such that
shells can efficiently run multiple programs connected by pipes, pausing the
producers to pause if they get ahead of the consumers and resuming them if the
consumers run out of data,  thus minimizing the amount of temporary disk space
usage.

R does not presume this to be among the fundamental capabilities of the
operating system, rather assuming single tasking capability by default. This
means that even if you do connect write.csv to a pipe then it will run to
completion before read.csv gets a  chance to process any of the data. MSDOS used
to simulate command line program chaining by writing all the data to a temporary
file before running the consumer program. R is similar... and like MSDOS there
is little reason to avoid temporary files in R.

set.seed( 42 )
DF <- data.frame( X=1:100, Y=rnorm( 100 ) )
frame <- tempfile()
write.csv( DF, file=fname, row.names=FALSE )
DF2 <- read.csv( file=fname )
all.equal( DF$X, DF2$X ) && all.equal( DF$Y, DF2$Y )
unlink( fname )

On July 9, 2018 7:42:00 AM PDT, Kevin Thorpe <kevin.thorpe at utoronto.ca>
wrote:>Hi.
>
>I have some data frames I created previously that seem to not be
>working correctly anymore. I *think* the problem is that some of the
>variables in the data frame are of a type called labelled. There are
>other attributes in the data frame as well. I thought that the easiest
>way to fix this was to convert to, say a csv and re-load.
>
>I tried something like read.csv(write.csv(df,row.names=FALSE)) but got
>the error
>
>Error in read.table(file = file, header = header, sep = sep, quote
>quote,? :
>? 'file' must be a character string or connection
>
>I guess there must be a way to send the output of write.csv to a
>connection that read.csv can use but I was mystified by the help page
>on connections, at least I could not determine how to achieve my
>desired result.
>
>I realize I could write to a file and read it back in, but that feels
>klunky somehow. Maybe my approach to convert my data to strip the
>"weird" stuff is wrong-headed and I would accept alternative
>strategies.
>
>I would like a more general solution to fix this because I expect to
>encounter it some more. For those wondering how I found myself in such
>a mess, the data frames were initially imported from SAS data sets
>through the haven package. I then did some standard manipulation and
>added some additional labels with the upData() function from Hmisc
>(both packages have been updated since initial creation of the data
>frames).
>
>Thanks,
>
>Kevin
> 
>--
> Kevin E. Thorpe
> Head of Biostatistics,? Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: kevin.thorpe at utoronto.ca? Tel: 416.864.5776? Fax: 416.864.3016
> 
>???? 
>______________________________________________
>R-help at r-project.org 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.
-- 
Sent from my phone. Please excuse my brevity.

R help - Jul 2018 - Using write.csv as a connection for read.csv

[R] Using write.csv as a connection for read.csv

[R] Using write.csv as a connection for read.csv

[R] Using write.csv as a connection for read.csv

[R] Using write.csv as a connection for read.csv

[R] Using write.csv as a connection for read.csv

[R] Using write.csv as a connection for read.csv

[R] Using write.csv as a connection for read.csv