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

[Kevin Thorpe]

Although your suggestion to provide the data is excellent and one I typically agree with, they data are currently unpublished and so should not be publicly available.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 using utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

________________________________
From: Eric Berger <ericjberger using 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 using utoronto.ca<mailto:kevin.thorpe using 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 using utoronto.ca<mailto:kevin.thorpe using utoronto.ca>  Tel: 416.864.5776  Fax: 416.864.3016


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