R help - Jul 2005 - CSV file and date. Dates are read as factors!

I am using read.csv to read a CSV file (produced by saving an Excel file
as a CSV file). The columns containing dates are being read as factors.
Because of this, I can not compute follow-up time, i.e.
Followup<-postDate-preDate. I would appreciate any suggestion that would
help me read the dates as dates and thus allow me to calculate follow-up
time.
Thanks
John

John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC

University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524

410-605-7119 
- NOTE NEW EMAIL ADDRESS:
jsorkin at grecc.umaryland.edu

John Sorkin wrote:
> I am using read.csv to read a CSV file (produced by saving an Excel file
> as a CSV file). The columns containing dates are being read as factors.
> Because of this, I can not compute follow-up time, i.e.
> Followup<-postDate-preDate. I would appreciate any suggestion that would
> help me read the dates as dates and thus allow me to calculate follow-up
> time.
> Thanks
> John
library(Hmisc)
?csv.get   (see datevars argument)

Frank
> 
> John Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> Baltimore VA Medical Center GRECC and
> University of Maryland School of Medicine Claude Pepper OAIC
> 
> University of Maryland School of Medicine
> Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> 
> 410-605-7119 
> -- NOTE NEW EMAIL ADDRESS:
> jsorkin at grecc.umaryland.edu
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
> 

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University

Working with dates is not easy (for me at least).  I always manage to
get it done, but the code is somewhat messy.  I have not tried using
the Hmisc package as Frank suggested, but I will show you my code as
an alternate way:

w <- unclass((as.Date(as.character(dataMat$fy1_period_end_date),
format="%m/%d/%Y") - as.Date(datec[i],
format="%m/%d/%Y"))/365)

w is the time (in days) between two dates.  You can see that I had to
"unclasss" the first date vector.  I read my files in csv also, so I
am sure something similar can be made to work for you.

HTH,

Roger




On 7/27/05, John Sorkin <jsorkin at grecc.umaryland.edu>
wrote:
> I am using read.csv to read a CSV file (produced by saving an Excel file
> as a CSV file). The columns containing dates are being read as factors.
> Because of this, I can not compute follow-up time, i.e.
> Followup<-postDate-preDate. I would appreciate any suggestion that would
> help me read the dates as dates and thus allow me to calculate follow-up
> time.
> Thanks
> John
> 
> John Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> Baltimore VA Medical Center GRECC and
> University of Maryland School of Medicine Claude Pepper OAIC
> 
> University of Maryland School of Medicine
> Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> 
> 410-605-7119
> -- NOTE NEW EMAIL ADDRESS:
> jsorkin at grecc.umaryland.edu
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>

Use the package chron. Before importing the data to R from the cvs file, 
convert dates to numeric format. Dates are just a sequence from a starting 
point. I use the following to work with dates. Asuming you have a column in 
your cvs file with header "date":
 options(chron.origin=c(month=12,day=31,year=1899))
 x <- read.csv("../bla/bla.csv")
x$date <- chron(x$date,format="y-m-d")
 Or if you have your cvs file with labels like "02/03/2005", then
replace
the last line with:
 x$date <- chron(as.character(x$date),format="y-m-d")
 Then you can use your field date to do date operations
 Hope this is useful.

 On 7/27/05, John Sorkin <jsorkin@grecc.umaryland.edu> wrote:
> 
> I am using read.csv to read a CSV file (produced by saving an Excel file
> as a CSV file). The columns containing dates are being read as factors.
> Because of this, I can not compute follow-up time, i.e.
> Followup<-postDate-preDate. I would appreciate any suggestion that would
> help me read the dates as dates and thus allow me to calculate follow-up
> time.
> Thanks
> John
> 
> John Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> Baltimore VA Medical Center GRECC and
> University of Maryland School of Medicine Claude Pepper OAIC
> 
> University of Maryland School of Medicine
> Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> 
> 410-605-7119
> -- NOTE NEW EMAIL ADDRESS:
> jsorkin@grecc.umaryland.edu
> 
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>
	[[alternative HTML version deleted]]

It's really pretty simple.

First, if you supply as.is=TRUE to read.csv() [or read.table()] then 
your dates will be read as character strings, not factors. That saves 
the step of converting them from factor to character.

Then, use as.Date() to convert the date columns to objects of class 
"Date". You will have to specify the format, if your dates are not in 
the default format.
>  tmp <- as.Date('2002-5-1')
>  as.Date(Sys.time())-tmp
Time difference of 1184 days

If your dates include times, then use as.POSIXct() instead of as.Date().
>  tmp <- as.POSIXct('2002-5-1 13:21')
>  Sys.time()-tmp
Time difference of 1183.746 days

If you don't want to use as.is, perhaps because you have other 
columns that you *want* to have as factors, then either supply 
colClasses to read.csv, or else just use format() to convert the 
factors to character.

as.Date(format(your_date_column))

As an aside, you might save yourself some time by using read.xls() 
from the gdata package.

And of course, there's always the ugly work-around. In your Excel, 
create new columns in which the dates are formatted as numbers, 
presumably as the number of days since whatever Excel uses for its 
origin. Then, in R, you can simply subtract the numbers. If you have 
date-time values in Excel, this might be a little trickier.

-Don

At 9:28 PM -0400 7/27/05, John Sorkin wrote:
>I am using read.csv to read a CSV file (produced by saving an Excel file
>as a CSV file). The columns containing dates are being read as factors.
>Because of this, I can not compute follow-up time, i.e.
>Followup<-postDate-preDate. I would appreciate any suggestion that would
>help me read the dates as dates and thus allow me to calculate follow-up
>time.
>Thanks
>John
>
>John Sorkin M.D., Ph.D.
>Chief, Biostatistics and Informatics
>Baltimore VA Medical Center GRECC and
>University of Maryland School of Medicine Claude Pepper OAIC
>
>University of Maryland School of Medicine
>Division of Gerontology
>Baltimore VA Medical Center
>10 North Greene Street
>GRECC (BT/18/GR)
>Baltimore, MD 21201-1524
>
>410-605-7119
>-- NOTE NEW EMAIL ADDRESS:
>jsorkin at grecc.umaryland.edu
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

-- 
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA