[R] How to write a Surv object to a csv-file?

[Charles C. Berry]

On Fri, 19 Dec 2008, Heinz Tuechler wrote:

> Dear David!
>
> Thank you for your response. I like csv files, because in that case I can 
> easily compare different versions of similar data.frames. Similar in this 
> case means that I may add a column or change some transformation command for 
> one column. With dput it's rather difficult, and when I tried the compare 
> package, I had no success comparing data.frames containing Surv objects.

Heinz,

Is this good enough?

> mat <- as.data.frame( lapply( df.soac, unclass ) )
> write.csv(mat,'mat.csv')
> read.csv('mat.csv')
   X soa.time soa.status char1
1 1        1          0     1
2 2        2          0     2
3 3        3          1     3
4 4        4          0     4
5 5        5          1     5
>


The bug seems to be in as.matrix.data.frame.

HTH,

Chuck

>
> Thanks again
>
> Heinz
>
> At 22:31 19.12.2008, David Winsemius wrote:
>
>> On Dec 19, 2008, at 2:04 PM, Heinz Tuechler wrote:
>> 
>> > Dear All,
>> > 
>> > trying to write a data.frame, containing Surv objects to a csv-file
>> > I get
>> > "Error in dimnames(X) <- list(dn[[1L]], unlist(collabs, use.names =
>> > FALSE)) :
>> >   length of 'dimnames' [2] not equal to array extent".
>> > 
>> > See example below.
>> > 
>> > May be, I overlooked something, but I expected that also data.frames
>> > containing Surv objects may be written to csv files.
>> > 
>> > Is there a better way to write to csv files?
>> 
>> Yes, if the goal is creating an ASCII structure that can be recovered
>> by an R interpreter:
>> 
>> ?dput
>> ?dget
>> 
>> >  dput(df.soac, "test")
>> >  copy.df.soac <- dget("test")
>> >  all.equal(df.soac, copy.df.soac)
>>
>>   Doesn't give you a result that you would want to read with Excel,
>> but that does not appear to be your goal. You can examine it with a
>> text editor.
>> 
>> --
>> David Winsemius
>> 
>> 
>> > 
>> > 
>> > Thanks,
>> > 
>> > Heinz Tüchler
>> > 
>> > 
>> > 
>> > ###   write Surv-object in csv-file
>> > library(survival)
>> > ## create example data
>> > soa <- Surv(1:5, c(0, 0, 1, 0, 1))
>> > df.soa <- data.frame(soa)
>> > write.csv(df.soa, 'df.soa.csv')    ## works as I expected
>> > read.csv('df.soa.csv')              ## works as I expected
>> > 
>> > df.soa2 <- data.frame(soa, soa2=soa)
>> > write.csv(df.soa2, 'df.soa2.csv')  ## works as I expected
>> > read.csv('df.soa2.csv')            ## works as I expected
>> > 
>> > char1 <- letters[1:5]
>> > df.soac <- data.frame(soa, char1)
>> > write.csv(df.soac, 'df.soac.csv')  ## generates the following error
>> > message:
>> > 
>> > Error in dimnames(X) <- list(dn[[1L]], unlist(collabs, use.names =
>> > FALSE)) :
>> >   length of 'dimnames' [2] not equal to array extent
>> > 
>> > df.csoa <- data.frame(char1, soa)
>> > write.csv(df.csoa, 'df.soac.csv')  ## generates the following error
>> > message:
>> > 
>> > Error in dimnames(X) <- list(dn[[1L]], unlist(collabs, use.names =
>> > FALSE)) :
>> >   length of 'dimnames' [2] not equal to array extent
>> > 
>> > 
>> > platform       i386-pc-mingw32
>> > arch           i386
>> > os             mingw32
>> > system         i386, mingw32
>> > status         Patched
>> > major          2
>> > minor          8.0
>> > year           2008
>> > month          11
>> > day            10
>> > svn rev        46884
>> > language       R
>> > version.string R version 2.8.0 Patched (2008-11-10 r46884)
>> > >  sessionInfo()
>> > R version 2.8.0 Patched (2008-11-10 r46884)
>> > i386-pc-mingw32
>> > 
>> > locale:
>> > LC_COLLATE=German_Austria.1252;LC_CTYPE=German_Austria. 
>> > 1252;LC_MONETARY=German_Austria. 
>> > 1252;LC_NUMERIC=C;LC_TIME=German_Austria.1252
>> > 
>> > attached base packages:
>> > [1] splines   stats     graphics  grDevices utils     datasets
>> > methods
>> > [8] base
>> > 
>> > other attached packages:
>> > [1] survival_2.34-1
>> > 
>> > ______________________________________________
>> > 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.
>
>

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901