How to write a Surv object to a csv-file?

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 T?chler

###   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

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