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?
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
How to write a Surv object to a csv-file?
5 messages · David Winsemius, Heinz Tuechler, Charles C. Berry
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
> 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.
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. 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 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.
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 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
Dear Charles, yes, your solution does what I need. Maybe, it offers also a way to use the compare package with Surv objects. Thank you, Heinz
At 23:30 19.12.2008, Charles C. Berry wrote:
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
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