Ista, you were right with the integer vs. double issue: I just found this
out while filing a bug to the R Bugzilla. You can find the bug report here:
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15411
Please let me know if it does not seem to cover all your comments, I'll add
more details in the bug report.
Let's see now how this one turns out...
Mathieu.
Le 08/01/2013 02:08 PM, Ista Zahn a écrit :
Hi Mathieu,
I don't have a full explanation, but here is some additional observations:
options(digits = 4)
## Simplified example
df2 <- data.frame(x = rnorm(21), y = rnorm(21), id = 99990:100010)
apply(df2, 1, function(dfi) format(dfi["id"], scientific = FALSE))
[1] "99990" "99991" "99992" "99993" "99994" " 99995" " 99996" "
99997" " 99998" " 99999" "100000" "100001" "100002" "100003"
[15] "100004" "100005" "100006" "100007" "100008" "100009" "100010"
## Based on magnitude of id (> 9994 gets padded regardless of position)
df2 <- data.frame(x = rnorm(21), y = rnorm(21), id = 100010:99990)
apply(df2, 1, function(dfi) format(dfi["id"], scientific = FALSE))
[1] "100010" "100009" "100008" "100007" "100006" "100005" "100004"
"100003" "100002" "100001" "100000" " 99999" " 99998" " 99997"
[15] " 99996" " 99995" "99994" "99993" "99992" "99991" "99990"
## The issue is that formatting a double leads to the originally noted behavior.
## The apply version coerces df2 to a matrix of type double which is why this
## happens there as well.
for(i in 1:nrow(df2)) print(format(df2[i, "id"], scientific=FALSE))
[1] "100010"
[1] "100009"
[1] "100008"
[1] "100007"
[1] "100006"
[1] "100005"
[1] "100004"
[1] "100003"
[1] "100002"
[1] "100001"
[1] "100000"
[1] "99999"
[1] "99998"
[1] "99997"
[1] "99996"
[1] "99995"
[1] "99994"
[1] "99993"
[1] "99992"
[1] "99991"
[1] "99990"
for(i in 1:nrow(df2)) print(format(as.double(df2[i, "id"]), scientific=FALSE))
[1] "100010"
[1] "100009"
[1] "100008"
[1] "100007"
[1] "100006"
[1] "100005"
[1] "100004"
[1] "100003"
[1] "100002"
[1] "100001"
[1] "100000"
[1] " 99999"
[1] " 99998"
[1] " 99997"
[1] " 99996"
[1] " 99995"
[1] "99994"
[1] "99993"
[1] "99992"
[1] "99991"
[1] "99990"
Best,
Ista
On Thu, Aug 1, 2013 at 11:31 AM, Mathieu Basille
<basille....@ase-research.org> wrote:
This problem does not seem to be widely popular, but at least affects two
users (both on Linux, maybe a hint here?). To me, it looks like a bug (is it
a R bug, or a OS-related bug, I don't know). Should I forward it to R-devel,
or some other place where R gurus may have a chance to look at it?
Mathieu.
Le 07/30/2013 02:34 PM, arun a écrit :
Hi Mathieu
yes, the original problem occurs in my system too. I am using R 3.0.1 on
linux mint 15. I guess the default case would be trim=FALSE, but still it
looks very strange especially in ?apply(), as it starts from " 99995"
onwards.
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] stringr_0.6.2 reshape2_1.2.2
loaded via a namespace (and not attached):
[1] plyr_1.8 tools_3.0.1
----- Original Message -----
From: Mathieu Basille <basille....@ase-research.org>
To: arun <smartpink...@yahoo.com>
Cc: R help <r-help@r-project.org>
Sent: Tuesday, July 30, 2013 2:29 PM
Subject: Re: [R] 'format' behaviour in a 'apply' call depending on
'options(digits = K)'
Thanks Arun for your answer. 'trim = TRUE' does indeed solve the symptoms
of the problem, and this is the solution I'm currently using. However, it
does not help to understand what the problem is, and what is the cause of
it.
Can you confirm that the original problem also occurs on your computer
(and
what is your OS)? It would be interesting since David is not able to
reproduce the problem with Mac OS X.
Mathieu.
Le 07/30/2013 02:15 PM, arun a écrit :
Hi,
Try using trim=TRUE, in ?format()
options(digits=4)
df2 <- data.frame(x = rnorm(110000), y = rnorm(110000), id = 1:110000)
df2$id2 <- apply(df2, 1, function(dfi) format(dfi["id"],
trim=TRUE,scientific = FALSE))
df2$id2[99990:100010]
# [1] "99990" "99991" "99992" "99993" "99994" "99995" "99996"
"99997"
# [9] "99998" "99999" "100000" "100001" "100002" "100003" "100004"
"100005"
#[17] "100006" "100007" "100008" "100009" "100010"
id2 <- format(1:110000, scientific = FALSE,trim=TRUE)
id2[99990:100010]
# [1] "99990" "99991" "99992" "99993" "99994" "99995" "99996"
"99997"
#[9] "99998" "99999" "100000" "100001" "100002" "100003" "100004"
"100005"
#[17] "100006" "100007" "100008" "100009" "100010"
A.K.
----- Original Message -----
From: Mathieu Basille <basille....@ase-research.org>
To: David Winsemius <dwinsem...@comcast.net>
Cc: r-help@r-project.org
Sent: Tuesday, July 30, 2013 2:07 PM
Subject: Re: [R] 'format' behaviour in a 'apply' call depending on
'options(digits = K)'
Thanks David for your interest. I have to admit that your answer puzzles
me
even more than before. It seems that the underlying problem is way beyond
my R skills...
The generation of id2 is indeed quite demanding, especially compared to a
simple 'as.character' call. Anyway, since it seems to be system specific,
here is the sessionInfo() that I forgot to attach to my first message:
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
In brief: last stable R available under Debian Testing... Hopefully this
can help tracking down the problem.
Mathieu.
Le 07/30/2013 01:58 PM, David Winsemius a écrit :
On Jul 30, 2013, at 9:01 AM, Mathieu Basille wrote:
Dear list,
Here is a simple example in which the behaviour of 'format' does not
make sense to me. I have read the documentation and searched the archives,
but nothing pointed me in the right direction to understand this behaviour.
Let's start with a simple data frame:
df1 <- data.frame(x = rnorm(110000), y = rnorm(110000), id = 1:110000)
Let's now create a new variable 'id2' which is the character
representation of 'id'. Note that I use 'scientific = FALSE' to ensure that
long numbers such as 100,000 are not formatted using their scientific
representation (in this case 1e+05):
df1$id2 <- apply(df1, 1, function(dfi) format(dfi["id"], scientific =
FALSE))
Let's have a look at part of the result:
df1$id2[99990:100010]
[1] "99990" "99991" "99992" "99993" "99994" "99995" "99996"
[8] "99997" "99998" "99999" "100000" "100001" "100002" "100003"
[15] "100004" "100005" "100006" "100007" "100008" "100009" "100010"
Some formating processes are carried out by system functions. In this
case I am unable to reproduce with the same code on a Mac OS 10.7.5/R 3.0.1
Patched
df1$id2[99990:100010]
[1] "99990" "99991" "99992" "99993" "99994" "99995" "99996"
"99997"
[9] "99998" "99999" "100000" "100001" "100002" "100003" "100004"
"100005"
[17] "100006" "100007" "100008" "100009" "100010"
(I did notice that generation of the id2 variable seemed to take an
inordinately long time.)
-- David.
So far, so good. Let's now play with the 'digits' option:
options(digits = 4)
df2 <- data.frame(x = rnorm(110000), y = rnorm(110000), id = 1:110000)
df2$id2 <- apply(df2, 1, function(dfi) format(dfi["id"], scientific =
FALSE))
df2$id2[99990:100010]
[1] "99990" "99991" "99992" "99993" "99994" " 99995" " 99996"
[8] " 99997" " 99998" " 99999" "100000" "100001" "100002" "100003"
[15] "100004" "100005" "100006" "100007" "100008" "100009" "100010"
Notice the extra leading space from 99995 to 99999? To make sure it
only happened there:
df2$id2[which(df1$id2 != df2$id2)]
[1] " 99995" " 99996" " 99997" " 99998" " 99999"
And just to make sure it only occurs in a 'apply' call, here is the
same directly on a numeric vector:
id2 <- format(1:110000, scientific = FALSE)
id2[99990:100010]
[1] " 99990" " 99991" " 99992" " 99993" " 99994" " 99995" " 99996"
[8] " 99997" " 99998" " 99999" "100000" "100001" "100002" "100003"
[15] "100004" "100005" "100006" "100007" "100008" "100009" "100010"
Here the leading spaces are for every number, which makes sense to me.
Is there anything I'm misinterpreting in the behaviour of 'format'?
Thanks in advance for any hint,
Mathieu.
PS: Some background for this question. It all comes from a Rmd
document, that knitr consistently failed to process, while the R code was
fine using batch or interactive R. knitr uses 'options(digits = 4)' as
opposed to 'options(digits = 7)' by default in R, which made one of my
function throw an error with knitr, but not with batch or interactive R. I
managed to solve the problem using 'trim = TRUE' in 'format', but I still do
not understand what's going on...
If you're interested, see here for more details on the original
problem:
http://stackoverflow.com/questions/17866230/knitr-vs-interactive-r-behaviour/17872176
--
~$ whoami
Mathieu Basille, PhD
~$ locate --details
University of Florida \\
Fort Lauderdale Research and Education Center
(+1) 954-577-6314
http://ase-research.org/basille
~$ fortune
« Le tout est de tout dire, et je manque de mots
Et je manque de temps, et je manque d'audace. »
-- Paul Éluard
______________________________________________
R-help@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.
David Winsemius
Alameda, CA, USA
On Jul 30, 2013, at 9:01 AM, Mathieu Basille wrote:
Dear list,
Here is a simple example in which the behaviour of 'format' does not
make sense to me. I have read the documentation and searched the archives,
but nothing pointed me in the right direction to understand this behaviour.
Let's start with a simple data frame:
df1 <- data.frame(x = rnorm(110000), y = rnorm(110000), id = 1:110000)
Let's now create a new variable 'id2' which is the character
representation of 'id'. Note that I use 'scientific = FALSE' to ensure that
long numbers such as 100,000 are not formatted using their scientific
representation (in this case 1e+05):
df1$id2 <- apply(df1, 1, function(dfi) format(dfi["id"], scientific =
FALSE))
Let's have a look at part of the result:
df1$id2[99990:100010]
[1] "99990" "99991" "99992" "99993" "99994" "99995" "99996"
[8] "99997" "99998" "99999" "100000" "100001" "100002" "100003"
[15] "100004" "100005" "100006" "100007" "100008" "100009" "100010"
Some formating processes are carried out by system functions. In this
case I am unable to reproduce with the same code on a Mac OS 10.7.5/R 3.0.1
Patched
df1$id2[99990:100010]
[1] "99990" "99991" "99992" "99993" "99994" "99995" "99996"
"99997"
[9] "99998" "99999" "100000" "100001" "100002" "100003" "100004"
"100005"
[17] "100006" "100007" "100008" "100009" "100010"
(I did notice that generation of the id2 variable seemed to take an
inordinately long time.)
______________________________________________
R-help@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@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@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.
