Re: [R] Plotting directly to memory?

[Jeroen Ooms]

On Sun, May 28, 2023 at 1:46 PM Duncan Murdoch  wrote:
>
> Is there a way to open a graphics device that plots entirely to an array
> or raster in memory?  I'd prefer it to use base graphics, but grid would
> be fine if it makes a difference.
>
> For an explicit example, I'd like to do the equivalent of this:
>
>filename <- tempfile(fileext = ".png")
>png(filename)
>plot(1:10, 1:10)
>dev.off()
>
>library(png)
>img <- readPNG(filename)
>
>unlink(filename)
>

The magick package has this capability too:

library(magick)
img <- magick::image_device()
plot(1:10, 1:10)
dev.off()
image_data(img)

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Re: [R] Rstudio does not run on ubuntu 20

[Jeroen Ooms]

On Mon, Jun 15, 2020 at 2:47 PM Luigi Marongiu  wrote:
>
> Hello,
> all of a sudden rstudio stopped working on ubuntu 20.04. I
> re-installed from `rstudio-1.3.959-amd64.deb` but it does not launch
> even if there is an icon. On terminal I got:
> ```
> $ rstudio
> rstudio: error while loading shared libraries: libssl.so.1.0.0: cannot
> open shared object file: No such file or directory
> $ sudo apt-get install libssl1.0.0 libssl-dev
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Package libssl1.0.0 is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
>
> E: Package 'libssl1.0.0' has no installation candidate


This happens when you install the wrong rstudio binary for your
version of debian/ubuntu. Go to
https://rstudio.com/products/rstudio/download-server/debian-ubuntu/
and scroll down to "Install for Debian 10 / Ubuntu 18" and try that
one.

I think you had downloaded the binary for Ubuntu 16, which depends on
an old version of openssl.

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Re: [R] Rtools required

[Jeroen Ooms]

On Wed, Apr 29, 2020 at 11:37 PM Steven  wrote:
>
> Hello John,
>
> Perhaps you can help me. I am an idiot. I visited the Rtools web page
> and learn to run the following lines in R: Still I am getting the same
> warning message.
>
>  > writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con =
> "~/.Renviron")
>  > Sys.which("make")
>make
> "C:\\rtools40\\usr\\bin\\make.exe"

That looks OK. Did you restart rstudio?

How exactly are getting this error? Are you using install.packages()
in R? Or using the pkgbuild package?

Also are you running the latest version of rstudio? I think old
versions may have had difficulty finding rtools40.

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Re: [R] Can't rsync extsoft/3.6 when compiling R 3.6

[Jeroen Ooms]

On Thu, May 2, 2019 at 9:36 AM Martin Maechler
 wrote:
>
> > Shuguang Sun
> > on Thu, 2 May 2019 12:57:37 +0800 writes:
>
> > Hi all,
> > When I try to compile R 3.6 in windows 10 in Rtools35, it raised the 
> error message:
> > --8<---cut here---start->8---
> > make rsync-extsoft
> > (mkdir -p ../../extsoft; \
> > cd ../../extsoft; \
> > rsync --timeout=60 -rcvp --delete 
> cran.r-project.org::CRAN/bin/windows/extsoft/3.6/ . )
> > receiving incremental file list
> > rsync: change_dir "/bin/windows/extsoft/3.6" (in CRAN) failed: No such 
> file or directory (2)
> > --8<---cut here---end--->8---
>
> > There is no "windows/extsoft/3.6/" and only up to 3.5.
>
> > Best Regards,
> > Shuguang Sun
>
> Indeed.
> If you look at this FTP directory in a capabable browser (such
> as Emacs), you see
>
> Dec 22 2014  3.2
> Jun 16 2016  3.3
> Jul  6 2016  3.4 -> 3.3
> May  8 2017  3.5 -> 3.3
>
> So it seems the CRAN team (or the R Core release master?) forgot
> to make that symbolic link there.

I think that might be my responsibility (not entirely sure honestly).
I'll add that directory and include the current versions of the libs
we use to build the official r-base on Windows.

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Re: [R] Problem installing libxml2 under Homebrew

[Jeroen Ooms]

You probably have a malconfigured homebrew installation of R. On MacOS
it is recommended to use the CRAN version of R
https://cran.r-project.org/bin/macosx/. The homebrew version depends
on gcc compilers and does not support cran binary packages.

If you really want to use the homebrew R try ruling out the following problems:

 - Check for conflicting compilers in your path (gcc, ccache, clang4).
Unless you have good reasons not to, you should use the native xcode
compilers to build R packages.
 - Comment out custom compilers/flags that you may have in your
~/.R/Makevars file.

Use the following script to check why the configuration is failing:

  CPP=$(R CMD config CPP)
  CFLAGS=$(xml2-config --cflags)
  echo '#include ' | $CPP $CFLAGS -E -xc - > /dev/null




On Sat, Feb 17, 2018 at 8:53 AM, Peter Meilstrup
 wrote:
> i am trying to install xml2 from CRAN, and it is throwing an error
> that it cannot find the libxml2 library configuration.
>
> The thing is that pkg-config seems to be set up correctly:
>
> $ echo $PKG_CONFIG_PATH
> :/usr/local/opt/libxml2/lib/pkgconfig:/usr/local/opt/libxml2/lib/pkgconfig
>
> $ pkg-config --cflags --libs libxml-2.0
> -I/usr/local/Cellar/libxml2/2.9.7/include/libxml2
> -L/usr/local/Cellar/libxml2/2.9.7/lib -lx
>
> Output of install.packages:
>
>> install.packages("xml2")
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.2.0.tar.gz'
> Content type 'application/x-gzip' length 251614 bytes (245 KB)
> ==
> downloaded 245 KB
>
> * installing *source* package ‘xml2’ ...
> ** package ‘xml2’ successfully unpacked and MD5 sums checked
> Found pkg-config cflags and libs!
> Using PKG_CFLAGS=-I/usr/include/libxml2
> Using PKG_LIBS=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
> - ANTICONF ERROR ---
> Configuration failed because libxml-2.0 was not found. Try installing:
>  * deb: libxml2-dev (Debian, Ubuntu, etc)
>  * rpm: libxml2-devel (Fedora, CentOS, RHEL)
>  * csw: libxml2_dev (Solaris)
> If libxml-2.0 is already installed, check that 'pkg-config' is in your
> PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
> is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
> R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
> 
> ERROR: configuration failed for package ‘xml2’
>
> Homebrew package info:
>
> dekkera:pkgconfig peter$ brew info libxml2 R
> libxml2: stable 2.9.7 (bottled), HEAD [keg-only]
> GNOME XML library
> http://xmlsoft.org
> /usr/local/Cellar/libxml2/2.9.7 (281 files, 10.4MB)
>   Poured from bottle on 2018-02-16 at 22:42:54
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/libxml2.rb
> ==> Options
> --HEAD
> Install HEAD version
> ==> Caveats
> This formula is keg-only, which means it was not symlinked into /usr/local,
> because macOS already provides this software and installing another version in
> parallel can cause all kinds of trouble.
>
> If you need to have this software first in your PATH run:
>   echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.bash_profile
>
> For compilers to find this software you may need to set:
> LDFLAGS:  -L/usr/local/opt/libxml2/lib
> CPPFLAGS: -I/usr/local/opt/libxml2/include
> For pkg-config to find this software you may need to set:
> PKG_CONFIG_PATH: /usr/local/opt/libxml2/lib/pkgconfig
>
> If you need Python to find bindings for this keg-only formula, run:
>   echo /usr/local/opt/libxml2/lib/python2.7/site-packages >>
> /usr/local/lib/python2.7/site-packages/libxml2.pth
>   mkdir -p /Users/peter/Library/Python/2.7/lib/python/site-packages
>   echo 'import site;
> site.addsitedir("/usr/local/lib/python2.7/site-packages")' >>
> /Users/peter/Library/Python/2.7/lib/python/site-packages/homebrew.pth
>
> R: stable 3.4.3 (bottled)
> Software environment for statistical computing
> https://www.r-project.org/
> /usr/local/Cellar/R/3.4.0_1 (2,246 files, 59.1MB)
>   Poured from bottle on 2017-05-20 at 17:10:29
> /usr/local/Cellar/R/3.4.1_2 (2,114 files, 55.3MB)
>   Poured from bottle on 2017-09-19 at 03:23:33
> /usr/local/Cellar/R/3.4.2 (2,111 files, 55.1MB)
>   Poured from bottle on 2017-11-13 at 22:23:36
> /usr/local/Cellar/R/3.4.3 (2,110 files, 55.1MB)
>   Poured from bottle on 2017-12-02 at 23:20:16
> /usr/local/Cellar/R/3.4.3_1 (3,773 files, 115.4MB)
>   Built from source on 2018-02-08 at 22:01:49 with: --with-x11
> --with-cairo --with-java
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/r.rb
> ==> Dependencies
> Build: pkg-config ✔
> Required: gcc ✔, gettext ✔, jpeg ✔, libpng ✔, pcre ✔, readline ✔, xz ✔
> Optional: openblas ✔
> ==> Requirements
> Optional: java ✔
> ==> Options
> --with-java
> Build with java support
> --with-openblas
> Build with openblas support

Re: [R] JSONlite import problem

[Jeroen Ooms]

On Sat, Oct 24, 2015 at 1:35 PM, Duncan Murdoch
 wrote:
>
> > However, editing the file with a text editor to create "proper" EOF
> > doesn't help.
>
> The problem is that you have valid-looking JSON objects on each odd
> numbered line, separated by single blank lines.  The parser expects an
> EOF at the end of the first object, but instead it found a blank line
> and another object.


Actually this is a common json streaming format called ndjson a.k.a.
jsonlines. Usually you can stream-import the data directly in jsonlite
using the stream_in function. See ?stream_in for examples.

However in this case there are white lines in between the json lines
which makes it a bit more tricky. I will add a feature to skip over
those lines.

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Re: [R] Installing pre-compiled R in Linux

[Jeroen Ooms]

> On Tue, Oct 6, 2015 at 9:42 PM, Sasikumar Kandhasamy  
> wrote:
>> Thanks a lot Mike. The Linux distribution we use is "Red Hat Enterprise
>> Linux Server release 6.2".

On RHEL and CentOS the easiest and most reliable way to get R and R
packages is via EPEL. Simply add the EPEL repositories and from there
on you can install R and R packages as you would do on Fedora.

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Re: [R] How to access https page

[Jeroen Ooms]

On Mon, Mar 9, 2015 at 3:39 PM, Hui Du hui...@savvyrookies.com wrote:

  readLines(url)
 Error in file(con, r) : cannot open the connection
 In addition: Warning message:
 In file(con, r) : unsupported URL scheme


Try:

library(curl)
readLines(curl(url))

[[alternative HTML version deleted]]

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Re: [R] Failure to execute R CMD SHLIB successfully

[Jeroen Ooms]

On Sat, Jan 31, 2015 at 1:36 PM, Fisher Dennis fis...@plessthan.com wrote:

 followed by a series of errors:
  gcc -m32 -shared -s -static-libgcc -o ../compiled/Windows32.so tmp.def
 ConvertSAS.o CKHashTable.o readstat_convert.o readstat_bits.o readstat_io.o
 readstat_sas.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386
 -Ld:/RCompile/CRANpkg/extralibs64/local/lib
 -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lR
  readstat_convert.o:readstat_convert.c:(.text+0x42): undefined reference
 to `_imp__libiconv'
  readstat_sas.o:readstat_sas.c:(.text+0x10b5): undefined reference to
 `_imp__libiconv_close'
  readstat_sas.o:readstat_sas.c:(.text+0x1126): undefined reference to
 `_imp__libiconv_open'
  readstat_sas.o:readstat_sas.c:(.text+0x1808): undefined reference to
 `dprintf'
  readstat_sas.o:readstat_sas.c:(.text+0x1da1): undefined reference to
 `_imp__libiconv_open'
  readstat_sas.o:readstat_sas.c:(.text+0x1de4): undefined reference to
 `_imp__libiconv_close'
  collect2: ld returned 1 exit status



The windows build of R includes a special version of iconv (Riconv.dll in
the same dir as R.exe). Therefore if you include iconv.h somewhere, you
also need to link to Riconv.dll in your Makevars.win:

PKG_LIBS= -lRiconv

[[alternative HTML version deleted]]

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Re: [R] Install R on linux Mint

[Jeroen Ooms]

On Wed, Jan 14, 2015 at 7:40 PM, Jeroen Ooms jeroen.o...@stat.ucla.edu wrote:
 Try 'precise' instead of 'utopic'

I meant 'trusty'. The version should match the underlying ubuntu:
http://www.linuxmint.com/oldreleases.php

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Re: [R] Install R on linux Mint

[Jeroen Ooms]

Try 'precise' instead of 'utopic'

On Wed, Jan 14, 2015 at 7:31 PM, John Sorkin
jsor...@grecc.umaryland.edu wrote:
 I am trying to install R on Linux mint 17.1. I followed the instructions 
 found on CRAN and got a messages about unmet dependencies. I detail below the 
 steps I took:

 I added deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu utopic/
 to /etc/apt/sources.list
 As can be seen below:

 john-OptiPlex-GX270 apt # more sources.list
 #deb cdrom:[Linux Mint 17.1 _Rebecca_ - Release i386 20141126]/ trusty 
 contrib main non-free
 deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu utopic/

 And then followed the instructions on CRAN:

 sudo apt-get update
 AND RECEIVED THE FOLLOWING MESSAGE:

 Fetched 316 kB in 8s (39.5 kB/s)
 Reading package lists... Done
 W: GPG error: http://lib.stat.cmu.edu utopic/ Release: The following 
 signatures couldn't be verified because the public key is not available: 
 NO_PUBKEY 51716619E084DAB9

 sudo apt-get install r-base
 AND RECEIVED THE FOLLOWING MESSAGE:

 The following packages have unmet dependencies:
  r-base : Depends: r-base-core (= 3.1.2-1utopic0) but 3.0.2-1ubuntu1 is to 
 be installed
   Depends: r-recommended (= 3.1.2-1utopic0) but it is not going to be 
 installed
 E: Unable to correct problems, you have held broken packages.

 John David Sorkin M.D., Ph.D.
 Professor of Medicine
 Chief, Biostatistics and Informatics
 University of Maryland School of Medicine Division of Gerontology and 
 Geriatric Medicine
 Baltimore VA Medical Center
 10 North Greene Street
 GRECC (BT/18/GR)
 Baltimore, MD 21201-1524
 (Phone) 410-605-7119
 (Fax) 410-605-7913 (Please call phone number above prior to faxing)

 Confidentiality Statement:
 This email message, including any attachments, is for ...{{dropped:12}}

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[R] Updates from the useR! 2014 organizing committee

[Jeroen Ooms]

Hi all,

We are exactly one month away from the useR! 2014 conference [1]. Time
for an update from the organizing committee.

This weekend, registrations passed the 500 mark, which is a new record
for useR! according to data collected by Gergely Daróczi [2]. Yet,
there is plenty of additional capacity, both for the conference
itself, as well as the beautiful on-campus housing at UCLA. We hope to
see many more registrations over the upcoming weeks and appreciate all
help in spreading the word to friends and colleagues that (should) use
R, but might not be actively following the blogs or mailing lists.

To those who are unsure whether to attend, we want to emphasize that
useR! is not just for seasoned professionals, but has lots to offer to
any R user. Abstracts and (free) tutorials cover a great diversity of
topics in both research and industry applications, ranging from
introductory to very advanced. The conference provides a great
opportunity to learn and mingle with the community, and is interesting
for beginner as well as experienced R users.

Tutorials this year are included with the conference ticket and no
separate registration is required. All registrants will receive an
email survey asking which tutorial they would like to attend, if any.
This information will be used for scheduling purposes and to
facilitate communication between presenters and participants (e.g.
distribution of preparation material).

Finally, we urge international guests to verify that their visa or
visa-waiver documents are valid to enter the United States. Citizens
from visa-waiver countries [3] that do not already have a US visa,
must apply online for an ESTA travel authorization at least 72 hours
prior to departure. Once approved, the ESTA is generally valid for a
period of 2 years, so now would be a good time to complete this
process.

We look forward to seeing all of you in California! Please keep an eye
on the conference website, which is continuously updated with most
recent news and information as it becomes available.

Best,

Jeroen, on behalf of the organizing committee


[1] http://user2014.stat.ucla.edu/
[2] http://rapporter.net/custom/R-activity/data/Rstats.csv
[3] http://www.esta.us/visa_waiver_countries.html

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[R] Call for abstracts to present at useR! 2014

[Jeroen Ooms]

We are happy to inform you that abstract submission for
useR! 2014 is now available online, see

http://user2014.stat.ucla.edu/

The R User Conference, useR! 2014 is scheduled for July 1-3, 2014 at
the University of California, Los Angeles.  Before the official
program, half-day tutorials will be offered on Monday, June 30.

Participants are encouraged to submit a one-page abstract for oral or
poster presentation at the conference.

For regular talks and posters, please use the recently updated LaTeX or
Microsoft Word/LibreOffice Writer abstract templates available at the
conference website:

http://user2014.stat.ucla.edu/

The deadline for abstract submission is March 30, 2014.

The preferred method of abstract and tutorial proposal submission is via
the web form at the conference website:

http://user2014.stat.ucla.edu/abstract-submission.html

We look forward to seeing you at useR! 2014 in California!

--
Jeroen, on behalf of the useR! 2014 local organizing committee

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[R] flatten lists

[Jeroen Ooms]

I am looking for a function to flatten a list to a list of only 1
level deep. Very similar to unlist, however I don't want to turn it
into a vector because then everything will be casted to character
vectors:

x - list(name=Jeroen, age=27, married=FALSE,
home=list(country=Netherlands, city=Utrecht))
unlist(x)

This function sort of does it:

flatlist - function(mylist){
  lapply(rapply(mylist, enquote, how=unlist), eval)
}

flatlist(x)

However it is a bit slow. Is there a more native way?

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Re: [R] flatten lists

[Jeroen Ooms]

Hmm that doesn't seem to work if the original list is nested more than
2 levels deep. I should have probably given a better example:

x - list(name=Jeroen, age=27, married=FALSE,
home=list(country=list(name=Netherlands, short=NL), city=Utrecht))




On Tue, Jun 26, 2012 at 3:04 PM, Neal Fultz nfu...@gmail.com wrote:
 do.call(c, x)

 maybe?

 On Tue, Jun 26, 2012 at 02:25:40PM -0700, Jeroen Ooms wrote:
 I am looking for a function to flatten a list to a list of only 1
 level deep. Very similar to unlist, however I don't want to turn it
 into a vector because then everything will be casted to character
 vectors:

 x - list(name=Jeroen, age=27, married=FALSE,
 home=list(country=Netherlands, city=Utrecht))
 unlist(x)

 This function sort of does it:

 flatlist - function(mylist){
   lapply(rapply(mylist, enquote, how=unlist), eval)
 }

 flatlist(x)

 However it is a bit slow. Is there a more native way?

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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] flatten lists

[Jeroen Ooms]

Alright, but I need something recursive for lists with arbitrary deepness.



On Tue, Jun 26, 2012 at 3:37 PM, arun smartpink...@yahoo.com wrote:
 Hi,

 Try:

 do.call(c,do.call(c,x))

 x1-do.call(c,do.call(c,x))
  x2-flatlist(x)
  identical(x1,x2)
 [1] TRUE



 A.K.



 - Original Message -
 From: Jeroen Ooms jeroen.o...@stat.ucla.edu
 To: Neal Fultz nfu...@gmail.com
 Cc: r-help@r-project.org
 Sent: Tuesday, June 26, 2012 6:23 PM
 Subject: Re: [R] flatten lists

 Hmm that doesn't seem to work if the original list is nested more than
 2 levels deep. I should have probably given a better example:

 x - list(name=Jeroen, age=27, married=FALSE,
 home=list(country=list(name=Netherlands, short=NL), city=Utrecht))




 On Tue, Jun 26, 2012 at 3:04 PM, Neal Fultz nfu...@gmail.com wrote:
 do.call(c, x)

 maybe?

 On Tue, Jun 26, 2012 at 02:25:40PM -0700, Jeroen Ooms wrote:
 I am looking for a function to flatten a list to a list of only 1
 level deep. Very similar to unlist, however I don't want to turn it
 into a vector because then everything will be casted to character
 vectors:

 x - list(name=Jeroen, age=27, married=FALSE,
 home=list(country=Netherlands, city=Utrecht))
 unlist(x)

 This function sort of does it:

 flatlist - function(mylist){
   lapply(rapply(mylist, enquote, how=unlist), eval)
 }

 flatlist(x)

 However it is a bit slow. Is there a more native way?

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[R] issues with read.spss

[Jeroen Ooms]

Someone supplied me with an SPSS datafile that caused a buffer
overflow and then a crash when reading it in R. Unfortunately I can't
supply the dataset at hand and I have a hard time reproducing it with
a toy example. But I found at least 2 issues that might be related. I
would like to know which of these are expected behavior, and which are
bugs. I reproduced it on R 2.14.1 both on Ubuntu Linux and Windows
7...

Below some code. The files that are referenced in the code are
available for download on http://www.stat.ucla.edu/~jeroen/spss/

#load library
library(foreign)

#problem one: long string variable is converted to multiple variables.
x - read.spss(longstring.sav);
summary(x); #4 variables??

#problem two: use.labels does not deal correctly with duplicate labels
and generates a bad factor.
x - read.spss(duplicate_labels.sav, use.value.labels=T);

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Re: [R] Standardized beta-coefficients in regression

[Jeroen Ooms]

Unfortunately I found myself in the same position as outlined above, where I
was requested to reproduce 'standardized regression coefficients' as
reported by SPSS. Below an example that produces something very similar to
the results table from an SPSS Linear Regression procedure, including the
standardized regression coefficients:

mylm - lm(Sepal.Width ~ ., data=iris, x=TRUE, y=TRUE)
sd.x - sd(mylm$x);
sd.y - sd(mylm$y);
std.coef - coef(mylm) * (sd.x / sd.y);
coef.table - as.data.frame(summary(mylm)$coefficients);
coef.table - cbind(coef.table, std.coef);
print(coef.table);

I do agree with B.R. but unfortunately the life of an applied statistician
is complex sometimes :-)

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Re: [R] Save generic plot to file (before rendering to device)

[Jeroen Ooms]

Bumping this one up because the 'before.plot.new' solution turned out
to be sub-optimal after all.

 It should be possible to do this with a before.plot.new hook, right?

 Yes, sure, if you treat the first and last plot separately.

It turns out that the before.plot.new hook does not is not triggered
at the right moments. I'm not sure if this is intended behavior or
incorrect implementation. What I was expecting is a hook/event that is
triggered every time before a new graphics frame is opened. E.g. if
there is an open PDF device and some plots are printed, the number of
times the hook is called should be exactly equal to the number of
pages in the resulting PDF document. Sometimes this works as expected,
sometimes it doesn't.

At the end of this message some example code. In the first example,
the hook works as expected is called 4 times, as there are 4 plots. In
all the other examples the event is either triggered too often or not
triggered at all. I guess the hook is called when the plot.new()
function is explicitly called, which might not always happen.

My question would be if (1) this is the intended behavior for
'before.plot.new', and (2) if yes, would it be possible to define an
additional event that always triggers, and only triggers, if a
completely new graphics device is opened. I.e. whenever a pdf device
would start a new page.

Thank you.


#set the hook (event listener)
setHook(before.plot.new, NULL);
setHook(before.plot.new, function(){ message(Yay! A new plot!)});

#works as expected:
plot(lm(speed~dist, cars), ask=F);

#triggered way too often, once for every partition of the plot
plot(mtcars);

#not triggered at all by lattice
library(lattice);
dotplot(speed~dist, cars);

#not triggered at all by ggplot2
library(ggplot2);
qplot(speed, dist, data=cars);

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Re: [R] Save generic plot to file (before rendering to device)

[Jeroen Ooms]

Thanks I didn't know about that. I ended up with something like this.
Is there a more elegant way to do it?

myplots - list();
hasplots - FALSE;
setHook(before.plot.new, function(...) {
    if(hasplots == FALSE){
      hasplots - TRUE;
    } else {
      myplots[[length(myplots)+1]] - recordPlot();
    }
});
myfn - function(mylm){
  plot(mylm, ask=F)
}
mylm - lm(dist~speed, data=cars);
pdf(tempfile())
dev.control(displaylist=enable)
myfn(mylm);
if(hasplots){
  myplots[[length(myplots)+1]] - recordPlot();
}
dev.off()





On Sat, Jul 16, 2011 at 8:17 PM, Hadley Wickham had...@rice.edu wrote:

  Thank you, this is very helpful. One final question regarding this method:
  suppose a function prints multiple plots, i.e. multiple pages to a PDF. Is
  it possible to record all of these plots at once? The code below only
  records the final plot. I would like to record all of them, without
  modifying myfn:
 
  You cannot, since this takes a snapshot from the current device. You will
  have to recordPlot() after each plot, actually.

 It should be possible to do this with a before.plot.new hook, right?

 Hadley

 --
 Assistant Professor / Dobelman Family Junior Chair
 Department of Statistics / Rice University
 http://had.co.nz/

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Re: [R] Save generic plot to file (before rendering to device)

[Jeroen Ooms]

 That warning is necessarily rather pessimistic.  We haven't changed the
 format for several years.  But we might, without notice.


Thank you, this is very helpful. One final question regarding this method:
suppose a function prints multiple plots, i.e. multiple pages to a PDF. Is
it possible to record all of these plots at once? The code below only
records the final plot. I would like to record all of them, without
modifying myfn:

myfn - function(mylm){
  plot(mylm, ask=F)
}

mylm - lm(dist~speed, data=cars);

pdf(tempfile())
dev.control(displaylist=enable)
myfn(mylm);
myplots - recordPlot()
dev.off()

save(myplot, file=myplot.RData)









 Another approach (or the start to one that you could build on) is the
 plot2script function in the TeachingDemos package (which uses recordPlot
 internally).

 But it is probably best to save the resulting data from the long process,
 that could then be quickly plotted as others have mentioned.

 --
 Gregory (Greg) L. Snow Ph.D.
 Statistical Data Center
 Intermountain Healthcare
 greg.s...@imail.org
 801.408.8111


  -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Jeroen Ooms
 Sent: Monday, July 11, 2011 12:22 PM
 To: David Winsemius
 Cc: r-help@r-project.org
 Subject: Re: [R] Save generic plot to file (before rendering to device)


 You can also save a data (or function) object to an .Rdata file with
 save(objname, file=filename.Rdata)  and your colleagues could then
 load(filename.Rdata) in R.


 Thanks for the responses. I found an old post by Gabor Grothendieck
 that
 shows what I want. Basically the trick is to save the displaylist to an
 object:

 dev.control(displaylist=**enable) # enable display list
 plot(1:10)
 myplot - recordPlot() # load displaylist into variable

 You can now store myplot and later fetch it and play it back via

 print(myplot)

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 PLEASE do read the posting guide 
 http://www.R-project.org/**posting-http://www.R-project.org/posting-
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 and provide commented, minimal, self-contained, reproducible code.


 __**
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 PLEASE do read the posting guide http://www.R-project.org/**
 posting-guide.html http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


 --
 Brian D. Ripley,  rip...@stats.ox.ac.uk
 Professor of Applied Statistics,  
 http://www.stats.ox.ac.uk/~**ripley/http://www.stats.ox.ac.uk/~ripley/
 University of Oxford, Tel:  +44 1865 272861 (self)
 1 South Parks Road, +44 1865 272866 (PA)
 Oxford OX1 3TG, UKFax:  +44 1865 272595


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Re: [R] Save generic plot to file (before rendering to device)

[Jeroen Ooms]

 You can also save a data (or function) object to an .Rdata file with
 save(objname, file=filename.Rdata)  and your colleagues could then
 load(filename.Rdata) in R.


Thanks for the responses. I found an old post by Gabor Grothendieck that
shows what I want. Basically the trick is to save the displaylist to an
object:

dev.control(displaylist=enable) # enable display list
plot(1:10)
myplot - recordPlot() # load displaylist into variable

You can now store myplot and later fetch it and play it back via

print(myplot)

[[alternative HTML version deleted]]

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[R] unwanted coercion using apply

[Jeroen Ooms]

I need to convert a dataframe to a record-structure, to be able to encode it
later in JSON. Suppose this is the data:

mydata - data.frame(foo=1:3, bar=c(M,M,F));

I would like to convert this to a unnamed list (json array) of key-value
pairs. For example like this:

apply(data.frame(foo=1:3, bar=c(M,M,F)),1,as.list)

However, when I do this, all the numeric values are converted to strings. I
don't understand why this is, because when I try to convert one record
simulataniously, this does not happen:

as.list(mydata[1,]);

I am not sure if this is indended behaviour or not, but is there an elegant
way to apply 'as.list' to all of the dataframe rows without coercing
everything to strings?


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Re: [R] unwanted coercion using apply

[Jeroen Ooms]

 apply() operates on arrays and a data frame will be coerced to a matrix
 (which requires all elements to be of the same type). This is documented in
 ?apply.


Thanks, I was not aware of that. I implicitly assumed there would be a
specific apply.data.frame.



 This may not be elegant, but why not just use a loop:


The thing is that were are going to use this operation on a (very) large
scale in a production environment, on datasets for which nrow  ncol. So I
would like the most efficient solution and if possibly, avoid looping over
the rows.

Thanks

Jeroen

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[R] regressing on variable with heavy tails

[Jeroen Ooms]

I have a dependent variable with is very peaked and has heavy tails,
something I haven't encountered before. (histogram:
http://postimage.org/image/2sw9bn8pw/). What could be an appropriate family
or transformation to do regress on this?--
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[R] matrix of higher order differences

[Jeroen Ooms]

Is there an easy way to turn a vector of length n into an n by n matrix, in
which the diagonal equals the vector, the first off diagonal equals the
first order differences, the second... etc. I.e. to do this more
efficiently:

diffmatrix - function(x){
n - length(x);
M - diag(x);
for(i in 1:(n-1)){
differences - diff(x, dif=i);
for(j in 1:length(differences)){
M[j,i+j] - differences[j]
}
}
M[lower.tri(M)] - t(M)[lower.tri(M)];
return(M);
}

x - c(1,2,3,5,7,11,13,17,19);
diffmatrix(x);



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[R] Read function that detects format automatically

[Jeroen Ooms]

I was wondering if there exists a function that automatically tries to detect
the format of a datafile. E.g. if it is an ascii datafile, that it can
detect appropriate defaults for the read.table() parameters. One could for
example read the first 10 lines of the file and analyze the format of the
first line in comparison with the others, count the number of dots, colons
and semicolons, etc. More generally, one could use the file extension or if
available the unix 'file' command to evaluate the filetype if it is non
ascii.

I think it should not be very complicated to get a very high accuracy for
detecting formats. For most datafiles it is for a human statistican easy to
see the format of the file by looking at a fragment, so it should be
possible to capture these rules in some code. It would be nice to have
something like a read.magic() function that reads a datafile using the
appropriate command, regardless of whether the user supplied an csv1, csv2,
tab delimited, excel, spss, stata, etc file. 

I actually started to code something like this, but then I figured that
maybe someone else has had the exact same idea.


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Re: [R] detect filetype (as in unix 'file')

[Jeroen Ooms]

 No, but what is wrong with using system()?

The application is running in a very sandboxed environment and might
not have permission to execute 'file'.

 'file' is large and complex because it tries to be comprehensive (but it
 still does not know about some common systems, e.g. 64-bit Windows
 binaries).  There simply is no point in replicating that in R: which is why
 we chose rather to port 'file' to Windows and provide in in Rools.

Alright that makes sense, thanks.

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[R] detect filetype (as in unix 'file')

[Jeroen Ooms]

Is there a way in R (in Linux) to detect the type of a file without invoking
a shell? E.g to do this:

 system(file density.plot)
density.plot: PDF document, version 1.4

but without using system()? I tried file() and file.info(), but both do
display the information I am looking for.



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Re: [R] svg malformed on CentOS (epel R)

[Jeroen Ooms]

The problem has been resolved thanks to Tom Callaway from Redhat:


Tom Callaway wrote:
 
 Looking at the R source code, it uses Cairo to do the SVG creation, and
 the Cairo in RHEL-5 is very (very) old (1.2.4).
 
 Digging through Cairo's changelogs post 1.2.4, I came across this:
 
 SVG: Fix bug preventing text from appearing in many viewers
 
 http://cairographics.org/news/cairo-1.4.0/
 
 Sure enough, I dug out an old cairo 1.4 series package from Fedora 7
 (1.4.4, to be specific), rebuilt it on RHEL-5 and it generates a good
 svg that views properly in Firefox.
 
 Looking at the code to see how they fixed that bug, it is pretty much
 what I suspected, they add the overflow=visible field when outputting
 the glyphs. This was trivial to backport and the patch is attached.
 
 In addition, since I had to make the packages to test, I have uploaded
 them here:
 
 http://spot.fedorapeople.org/cairo-invisible-text-fix-el5/
 
 Last but not least, I have opened a bug against RHEL 5 on this issue. I
 do not know if they will push a cairo update for this, but at least, it
 is now on their radar:
 
 https://bugzilla.redhat.com/show_bug.cgi?id=691844
 

So to fix the problem, grab the updated Cairo binary from the link he gives
and do a: rpm -Uvh cairo-1.2.4-5.spot.i386.rpm

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Re: [R] recursive do.call

[Jeroen Ooms]

Hmmm I was hoping there would be a more natural way to do it. For example,
if you actually try to call the first function with all arguments:

lm(formula=dist~speed, digits=3, data=cars)

R will match whatever it can, and give you a warning with the names of
remaining unmatched arguments. The only thing I really need is instead of a
warning take these arguments and pass them on to the next function.




On Mon, Mar 14, 2011 at 3:34 AM, Felix Andrews fe...@nfrac.org wrote:

 It is complicated if the argument list is all mixed in together as in
 your example. You would have to look up argument lists for possible S3
 methods (e.g. 'digits' is an argument to print.default), and then
 there is S4 to think about. Also, can arguments be matched by partial
 names? Can they be given in the argument list without a name?

 My point is that you had better have a good reason to want to do it this
 way...

 Cheers
 Felix


 On 14 March 2011 14:24, Jeroen Ooms jeroeno...@gmail.com wrote:
  I would like to define a recursive equivalent to call or do.call, which
 takes
  a vector of multiple function names and 'chains' them, by greedy matching
 of
  arguments down the chain. For example, I would like to be able to do:
 
  rec.do.call(c(glm,coef,print), list(formula=dist~speed, digits=3,
  data=cars));
 
  which would then be equivalent to:
 
  print(coef(glm(formula=dist~speed, data=cars)), digits=3);
 
  I've been playing around with a recursive function with ellipses, but I
  can't wrap my head around it.
 
  --
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 --
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 http://www.neurofractal.org/felix/


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Re: [R] recursive do.call

[Jeroen Ooms]

I see what you are saying. The application I am working with is making
convenient single-call (user) interfaces for R functions, and I don't
want to write a wrapper for every possible combination (like Gene
suggested below). If we don't consider the ... arguments for a second,
and only consider first class arguments of all the functions. Maybe we
could do something like this:

rec.do.call - function(fnnames, fnargs, object=NULL){
if(length(fnnames) == 1){
cat(fnnames, (, paste(names(fnargs), collapse=,), ).\n\n, 
sep=);
return(do.call(fnnames, c(object, fnargs)));
}

thisfn - head(fnnames, 1);

if(is.null(getS3method(thisfn, class(object[[1]]), T))){
fnformals - formals(thisfn);
} else {
fnformals - formals(getS3method(thisfn, class(object[[1]])));
}

matchindex - na.omit(pmatch(names(fnformals), names(fnargs)));
cat(Matched: , thisfn, (, paste(names(fnargs[matchindex]),
collapse=,), ). , sep=);

myobj - do.call(thisfn, c(object, fnargs[matchindex]));

if(length(matchindex)==0){
remaining.fnargs - fnargs; 
} else {
remaining.fnargs - fnargs[-matchindex];
}

cat(Remaining:, (, paste(names(remaining.fnargs), collapse=,),
). \n, sep=);

rec.do.call(tail(fnnames, -1), remaining.fnargs, list(myobj));
}

#two examples:
rec.do.call(c(glm,anova,print), list(formula=dist~speed,
data=cars, test=Chisq, digits=1, signif.stars=F))
rec.do.call(c(glm,coef,round), list(formula=dist~speed,
data=cars, digits=1))

This seems to work for the examples above. Would this generally hold,
or is this asking for trouble?




     -thomas

 
 
  On Mon, Mar 14, 2011 at 3:34 AM, Felix Andrews fe...@nfrac.org wrote:
 
  It is complicated if the argument list is all mixed in together as in
  your example. You would have to look up argument lists for possible S3
  methods (e.g. 'digits' is an argument to print.default), and then
  there is S4 to think about. Also, can arguments be matched by partial
  names? Can they be given in the argument list without a name?
 
  My point is that you had better have a good reason to want to do it this
  way...
 
  Cheers
  Felix
 
 
  On 14 March 2011 14:24, Jeroen Ooms jeroeno...@gmail.com wrote:
   I would like to define a recursive equivalent to call or do.call, which
  takes
   a vector of multiple function names and 'chains' them, by greedy matching
  of
   arguments down the chain. For example, I would like to be able to do:
  
   rec.do.call(c(glm,coef,print), list(formula=dist~speed, digits=3,
   data=cars));
  
   which would then be equivalent to:
  
   print(coef(glm(formula=dist~speed, data=cars)), digits=3);
  
   I've been playing around with a recursive function with ellipses, but I
   can't wrap my head around it.
  
   --
   View this message in context:
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   and provide commented, minimal, self-contained, reproducible code.
  
 
 
 
  --
  Felix Andrews / 安福立
  http://www.neurofractal.org/felix/
 
 
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 --
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 University of Auckland

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[R] svg malformed on CentOS (epel R)

[Jeroen Ooms]

There is an issue with the default svg device on a centos workstation that I
am using. It does not result in an error, but it produces malformed svg
images. Exactly the same script works just fine on an ubuntu box. On Ubuntu
I am using R binary that comes with maverick, on centos I am using the
latest R binary from EPEL. Other than that both boxes are pretty clean, with
only the dependencies installed that are automatically installed when
installing R.

For example a testscript like this
svg(plot.svg);
plot(cars);
dev.off();

should produce this: http://www.stat.ucla.edu/~jeroen/files/plot_good.svg
(ubuntu), but on centos it produces this:
http://www.stat.ucla.edu/~jeroen/files/plot_bad.svg. 

It looks very much as if there is something wrong with the fronts; maybe I
am missing some library. However, as this is a production server, I don't
want to go install random packages to see if this fixes the problem.

Some questions:

- How could I fix it?
- Why is R not throwing an error instead of producing a malformed plot?
- Maybe we could notify the R binary maintainers from fedora to add a formal
dependency so that it works 'out of the box'?

Jeroen

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[R] recursive do.call

[Jeroen Ooms]

I would like to define a recursive equivalent to call or do.call, which takes
a vector of multiple function names and 'chains' them, by greedy matching of
arguments down the chain. For example, I would like to be able to do:

rec.do.call(c(glm,coef,print), list(formula=dist~speed, digits=3,
data=cars));

which would then be equivalent to:

print(coef(glm(formula=dist~speed, data=cars)), digits=3);

I've been playing around with a recursive function with ellipses, but I
can't wrap my head around it.

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Re: [R] getting attributes of list without the names.

[Jeroen Ooms]

Thank you, this is very helpful. I am a little confused now about the
structure of a list though. If the names of the list-elements is truly an
attribute that is stored in another list this would lead to an infintely
recursing object?

How could I iterate over the full object tree, without getting into infinite
recursion if every list's attributes is another list with at least a 'names'
attribute?





On Tue, Mar 1, 2011 at 2:30 AM, Duncan Murdoch murdoch.dun...@gmail.comwrote:

 On 11-02-28 11:17 PM, Jeroen Ooms wrote:

 I am trying to encode arbitrary S3 objects by recursively looping over the
 object and all its attributes. However, there is an unfortunate feature of
 the attributes() function that is causing trouble. From the manual for
 ?attributes:

 The names of a pairlist are not stored as attributes, but are reported as
 if
 they were (and can be set by the replacement method for attributes).

 Now because of this, my program ends up in infinite recursion, because it
 will try to encode
 attributes(attributes(attributes(attributes(list(foo=123 etc. I can't
 remove the 'names' attribute, because this will actually affect the list
 structure. And even when I do:

 attributes(attributes(obj)[names(attributes(obj)) != names])

 This will keep giving me a named list. Is there any way I can get the
 attributes() of a list without it reporting the names of a list as
 attributes? I.e it should hold that:

 atr1- attributes(list(foo=bar));
 atr2- attributes(list());
 identical(atr1,atr2);


 The names of a list (a generic vector) are attributes, just like the names
 of other vectors.  The documentation is talking about pairlists, a mostly
 internal structure, used for example to store parts of expressions.  So your
 premise might be wrong about the cause of the recursion...

 But assuming you really want to see all attributes except names.  Then just
 write your own version:

 nonameattributes - function(obj) {
  result - attributes(obj)
  if (!is.null(result$names))
result$names - NULL

  # This removes the empty names of the result if there were no other
  # attributes.  It's optional, but you said you wanted
  # identical(atr1, atr2)

  if (!length(result))
names(result) - NULL

  result
 }

 You can make the conditional more complicated, only making the change for
 pairlists, etc., using tests on typeof(obj) or other tests.

 Duncan Murdoch




[[alternative HTML version deleted]]

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[R] getting attributes of list without the names.

[Jeroen Ooms]

I am trying to encode arbitrary S3 objects by recursively looping over the
object and all its attributes. However, there is an unfortunate feature of
the attributes() function that is causing trouble. From the manual for
?attributes:

The names of a pairlist are not stored as attributes, but are reported as if
they were (and can be set by the replacement method for attributes).

Now because of this, my program ends up in infinite recursion, because it
will try to encode
attributes(attributes(attributes(attributes(list(foo=123 etc. I can't
remove the 'names' attribute, because this will actually affect the list
structure. And even when I do:

attributes(attributes(obj)[names(attributes(obj)) != names])

This will keep giving me a named list. Is there any way I can get the
attributes() of a list without it reporting the names of a list as
attributes? I.e it should hold that:

atr1 - attributes(list(foo=bar));
atr2 - attributes(list());
identical(atr1,atr2);



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[R] Parsing JSON records to a dataframe

[Jeroen Ooms]

What is the most efficient method of parsing a dataframe-like structure that
has been json encoded in record-based format rather than vector based. For
example a structure like this:

[ {name:joe, gender:male, age:41}, {name:anna,
gender:female, age:23} ]

RJSONIO parses this as a list of lists, which I would then have to apply
as.data.frame to and append them to an existing dataframe, which is terribly
slow. 


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Re: [R] Chrooted R + Rserve

[Jeroen Ooms]

I am trying to reproduce this setting, but it does not seem to work anymore.
I keep getting the error: execve failed: No such file or directory.

One of the reasons is that /usr/local/bin/Rserve is no longer a standalone
executable, and is now initiated using R CMD Rserve. However, after making
the appropriate changes to the .ini, I still get the same error.

Anyone successfully reproduced this setting with a recent R/Rserve/Jailkit?
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[R] Setting R_Interactive

[Jeroen Ooms]

We're using Rserve as a back-end in our application. A problem that we
experienced is that the Rserve connection gets stuck when R is asking for
some kind of user interaction. For example, when executing an
'install.packages' command for the first time without specifying the repos
argument, R will prompt a list to specify a mirror, and does not return. To
solve this, we need to set R to non-interactive (see ?interactive), but it's
hard to find out how.

Jeffrey Horner has been so kind to write a little piece of c code that sets
the C level global variable
R_Interactive (see package 'interactivity' on cran), but I was wondering if
there is an easier way to start R in non interactive mode.



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[R] read.table behavior for Dates.

[Jeroen Ooms]

When read.table imports a table that includes a header called 'Date', it
tries to recognize the date format. For example, if one imports this data
from Yahoo finance, the Date column is automatically transformed to Y-m-d,
whereis in the data it appears as m/d/Y:

myData -
read.csv(http://ichart.finance.yahoo.com/table.csv?s=GOOGa=07b=19c=2004d=03e=16f=2010g=dignore=.csv;)

However, it does not actually convert the variable to Date format.
MyData$Date is still a factor. This combination of converting the format but
not attributing the 'Date' class is for me extremely unfortunate behavior.
My scripts still don't recognize the variable as being a date, but it also
becomes harder to manually convert it using as.Date() because it is no
longer in the original format.

Is there a way to either automatically convert to as.Date() when a date
format has been detected, or otherwise disable this transformation at all?


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Re: [R] read.table behavior for Dates.

[Jeroen Ooms]

Yes I know I can manually do it, but I am using it for scripts in which users
upload files. Hence, I don't know what's going to come; I don't know on
before hand whether data will contain Dates, and in which columns they
appear. This is why I was surprised that read.table has some (undocumented)
behavior of converting columns that look like Dates to a different format.

I would like to control this default behavior of the read.table function,
rather than set a type for a specific column of a specific file. 


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Re: [R] read.table behavior for Dates.

[Jeroen Ooms]

Ah Phil Spector is right, nothing is converted. I'm almost too embarrassed to
admit it, but actually, it was Excel that tricked me. It displays date
fields differently than they are stored in the csv file, and once you press
'save', it saves everything to a different format, completely unasked.

Nevertheless I got some valuable insight in the topic. What I'm trying to do
here is make it easier for people to upload files that might contain dates
to my webapp at yeroon.net/ggplot2. Currently, dates are imported as
factors. I would like to implement something that Henrique described, to
automatically convert variables to Date that are obviously dates.

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[R] [announce] yeroon.net/ggplot2 web application v0.2

[Jeroen Ooms]

A new version of the ggplot2 web interface has been released. Info and a demo
video are available here: http://www.stat.ucla.edu/~jeroen/ggplot2/. The new
version has a lot of new features, like advanced data import, integration
with Google docs, converting variables from numeric to factor to dates and
vice versa, and a lot of new geom's. 

For those that missed it: http://yeroon.net/ggplot2 is a web interface for
Hadley Wickham's R package ggplot2. It is used as a tool for rapid
prototyping, exploratory graphical analysis and education of statistics and
R. The interface is written completely in javascript, therefore there is no
need to install anything on the client side: a standard browser will do. All
major browsers are supported but a recent and standards-compliant browser is
highly recommended. Best performance is achieved by using Google Chrome. 

The easiest way to learn how to use the application is by taking 5 minutes
to watch the introductory demo video. 
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Re: [R] yeroon.net/ggplot2 web application v0.11

[Jeroen Ooms]

Hi Felipe,

my apps are completely webbased, so you cannot use them offline,
unless you are hosting a mirror locally or in your LAN (which can be
arranged if you are interested).

Jeroen



2009/12/7 Felipe Carrillo mazatlanmex...@yahoo.com:
 Hi Jeroen:
 This is great for someone who is point and click oriented. Can this program 
 be downloaded to be used offline or its just web based? My field crew usually 
 take toughbooks to the field and since they don't know how to program it will 
 be nice to make the graphics just by pointing and clicking. Thanks


 Felipe D. Carrillo
 Supervisory Fishery Biologist
 Department of the Interior
 US Fish  Wildlife Service
 California, USA


 --- On Sun, 12/6/09, Jeroen Ooms jeroen.o...@stat.ucla.edu wrote:

 From: Jeroen Ooms jeroen.o...@stat.ucla.edu
 Subject: [R] yeroon.net/ggplot2 web application v0.11
 To: r-help@r-project.org
 Date: Sunday, December 6, 2009, 5:07 PM
 A new version of the ggplot2 web
 application is available at
 http://www.yeroon.net/ggplot2. New features include 1D
 geom’s
 (histogram, density, freqpoly), syntax mode (by clicking
 the tiny
 arrow at the bottom), and some additional facet options.
 Furthermore
 some minor improvements and fixes, most notably for
 Internet Explorer.

 As usual, a little demo video that shows how to use the new
 features:
 http://www.youtube.com/watch?v=7XGN6OSCq6Ehd=1 (watch
 in full
 screen). The datafile from the demo is available at
 http://www.yeroon.net/ggplot2/myMovies.csv.

 The data upload has not been improved yet, I am working on
 that. For
 now, it supports .csv, .sav (spss), and tab delimited data.
 Please
 make sure your filename has the appropriate extension and
 every column
 has a header in your data. If you export a dataframe from
 R, use:
 write.csv(mydf, ”mydf.csv” , row.names=F). If you
 upload an spss
 datafile, none of this should be a concern.

 Supported browsers are IE6-8, FF, Safari, and Chrome, but a
 recent
 browser is highly recommended. As always, feedback is more
 than
 welcome.

 Jeroen

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 reproducible code.






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[R] yeroon.net/ggplot2 web application v0.11

[Jeroen Ooms]

A new version of the ggplot2 web application is available at
http://www.yeroon.net/ggplot2. New features include 1D geom’s
(histogram, density, freqpoly), syntax mode (by clicking the tiny
arrow at the bottom), and some additional facet options. Furthermore
some minor improvements and fixes, most notably for Internet Explorer.

As usual, a little demo video that shows how to use the new features:
http://www.youtube.com/watch?v=7XGN6OSCq6Ehd=1 (watch in full
screen). The datafile from the demo is available at
http://www.yeroon.net/ggplot2/myMovies.csv.

The data upload has not been improved yet, I am working on that. For
now, it supports .csv, .sav (spss), and tab delimited data. Please
make sure your filename has the appropriate extension and every column
has a header in your data. If you export a dataframe from R, use:
write.csv(mydf, ”mydf.csv” , row.names=F). If you upload an spss
datafile, none of this should be a concern.

Supported browsers are IE6-8, FF, Safari, and Chrome, but a recent
browser is highly recommended. As always, feedback is more than
welcome.

Jeroen

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[R] multivariate numerical integration.

[Jeroen Ooms]

I am currently using the package 'adapt' for multivariate integration.
However this package seems to be removed from CRAN (It is still referred to
in the help file for integrate(stats) though).

I assume it has been deprecated for a reason? Is there an alternative for
multivariate numerical integration?

-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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[R] 1 dimensional optimization with local minima

[Jeroen Ooms]

I am using numerical optimization to fit a 1 parameter model, in which the
input parameter is bounded. I am currently using optimize(), however, the
problem turns out to have local minima, and optimize does not always seem to
find the global minimum. I could to write a wrapping function that tries
multiple intervals or starting values, but I would prefer a package that has
built-in methods to make it more robust against local minima.

I checked the CRAN Task View for Optimization, however there seem to be a
lot of alternatives, and not being an optimization expert, I could use some
advice. What could be an appropriate package or function for one-dimensional
bounded optimization, that includes some protection against local minima? 



-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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[R] Announce: lme4 web application

[Jeroen Ooms]

inspired by useR! 2009, yeroon.net is a new project developing statistical
web applications to make popular R packages easier available. A first
version of the lme4 web interface is available at  http://yeroon.net/lme4/
http://yeroon.net/lme4/ . It implements most lme4 features and some more.

A short 2minute how-to demo video that illustrates how to use the
application is available on youtube:
http://www.youtube.com/watch?v=_OHps7z3Pqchd=1. More information and
details are available on my website http://www.jeroenooms.com/lme4.html

We hope you will give it a try, and that you like it. Any
feedback/suggestions/bugreports are welcome of course.

note: because this is a public demo server, R sessions are currently limited
to 40seconds. If you experience timeouts, try again later (server can be
busy).

Thank you!

Jeroen


-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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[R] [Hmisc] Latex to pdf

[Jeroen Ooms]

I would like to print some tables and figures to a PDF device on a CentOS 5
vps. However, I cannot seem to get the latex function from Hmisc working. I
followed the example, and got an error: sh: xdvi: command not found. I tried
installing the 'tetex-xdvi' linux package, and now it returns: Error: Can't
open display. I guess the reason for this is that the machine is a VPS
terminal, so it has no display, however I dont understand why it does not
write to the PDF device. Some code:

 pdf(test.pdf)
 x - matrix(1:6, nrow=2, dimnames=list(c('a','b'),c('c','d','this that')))
 latex(x)   # creates x.tex in working directory
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
entering extended mode
(/tmp/Rtmp7bbXMN/file643c9869.tex
LaTeX2e 2003/12/01
Babel v3.8d and hyphenation patterns for american, french, german,
ngerman, b
ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch,
esperanto, e
stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk,
polis
h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish,
tur
kish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf/tex/latex/base/report.cls
Document Class: report 2004/02/16 v1.4f Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/size10.clo))
(/usr/share/texmf/tex/latex/geometry/geometry.sty
(/usr/share/texmf/tex/latex/graphics/keyval.sty)
(/usr/share/texmf/tex/latex/geometry/geometry.cfg))
No file file643c9869.aux.
[1] (./file643c9869.aux) )
Output written on file643c9869.dvi (1 page, 372 bytes).
Transcript written on file643c9869.log.
Error: Can't open display:


-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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[R] Convert dataframe to array of records

[Jeroen Ooms]

I would like to convert a dataframe to an array of lists, one for every
record. A natural choide is apply as.list to the rows. However, as it seems,
as.list() automatically converts all list elements to the same datatype. Eg:

myData - data.frame(a=foo,b=as.logical(rbinom(10,1,.5)));
apply(myData,1,as.list);

In this output, all boolean values have been converted to character strings.
I don't understand why this happens; a list does not require that every
element is of the same datatype. Is there an easy way (ie avoid for-loops
etc) to convert the dataframe to an array of records, while keeping the
datatypes for every field? 

-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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[R] Anova over a list of models

[Jeroen Ooms]

I have a list object, in which I have stored n lme4-models. For example:

library(lme4);
myModels - list();
myModels[1] - lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
myModels[2] - lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject),
sleepstudy)

Now I would like to perform an anova over all models in the list. However,
the anova function requires that every model is inserted as a seperate
argument, i.e. anova(model1,model2). I run into two problems:
1) anova(myModels[1],myModels[2]) returns an error.
2) if n, the number of models, is unknown, how do I add all models as a
seperate argument? 



-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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Re: [R] Anova over a list of models

[Jeroen Ooms]

2009/9/5 Henrique Dallazuanna www...@gmail.com

 Try this:
 anova(myModels[[1]],myModels[[2]])

 do.call(anova, myModels)

Does this work for you? Both functions are failing here:

 anova(myModels[[1]],myModels[[2]])
Error in names(mods) - sapply(as.list(mCall)[c(FALSE, TRUE, modp)],
as.character) :
  'names' attribute [6] must be the same length as the vector [2]
 do.call(anova, myModels)
Error in as.character.default(X[[1L]], ...) :
  no method for coercing this S4 class to a vector

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[R] Problem Installing R 2.9.1.1 RHEL x86_64 binary

[Jeroen Ooms]

I just grabbed the new EL5 binary's for my x64 VPS from CRAN. However, where
updates usually go smoothly, I now get these errors:

-bash-3.2# rpm -i R-2.9.1-1.el5.x86_64.rpm
error: Failed dependencies:
R-devel = 2.9.1-1.el5 is needed by R-2.9.1-1.el5.x86_64

-bash-3.2# rpm -i R-core-2.9.1-1.el5.x86_64.rpm
error: Failed dependencies:
perl(File::Copy::Recursive) is needed by R-core-2.9.1-1.el5.x86_64

-bash-3.2# rpm -i R-devel-2.9.1-1.el5.x86_64.rpm
error: Failed dependencies:
R-core = 2.9.1-1.el5 is needed by R-devel-2.9.1-1.el5.x86_64
pcre-devel is needed by R-devel-2.9.1-1.el5.x86_64

What could be the problem?

-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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[R] popular R packages

[Jeroen Ooms]

I would like to get some idea of which R-packages are popular, and what R is
used for in general. Are there any statistics available on which R packages
are downloaded often, or is there something like a package-survey? Something
similar to http://popcon.debian.org/ maybe? Any tips are welcome! 

-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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Re: [R] popular R packages

[Jeroen Ooms]

 I agree with Thomas, over the years I have installed R on at least 5
 computers.


I don't see why per-marchine statistics would not be useful. When you
installed a package on five machines, you probably use it a lot, and it is
more important to you than packages that you only installed once.

Furthermore I don't think the distribution of packages has to be
problematic. I guess downloads are only slightly related to the specific
mirror, so download statistics from one of the popular mirror's would do for
me.

Of course these statistics are never perfect, but they could be
informative...

[[alternative HTML version deleted]]

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[R] lme4 and Variable level detection

[Jeroen Ooms]

I am making a little GUI for lme4, and I was wondering if there is a function
that automatically detects on which level every variable exists.
Furtheremore I got kind of confused about what a random effects model
actually calculates.

I have some experience with commercial software packages for multilevel
analysis, like HLM6, and I was surprised that lme4 does not require the user
to specify the level for every predictor variable. Is this because the
function automatically detects the level by testing on which levels the
predictor has variance, or is this information simply not needed?

I was taught that a crosslevel interaction predicts the regression
coefficient of the lower level variable, which is also what is implied by
the HLM gui. However, in an lme4 formula, a crosslevel interaction has the
same syntax as a regular interaction term. Furthermore, lme4 also allows
adding crosslevel interactions without a random slope for the lower level
variable. Now I'm confused. Is there a fundamental difference between a
crosslevel interaction, or is the same thing as a regular interaction when
the model also holds an error term for the lower level variable?




-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University 

Visit  http://www.jeroenooms.com www.jeroenooms.com  to explore some of my
current projects.





 
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[R] package install error in CentOS

[Jeroen Ooms]

I am trying to install package Cairo on CentOS 5.2, but I keep getting this
error:

* Installing *source* package 'Cairo' ...
/usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission
denied
ERROR: configuration failed for package 'Cairo'
** Removing '/usr/lib64/R/library/Cairo'

The downloaded packages are in
/tmp/Rtmp8ML568/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(Cairo) :
  installation of package 'Cairo' had non-zero exit status

I tried to do it manually but with no luck:

[jer...@138 shizzle]$ sudo R CMD INSTALL Cairo_1.4-4.tar.gz
* Installing to library '/usr/lib64/R/library'
* Installing *source* package 'Cairo' ...
/usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission
denied
ERROR: configuration failed for package 'Cairo'
** Removing '/usr/lib64/R/library/Cairo'

I have tried to changing the $TMPDIR to another dir, and giving it 777
permissions, but I keep getting the error. Some info:

 sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-redhat-linux-gnu

locale:
C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base


[jer...@138 shizzle]$ gcc --version
gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


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[R] png() and jpg() devices acting weird.

[Jeroen Ooms]

I use a CentOS 5.2 VPS to generate graphs through an R web-application. I
generate generate both pdf() and png() formats of the graphs. The pdf works
just fine and generates perfect pictures. However, the figures generated by
the png() (and also the jpg) device are messed up. 

The weird thing is that it does not generate an error. It does generate a
file with a figure of the correct size, but the figures are mostly just
white space, or small parts of the actual figure.

X11 is not installed on the machine so I have to use type=cairo. I have
tried installing and updating cairo, glib2, gtk+ in linux, and installed the
R-package Cairo, but with no result. 

 sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-redhat-linux-gnu

locale:
C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] Cairo_1.4-4


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Re: [R] package install error in CentOS

[Jeroen Ooms]

solved:

There was indeed a problem with exec rights in the /tmp dir as they were set
by my VPS host. I fixed it by creating a dir 'tempdir' in my homedir, and
giving it 777 rights. Then set the environment variable TMPDIR in R:

Sys.setenv(TMPDIR=/home/jeroen/tempdir);
install.packages(Cairo);

thank you :)



Jeffrey Horner wrote:
 
 Check that your data partitions have the 'exec' flag set in /etc/fstab, 
 particulary the /tmp partition:
 
 http://www.centos.org/modules/newbb/viewtopic.php?topic_id=1687forum=31
 
 Jeff
 
 Jeroen Ooms wrote:
 I am trying to install package Cairo on CentOS 5.2, but I keep getting
 this
 error:

 * Installing *source* package 'Cairo' ...
 /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter:
 Permission
 denied
 ERROR: configuration failed for package 'Cairo'
 ** Removing '/usr/lib64/R/library/Cairo'

 The downloaded packages are in
 /tmp/Rtmp8ML568/downloaded_packages
 Updating HTML index of packages in '.Library'
 Warning message:
 In install.packages(Cairo) :
   installation of package 'Cairo' had non-zero exit status

 I tried to do it manually but with no luck:

 [jer...@138 shizzle]$ sudo R CMD INSTALL Cairo_1.4-4.tar.gz
 * Installing to library '/usr/lib64/R/library'
 * Installing *source* package 'Cairo' ...
 /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter:
 Permission
 denied
 ERROR: configuration failed for package 'Cairo'
 ** Removing '/usr/lib64/R/library/Cairo'

 I have tried to changing the $TMPDIR to another dir, and giving it 777
 permissions, but I keep getting the error. Some info:

   
 sessionInfo()
 
 R version 2.8.0 (2008-10-20)
 x86_64-redhat-linux-gnu

 locale:
 C

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base


 [jer...@138 shizzle]$ gcc --version
 gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
 Copyright (C) 2006 Free Software Foundation, Inc.
 This is free software; see the source for copying conditions.  There is
 NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
 PURPOSE.



 
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[R] a ratio-variable predictor

[Jeroen Ooms]

Maybe this is more of a statistical question than an R question, but I am
going to ask it anyway :) Cortisol and Testosteron are known to interact in
the body, and some literature suggest that especially the ratio between the
two is a good predictor. So I want to add the ratio predictor (y~cort/test)
to a glm, and later a multilevel model, however I have no experience with
ratio variables.

Intuitively, I would think that a ratio is very similar to an interaction
effect, only with an inverse scale for the second term (cort* 1/test).
However, I found that even more than with normal interaction effects, the
scaling of the variables becomes important. Furthermore there is the obvious
problem (which is not too big of a problem in my case), of values that are
close to zero on the second term. 

So what is an appropriate way to incorporate a ratio-predictor? Any tips on
R procedure/package that I could use, or any other experiences with
ratio-predictors are welcome.
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[R] Multivariate kernel density estimation

[Jeroen Ooms]

I would like to estimate a 95% highest density area for a multivariate
parameter space (In the context of anova). Unfortunately I have only
experience with univariate kernel density estimation, which is remarkebly
easier :)

Using Gibbs, i have sampled from a posterior distirbution of an Anova model
with k means (mu) and 1 common residual variance (s2). The means are
independent of eachother, but conditional on the residual variance. So now I
have a data frame of say 10.000 iterations, and k+1 parameters.

I am especially interested in the posterior distribution of the mu
parameters, because I want to test the support for an inequalty constrained
model (e.g. mu1  mu2  mu3). I wish to derive the multivariate 95% highest
density parameter space for the mu parameters. For example, if I had a
posterior distirbution with 2 means, this should somehow result in the
circle or elipse that contains the 95% highest density area. 

Is something like this possible in R? All tips are welcome.
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Re: [R] plotting density for truncated distribution

[Jeroen Ooms]

thank you, both solutions are really helpful!
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[R] plotting density for truncated distribution

[Jeroen Ooms]

I am using density() to plot a density curves. However, one of my variables
is truncated at zero, but has most of its density around zero. I would like
to know how to plot this with the density function.

The problem is that if I do this the regular way density(), values near zero
automatically get a very low value because there are no observed values
below zero. Furthermore there is some density below zero, although there are
no observed values below zero. 

This illustrated the problem: 

mydata - rnorm(10);
mydata - mydata[mydata0];
plot(density(mydata));

the 'real' density is exactly the right half of a normal distribution, so
truncated at zero. However using the default options, the line seems to
decrease with a nice curve at the left, with some density below zero. This
is pretty confusing for the reader. I have tried to decrease the bw, masks
(but does not fix) some of the problem, but than also the rest of the curve
loses smoothness. I would like to make a plot of this data that looks like
the right half of a normal distribution, while keeping the curve relatively
smooth.

Is there any way to specify this truncation in the density function, so that
it will only use the positive domain to calculate density?
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Re: [R] R 2.8.0 is released

[Jeroen Ooms]

I'm getting a unexpected compiling error when doing make:

gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2
-I../../src/extra/pcre  -I. -I../../src/include -I../../src/include
-I/usr/local/include -DHAVE_CONFIG_H   -fpic  -g -O2 -c platform.c -o
platform.o
platform.c: In function 'do_capabilities':
platform.c:1661: error: expected ',' or ';' before 'Rf_checkArityCall'
make[3]: *** [platform.o] Error 1

R.2.7.2 compiled without any problems on the same machine.
Here is my config.log: http://jeroen.xslhosting.net/config.log.zip
 
Am I doing anything wrong? And will their be binary Debian packages for this
release (they never appeared for R-2.7.2)?


thank you!



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Re: [R] R 2.8.0 is released

[Jeroen Ooms]

I'm getting a unexpected compiling error when doing make: 

gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2
-I../../src/extra/pcre  -I. -I../../src/include -I../../src/include
-I/usr/local/include -DHAVE_CONFIG_H   -fpic  -g -O2 -c platform.c -o
platform.o 
platform.c: In function 'do_capabilities': 
platform.c:1661: error: expected ',' or ';' before 'Rf_checkArityCall' 
make[3]: *** [platform.o] Error 1 

R.2.7.2 compiled without any problems on the same machine. 
Here is my config.log: http://jeroen.xlshosting.net/config.log.zip
  
Am I doing anything wrong? And will their be binary Debian packages for this
release (they never appeared for R-2.7.2)? 


thank you! 
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Re: [R] drop1() seems to give unexpected results compare to anova()

[Jeroen Ooms]

Thomas Chu wrote:
 
 Neither of those 3 lines of commands managed to drop x4 and its P value 
 magically decreased from 0.94 to almost 0! I am also baffled by how R 
 calculated those RSS. 
 
Maybe it is using a different type of SS. If i have a lm() model, and i do:
options(contrasts=c(contr.sum, contr.poly));
anovafit - drop1(model,attributes(model$terms)$term.labels,test=F);
then i get identical SS, F and p values as in SPSS. Maybe 
http://www.nabble.com/set-type-of-SS-in-anova()-to18287076.html#a18287076
this post  is helpfull. Also check out the post on 
http://myowelt.blogspot.com/ this blog  from 2008-05-24: Obtaining the same
ANOVA results in R as in SPSS - the difficulties with Type II and Type III
sums of squares .

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[R] Link functions in SEM

[Jeroen Ooms]

Is it possible to fit a structural equation model with link functions in R? I
am trying to build a logistic-regression-like model in sem, because
incorporating the dichotomous variables linearly seems inappropriate. Mplus
can do something similar by specifying a 'link' parameter, but I would like
to be able to do it in R, ofcourse. 

I have explored the 'sem' package from John Fox, but it does not seem to be
able to fit non-linear relations. Is there some R-package or way to get this
done? I have also considered creating a seperate latent variable in the sem
model for the systematic component of the predictors, but then I still need
a way to fix a non-linear link from the systematic component to the
dichotomous Y variable. 
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Re: [R] Object-oriented programming in R for Java programmers?

[Jeroen Ooms]

Werner Wernersen wrote:
 
 I have done oo programming in C++ and Java before but the first few
 tutorial on R oo were a bit confusing for me. 
 
My personal experience is that the type of OO programming that makes for
example Java code nice and easy to structure is not possible in R. The
biggest problem for me is, correct me if i'm wrong, that R does not store
memory references in its identifiers (variables), but a creates new 'object'
for every identifier. For example, if you do in R:
a - 123
b - 456
a - b
a - 789
b

If you would do a similar thing in Java, bot the variables 'a' and 'b' would
have changed to the value 789, because both the variables now refer to the
same object. So manipulating one also manipulates the other. However, in R,
variable 'b' still stores the value of 456 at the end of this example.

What this means for OO programming is that there is no easy way to reference
to objects. For example, if you have want to access a variable which is part
of a dataframe object, which is nested in a list object, you can only
reference this object every time using list$dataframe$varname, where in
Java, you could create a new variable that references to this specific
object. Once datastructures become more complex, this handicap gets bigger
and bigger.

However, please don't take this for granted since I am only a beginning R
programmer (and slightly more advanced Java programmer). I am also really
curious what others have to say because I am having the same problem of my
R-code quickly getting messy and confusing.
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