[R] Correlation when one variable has zero variance (polychoric?)

2007-12-19 Thread Jose Quesada
Hi,

I'm running this for a simulation study, so many combinations of parameter  
produce many predictions that I need to correlate with data.

The problem

I'm using rating data with 3 to 5 categories (e.g., too low, correct, too  
high). The underlying continuous scales should be normal, so I chose the  
polychoric correlation. I'm using library(polychor) in its latest version  
0.7.4

The problem is that sometimes the models predict always the same value  
(i.e., the median). Example frequency table:

> table(med$ADRI_LAN, rate$ADRI_LAN)
   2   3   4   5
   3  28 179 141  50

That is, there is no variability in one of the variables (the only value  
is 3, the median).

Pearson Product Moment Correlation consists of the covariation divided by  
the square root of the product of the standard deviations of the two  
variables. If the standard deviation of one of the variables is zero, then  
the denominator is zero and the correlation cannot be computed. R returns  
NA and a warning.

If I add jitter to the variable with no variability, then I get a  
virtually zero, but calculable, Pearson correlation.

However, when I use the polychoric correlation (using the default  
settings), I get just the opposite: a very high correlation!

> polychoric= polychor( med$ADRI_LAN, rate$ADRI_LAN ) #, ML=T,  
> std.err=T
> polychoric
[1] 0.59

This is very counterintuitive. I also ran the same analysis in 2005 (what  
has changed in the package polycor since then, I don't know) and the  
results were different. I think back then I contrasted them with SAS and  
they were the same. Maybe the approximation fails in extreme cases where  
most of the cells are zero? Maybe the approximation was not used in the  
first releases of the package? But it seems that the ML estimator doesn't  
work at all (at least in the current version of the package) with those  
tables when most cells are zero due to no variability on one variable):

> polychor(med$ADRI_LAN, rate$ADRI_LAN, ML=T)
Error in tab * log(P) : non-conformable arrays

I've seen some posts where sparse tables were trouble, eg:  
http://www.nabble.com/polychor-error-td5954345.html#a5954345
  "You're expecting a lot out of ML to get estimates of the first couple of  
thresholds for rows and the first for columns. [which were mostly zeroes]"

Are the polychoric estimates using the approximation completely wrong? Is  
there any way to compute a polychoric correlation with such a dataset?  
What should I conclude from data like these?
Maybe using correlation is not the right thing to do.

Thanks,
-Jose

-- 
Jose Quesada, PhD.
http://www.andrew.cmu.edu/~jquesada

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[R] Test Driven Development in R

2009-01-31 Thread Jose Quesada

Hi,
I wonder what kind of interest there is on Test Driven Development (TDD) in R.

Test Driven Development consists of writing the test before the function, and 
iteratively build the function until it passes the test.


Python and Ruby (specially Ruby) have very strong test-oriented cultures. In 
fact, in Ruby at least the custom is to do TDD and lately Behavior-driven 
development (BDD). In BDD, one writes a story of what one would want the code to 
do. This story is almost native English, and then the test suite converts it 
into something that the language understand as tests.


There are some posts on the list about this, but they are about testing in 
general (Runit), not TDD. Example:

http://thread.gmane.org/gmane.comp.lang.r.general/85047

Recently, I found there is an alpha, but working implementation of TDD for 
Komodo edit:

www.sciviews.org/SciViews-K/index.html

The editor has a green bar that becomes red as soon as one edits a function, and 
that edit breaks the tests. This is tremendously useful.


Using Gmane search, the only mention I could find on svUnit was:
http://thread.gmane.org/gmane.comp.lang.r.general/136632/focus=136662

I think this could make a great UseR 2009 talk. Ideally, by someone with more R 
experience than me, and even more ideally by Philippe Grosjean :), but it push 
comes to shove, I could prepare such a talk.


Would this be interesting at all? Are there any resources that I have missed? 
How many people are using this kind of testing or Komodo -sciViews at all?


Best,
-Jose
--
Jose Quesada, PhD.
Max Planck Institute, Human Development, Berlin
http://www.josequesada.name/

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[R] R vs Python performance-wise

2008-12-06 Thread Jose Quesada

Hi,

Has anyone run any R vs Python (numpy) tests?
I'd love to see what the differences performance-wise are, specially  
handling large sparse matrices.
Since both rely on external C code, there might not be much of a  
difference.


If you know and use both languages, what are the main differences and what  
made you stick to one over another?


I also noticed that there are strong libraries for social networks on both.

python:
networkX: https://networkx.lanl.gov/wiki
pySNA: http://www.menslibera.com.tr/pysna/

R:
sna, network etc. see:
http://www.jstatsoft.org/v24

Has anyone run a bechmark of the two systems doing the same operation?

Which is the right environment for large social networks? Some packages  
have bindings for both languages, and of course, there's  a reliable way  
to bind the two languages together, Rpy:

http://rpy.sourceforge.net/

So this may not be a big deal which one to pick.

Thanks,
-Jose

--
Jose Quesada, PhD.
Max Planck Institute, Human Development, Berlin
http://www.andrew.cmu.edu/~jquesada

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[R] Working with RDF

2009-02-09 Thread Jose Quesada
Dear list,

I will be working with RDF in the future, and was wondering if there's
anyone else in this list doing this.
Any libraries/resources to check?

Thanks,
-Jose

-- 
Jose Quesada, PhD.
Max Planck Institute, Human Development, Berlin
http://www.josequesada.name/

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[R] twitter useRs?

2009-02-09 Thread Jose Quesada
I wonder if there are any useRs sharing day-to-day realizations/tricks
on twitter...
Seems like a good place for those things that are good findings, but
one is too lazy to blog about them...

-- 
Jose Quesada, PhD.
Max Planck Institute, Human Development, Berlin
http://www.josequesada.name/

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Re: [R] R and vim (gvim) on ubuntu

2009-03-06 Thread Jose Quesada
-BEGIN PGP SIGNED MESSAGE-
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> when I try to run an R command eg, "x <- rnorm(100,10,5)" vim returns this
> error:
> "~/.pipe" E212: can't open file for wirting"

Hi Andreas,

I'd recommend to use this script instead. It uses screen to
communicate R and vim, it works well.
http://www.vim.org/scripts/script.php?script_id=2551

Best,
- -Jose

- --
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and cognition,
Berlin
http://www.josequesada.name/  
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[R] using chm help files under linux

2009-03-10 Thread Jose Quesada
Hi,

Chm (compiled help) is a microsoft invention. It's the default help
system under windows, but not so under linux.
I found that (at times) I like better how chm help looks.
Since there are chm viewers under linux, using chm help files should
be possible.
Has anybody tried to set R so it opens chm by default? I'm sure
there's some flag or Rprofile var that could get this done.

Thanks,

-- 
-Jose
--
Jose Quesada, PhD
http://josequesada.name

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[R] Comparison of data analysis packages: R, Matlab, SciPy, Excel, SAS, SPSS, Stata - Brendan O'Connor's Blog

2009-03-14 Thread Jose Quesada
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Hi All,

I found an interesting thread discussing R and other packages here:

http://anyall.org/blog/2009/02/comparison-of-data-analysis-packages-r-matlab-scipy-excel-sas-spss-stata/


Plenty of well-reasoned comments.
I thought it may be informative for people on this list.
Best,
- -Jose

- --
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and cognition,
Berlin
http://www.josequesada.name/   
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[R] dpaste, pastebin etc. Syntax highlighting for R?

2009-03-16 Thread Jose Quesada
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Hi All,

There are many sites to get bite-sized chuncks of code.
The nice thing is that they use syntax highlighting.

Examples:
http://dpaste.com/
http://pastie.org/
http://pastebin.com/

Twitter with a link to a syntax highlighting site would do wonders.
There are plugins for most (good) editors to post directly to the site
from the editor.
Example:
http://www.vim.org/scripts/script.php?script_id=1624

The wiki shows that there are good working solutions to get R syntax
highlighting coverted to html.
The code for such a thing is here:
http://www.andre-simon.de/

Does anyone know of any of those pastebin-like sites that uses
R-friendly syntax highlighting?

Hmm, I had another idea, but maybe I'll use an independent thread.

- -Jose

- --
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and cognition,
Berlin
http://www.josequesada.name/   
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[R] R-code in html help pages: syntax highlighting

2009-03-16 Thread Jose Quesada
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Hi,

A follow up to my previous post. It'd be good to have syntax
highlighting in the html help pages. There is highlight
(http://www.andre-simon.de/) which seems to be open source. Since code
is delimited in the help file format, it should not be too difficult
to run a highlighting program (actually, vim and emacs do this too)
recursively and pretty-print all the R examples in the entire CRAN.
Including the highlighter with R, or whatever supplementary tools
people use to make R html help files could simplify things. I've never
written docs or released a package, so I may be understimating the
effort it'd take to get this working.

Using the r-help gmane archives also leads to plain code.
This is probably more trouble than it's worth, since there's no
metadata delimiting a block of code and it might be difficult... but
grepping through all R-help posts and coloring code would be really
nice too. Again, this lands straight into 'nice to have, but not
essential' territory.

If anyone wants to do this, feel free to.

Best,
- -J

- --
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and cognition,
Berlin
http://www.josequesada.name/   
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[R] How do I set the working directory when using ESS and R under windows?

2009-04-30 Thread Jose Quesada
Hi,

While I'm a devoted vim user, I'm testing ESS :)
How do I set the working directory when using ESS and R under windows?
When I try to launch R, it asks for a directory. In windows, it simply
doesn't let you pick a directory on the 'open' dialog.
It may be a problem with windows server 2008 64 bit, though, as it seems
really basic. Thanks.

Best,
-Jose

-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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[R] RMySQL and non-installer mysql

2009-05-06 Thread Jose Quesada
Hi all,

I'm running mysql on windows server 2008 64, but I just unzipped files.
There's no installer and no registry entry.

When using RMySQL, it seems that it needs to look at the registry:

> library("RMySQL")
Loading required package: DBI
Error in utils::readRegistry("SOFTWARE\\MySQL AB", hive = "HLM",
maxdepth = 2) :
  Registry key 'S' not found
Error : .onLoad failed in 'loadNamespace' for 'RMySQL'
Error: package/namespace load failed for 'RMySQL'

Thus, it finds nothing.

Is there any workaround?
Thanks!

-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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[R] Rmysql linking to an old-ish mysql build

2009-05-08 Thread Jose Quesada
Hi,

I'm trying to get Rmysql to work o windows server 2008 64-bit.
I have the latest build of mysql installed (mysql-5.1.34-winx64).

When trying to load Rmysql, I got a warning that Rmysql is linking to an
old-ish mysql build (5.0.67).
I could do some basic stuff (the connection works) but it breaks when
trying to read a large table.

So I set up to use the buld 5.0.67 that Rmysql likes.

10 hrs later and after lots of sysadmin work, I have to call it quits. I
couldn't make it work.

Since this mysql 5.0.67 is pretty old, I was wondering if anyone has
binaries for Rmysql that work for a more recent version.
Maybe the authors of the package have plans to update it soon?

I've tried the package on both R 2.9.0 and R2.8.1.

If nothing comes up, I'll try to spend a few more hours on getting the
old version to work.

Thanks!

Best,
-Jose

-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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Re: [R] Vim R plugin-2

2009-05-09 Thread Jose Quesada
Jakson A. Aquino  gmail.com> writes:

>
> Dear R users,
>
> People who uses vim in Linux/Unix may be interested in checking the
> plugin for R that I'm developing:
>
>   http://www.vim.org/scripts/script.php?script_id=2628
>
> The plugin includes omni completion for R objects, code indentation
> and communication with R running in a terminal emulator (xterm or
> gnome-terminal). This last feature was already present in Johannes
> Ranke's plugin.
>
> I would like to know if you have any suggestions of improvements.
>
> Best regards,
>


Excellent work!
I wonder if this could be made more portable (e.g., it depends on perl, + R
being on a tty terminal, which is not always the case).

I'll try to look at it and see if I can port it so it works on windows.
But the
current communication method I use there are just the clipboard, not sure if
it'll be possible.

Any alternative ways of sending info both ways from R to any open
process (vim)
in windows?

I have, and like, perl; the only think that is missing is the tty support on
windows (I think!)

-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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Re: [R] Vim R plugin-2

2009-05-09 Thread Jose Quesada
Jakson Alves de Aquino wrote:
> Jose Quesada wrote:
>   
>> I'll try to look at it and see if I can port it so it works on windows.
>> But the
>> current communication method I use there are just the clipboard, not sure if
>> it'll be possible.
>> 
>
> Unfortunately, I cannot help on Windows environment.
>
>   
>> Any alternative ways of sending info both ways from R to any open
>> process (vim)
>> in windows?
>> 
>
> Netbeans could be a fast and portable route for communication between R
> and vim without the need of using either pipes or files saved in disk as
> intermediary. Typing ":help netbeans" in vim should show netbeans
> documentation. R also has TCP support: write.socket(), read.socket(),
> etc. We could begin to explore this route...
>
>   
Great finding!
I wish I had more time to dedicate to this.

Have you seen:
http://pyclewn.wiki.sourceforge.net/features+

In my view, R as a language is very good but the tools around it are not
good.
When a matlab person tries R, their first comments are always how poor
the environment is.
Sure, one can have a debugger (with a crappy GUI in TK), and there's
some editor support, but it's kind of painful.

Integreting an R debugger with something like pyclewn would be very good.

Best,
-jose


-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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[R] alternative to built-in data editor

2009-05-27 Thread Jose Quesada
Hi all,

I often have to peek at large data.
While head and tail are convenient, at times I'd like some more
comprehensive.
I guess I debug better in a more visual way?
I was wondering if there's a way to override the default data editor.
I could of course dump to a txt file, and look at it with an
editor/spreadsheet, but after doing it a few times, it gets boring.
Maybe it's time for me to write a function to automatize the process?
I'd ask first in case there's an easier way.

Thanks!
-Jose

-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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


[R] a simple trick to get autoclose parenthesis on windows

2009-05-27 Thread Jose Quesada
Hi,

This is a simple trick to get autoclose parenthesis on windows.
If you like how StatET autocloses parens, but like to use the lighter
Vanilla R, you can use autohotkey (http://autohotkey.net) to provide
this functionality.

Simply put the below code in a text file, rename extension as .ahk and
doubleclick on it to execute.


-- code starts here 8< --


; Vanilla R
; =
#IfWinActive, ahk_class Rgui
; autoclose parens
(::Send (){left}
"::Send ""{left}
return

-- code ends here 8< --

Silly, but I find it very convenient.

Best,
-Jose

-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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


Re: [R] a simple trick to get autoclose parenthesis on windows

2009-05-31 Thread Jose Quesada
Gabor Grothendieck wrote:
> Hi, I was looking for your sendcodetoR.ahk autohotkey script
> but couldn't find it.  Would you be able to point me to it.
> Thanks.
>   
Here's what I have right now, it also maps right alt to send code to R.
You should change the ahk_class to your editor of choice (here it's
vim). To get the ahk_class, you need to run the atoit_spy (comes with
every autohotkey install).

HTH,
-Jose

; F3 and right alt will send selection to open Rgui
#WinActivateForce
F3::
IfWinExist, ahk_class Rgui
{
Send ^c; copy selection to clipboard
WinActivate ; R Console
save = %clipboard%
sendinput, {Raw}%save%
sendinput,{enter}
Sleep 1000
WinActivate, ahk_class Vim
}

Ralt::
IfWinExist, ahk_class Rgui
{
Send ^c; copy selection to clipboard
WinActivate ; R Console
save = %clipboard%
sendinput, {Raw}%save%
sendinput,{enter}
Sleep 1000
WinActivate, ahk_class Vim
}
return


-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

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


[R] Scrolling behavior in View()

2009-06-07 Thread Jose Quesada
Hi,

I've realized that the scrolling behavior in View() is unlike most other
applications. It seems that the minimum scroll size is very large for
large objects( i.e., a vector of 1M integers), and it might be that this
scroll is proportional to the size of the object.
Try this:
a = 1:100
View(a)
Click once on the scroll arrow down. It will move to item 1001.

It could be that the scroll size is 1/1000 object length.

If this is so, it's a bit of a problem, since there's no way to View say
cell 500... unless one does a View(head(a, 500)), which kind of defeats
the point of view.

Is this behavior by design? If so, wouldn't it be better to make it
optional (as it breaks GUI conventions of mostly any OS for scrolling
behavior)? An argument for view to turn this off would be great.

Thanks!

Best,
-Jose

-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/

__
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.