date:20110625




On 25.06.2011 02:12, Saptarshi Guha wrote:

Hello,

I'm trying to use rjson to parse a JSON object. The object can be found here

http://pastebin.com/np0s5hgM

(you'll probably need to add quotes around the content)


fromJSON returns the error
  glibc detected home/sguha/lib64/R/bin/exec/R: realloc(): invalid next
size: 0x0209e210 ***

Is there a fix coming soon? Maybe CRAN should also have an outstanding
bug field  - packages with unfixed bugs could be removed.


But rather than posting to this list, you should send a message to the 
package maintainer including reproducible examples. Otherwise the 
package maintainer may not even be aware of any bug nor can he or she 
reproduce.


Uwe Ligges





Cheers
Joy


rjson- 0.2.3
and

R.version
_
platform   x86_64-unknown-linux-gnu
arch   x86_64
os linux-gnu
system x86_64, linux-gnu
status
major  2
minor  13.0
year   2011
month  04
day13
svn rev55427
language   R
version.string R version 2.13.0 (2011-04-13)

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Problems setting language in R-2.13.0 and opening RData

2011-06-25 Thread Manabu Sakamoto

Dear list,

I just recently installed R-2.13.0 on my Windows7. I used to run R-2.10.0.

First of all, I used to be able to install R in English (in R-2.10.0)
during the installation procedure. My PC is in a Japanese environment
but I want R to be in English because I won't be able to interpret any
errors if they are in Japanese (I am Japanese so I can read them but I
won't be able to understand them). However, it seems that under
R-2.13.0, the option to install in English simply does not exist and I
have to associate LANGUAGE=en in the properties of all short cuts to
R.

This leads to my second problem. I usually open a saved work space by
double clicking on a .RData file. I had no problems in R-2.10.0 but in
R-2.13.0, even though I associated R-2.13.0 with RData files during
installation, I had problems opening them by double-clicking (it
always came up with a RTerm window) but I found a R for Windows GUI
front-end that I can associate my RData with which enabled me to open
RData in the R GUI. However, this R window is in Japanese.

So my question is: is there a way to set R itself in English
(including this R for Windows GUI front-end) and not just the pathways
from short cuts? Any suggestions would be most appreciated.

many thanks in advance.
Manabu
-- 
Manabu Sakamoto, PhD
School of Earth Sciences
University of Bristol
manabu.sakam...@googlemail.com

__
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.

Re: [R] Extract character from the end of a string

1. Please always quote the original message when sending messages to 
this *mailing list*.
2. Please send your answers and comments also to the original poster who 
may not be aware you posted to the list.


Uwe Ligges




On 25.06.2011 06:55, jwehr wrote:

Thank you, Joshua!

I got what I was looking for using this command:

as.numeric(grepl(\\*$, qb$Player))

Where the variable name is Player in dataset qb.

--
View this message in context: 
http://r.789695.n4.nabble.com/Extract-character-from-the-end-of-a-string-tp3621732p3624124.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Time-series analysis with treatment effects - statistical approach

2011-06-25 Thread Mike Marchywka

Date: Thu, 23 Jun 2011 15:41:25 -0700
From: jmo...@student.canterbury.ac.nz
To: r-help@r-project.org
Subject: Re: [R] Time-series analysis with treatment effects - statistical
approach

Mike Marchywka wrote:

I discovered a way to do repetitive tasks that can be concisely specified
using
something called a computer.

Now that's funny :)

well, there is a point to that and that is that with cheap computations you can
do different analyses than you did in the past.

There were not controlled tests. It was a field experiment testing the
effects that various pavement designs have on underlying soil moisture. Two
designs incorporated a porous pavement surface course, while two others were
based on standard impervious concrete pavement...the control was just bare,
exposed soil.

As you can see from the graph, the control responds quickly to rainfall
events, but dries out quickly as well due to evaporation. The porous
pavement allows for quick infiltration of precipitation, while the
impervious pavement eventually allows infiltration of rainfall, but it's
delayed.

My objective is to be able to differentiate between the pavement treatments,
such that I can state with statistical confidence that porous pavements
affects underlying soil moisture differently than impervious pavements.

I think this is obvious just looking at it, but I wanted to be able to back
it up with stats. What I'd done previously is to average by week. But as I
mentioned, I thought that an anova table with 104 rows relating to each week
was a poor way of analyzing the data. But that being said, it effectively
allows me to check for treatment-related differences.

I don't think we've mentioned R in the past few posts but I guess pointing
people to useful things that R can do is not too big a problem and
if you have ever dealt with analysis for the sake of rationalization
you can appreciation that is a huge problem :) Generally you'd
like to have reproducible results and if you don't have IID ( stationary
parameters of the population you wish to characterize) you
are not even asking a good question about the system. It may
be helpful as quick check of something but otherwise difficult to
interpret- do your results mean these things are different in the
desert? You appear to have data points from a bunch of different situations.
After the fact selection is often helpful but generally stats people frown
on that as backing up anything ( unless it supports sponsor's opinion LOL).

http://www.itl.nist.gov/div898/handbook/prc/section4/prc432.htm

I guess I'd either go with dynamic model or convert into dollars and then
see if you have clinically and statistically significant differences in things
of relevance.

Thanks for the suggestions to date. Maybe the more I explain what I'm trying
to achieve, the more focussed the suggestions will be. The vaguer the
question, the broader the response, right?

Thanks again,
Justin

--
View this message in context:
http://r.789695.n4.nabble.com/Time-series-analysis-with-treatment-effects-statistical-approach-tp3615856p3621179.html
Sent from the R help mailing list archive at Nabble.com.

__
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.

[[alternative HTML version deleted]]

Re: [R] Need help on a R script part

2011-06-25 Thread Hugo Mildenberger

Lusk, 

if I were in your business, I would tackle such a problem with 
help from a little formatting ...

  e1=x1-mean(x1)
  e2=x2-mean(x2)
  n1=length(x1)
  n2=length(x2)
  N=(n1 + n2)
  nu2=sum( c(  ( x1 -mean(x1)  )^2 , ( x2-mean(x2)  )^2  ) )/N
  ss=c(e1,e2) 
  b3=N*sum(ss^4)/(sum( ss^2)^2)

  for(j in 1:B){ ss11=sample(x1, n1, replace=TRUE) 
  ss12=sample(x2, n2, replace=TRUE) } 


... afterwards I'd correct for missing parenthesis and such. But I 
understand that this approach was really not conducive when the 
main intention was to target the public by giving the unhappy college 
student who infelicitously bumped into a mountain of WWI-style 
razor wire. The wire-cutter equivalent tool the R interpreter provides 
you with is the question mark. Here are some examples how to use it:

?mean
?length
?sum
?sample
?^
?for
?in
?:
?=
?-
?+
?*
?/


Hope this helps.

Kind regards




On Friday 24 June 2011 15:31:44 Lusk Aris wrote:
 
 Hi all,
 I need all your help on this. I have the next part of 
 code:e1=x1-mean(x1)e2=x2-mean(x2)n1=length(x1)n2=length(x2N=(n1 + 
n2)nu2=sum( c(  ( x1 -mean(x1) )^2 , ( x2-mean(x2) )^2  ) )/Nss=c(e1,e2) b3= 
N*sum(ss^4)/ (sum( ss^2)^2)what do lines 6-8 (mathematical 
notation)?Also the, what means part?for(j in 1:B){ ss11=sample(x1, 
n1, replace=TRUE) ss12=sample(x2, n2, replace=TRUE) 
}I would appreciate you could help on my inquiry, 
and I am awaiting for your soon answer Thx in advance, Lusk 

   [[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Competing-risks nomogram

2011-06-25 Thread Firas Abdollah

Many thanks for the prompt response.
However, I am afraid that it is not completely clear for me. I
apologize, I am not a statistician.
Sorry, may be what I will say make totally non sense, but what I
understood is the following:
Let's suppose that I need to predict cancer-specific survival using
the variables X and Y. What I need to do is to develop a model that
include these variables and predict cancer-specific survival using the
competing-risks regression. Then, I shall calculate the predictions
of this model at a certain time point, then I shall use these
prediction as an endpoint, and predict it using a linear regression
model that include the same variables, i.e X and Y. Finally, I use the
coefficients of this final model to develop a nomogram. Is that
correct?

Many thanks again




Should I calculate the prediction of the competing-risks regression
model, and then use this prediction as an endpoint and predict it
using a linear regression by including the same variables as
predictors?

On Fri, Jun 24, 2011 at 1:27 PM, Frank Harrell [via R]
ml-node+3622291-345449798-247...@n4.nabble.com wrote:
 Replace the Design package with the rms package. Â Use the ordinary linear
 regression trick to predict the linear predictor from the competing risk
 regression, then use nomogram on this new model (that merely represents the
 fit of interest).
 Frank

 Firas Abdollah wrote:
 Hi R users,

 I'd like to draw a nomogram using a competing-risks regression (crr function
 in R), rather than a cox regression. However, the nomogram function provided
 in the Design package is not good for this purpose.
 Do you have any suggestion.
 I really appreciate your help

 Many thanks

 F.Abdollah, MD
 San-Raffele hospital
 Milan, Italy

 Frank Harrell
 Department of Biostatistics, Vanderbilt University

 
 If you reply to this email, your message will be added to the discussion
 below:
 http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3622291.html
 To unsubscribe from Competing-risks nomogram, click here.



-- 
Firas Abdollah, MD
Dept. of Urology
San Raffaele Hospital
Vita-Salute University,
Via Olgettina 60, 20132, Milan, Italy
Tel. +39 02 2643 7286
Fax. +39 02 2643 7298
E-mail: firas.abdol...@gmail.com


--
View this message in context: 
http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3624283.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]

__
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.

Re: [R] Access R functions from web

2011-06-25 Thread Mike Marchywka

 From: orvaq...@gmail.com
 To: r-help@r-project.org
 Subject: [R] Access R functions from web

 I need a way to send R objects and call R functions from web. Is there any
 project close or similar to that?

 I want to be able to send an HTTP rquest from an existing application with
 some data. And obtain a plot from R.

This should be a faq but it can take a while to find, see Rserve and Rapache.
I have been using Rapache now on red hat and debian  and it works nicely.
Also, the goog visualization API works in some limited testing but apparently
a lot of that requires flash ( which I either did not have or had turned off 
LOL).

 Thanks in advance
 Caveman

   [[alternative HTML version deleted]]

 __
 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.

[[alternative HTML version deleted]]

__
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.

Re: [R] Problems setting language in R-2.13.0 and opening RData




On 25.06.2011 11:48, Manabu Sakamoto wrote:

Dear list,

I just recently installed R-2.13.0 on my Windows7. I used to run R-2.10.0.

First of all, I used to be able to install R in English (in R-2.10.0)
during the installation procedure. My PC is in a Japanese environment
but I want R to be in English because I won't be able to interpret any
errors if they are in Japanese (I am Japanese so I can read them but I
won't be able to understand them). However, it seems that under
R-2.13.0, the option to install in English simply does not exist and I
have to associate LANGUAGE=en in the properties of all short cuts to
R.


The choice for a language in the installer was always just for the 
installer itself, not for R. This has not changed.


Of course you can set a glöobal environment variable LANGUAGE=en, which 
would be used by any R started on your machine (as well as for any other 
software that reads such a variable)


Uwe Ligges




This leads to my second problem. I usually open a saved work space by
double clicking on a .RData file. I had no problems in R-2.10.0 but in
R-2.13.0, even though I associated R-2.13.0 with RData files during
installation, I had problems opening them by double-clicking (it
always came up with a RTerm window) but I found a R for Windows GUI
front-end that I can associate my RData with which enabled me to open
RData in the R GUI. However, this R window is in Japanese.

So my question is: is there a way to set R itself in English
(including this R for Windows GUI front-end) and not just the pathways
from short cuts? Any suggestions would be most appreciated.

many thanks in advance.
Manabu


__
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.

Re: [R] try to generate graph for each element of my list




On 24.06.2011 21:29, n.via...@libero.it wrote:

Dear all,
I have the following problem. I have a List of time series dataframe.I'm
trying to produce specific graph for each element of my list. The code is:
This is my list:
Lista_import-lapply(Lista_import, function(x){
x2-subset(x, select=c(ANNO,DICHIARANTE,PARTNER, quota))
x2-cast(x2, ANNO+DICHIARANTE~PARTNER)
x2- as.xts(as.matrix(as.timeSeries(x2)))
return(x2)})


each list have the following  shape:
$AUS
$DEU
and data inside...I'm not showing you the content cause I think is not
relevant


For the GRaph the code is

c-lapply(Lista_import,function(x){
for(i in names(Lista_import)){

legenda- read.csv
(/home/fturrini/Tessile/01_Dati_complementari/Legenda_paese.csv,header=TRUE)


The lihne above is independent from i in the loop, hence move it outside 
and rename the stuff below.



leg- data.frame(ISO3=colnames(x),inutile=1)
legenda- merge(legenda,leg, by=ISO3, all.y=TRUE)

png(paste(/home/Tessile/Output/Gra/MaxM/QuoteEXperPaese_,i,.png),
width=1661,height=828)



- ou should really prettify your code in order to make it readable. Use 
tabs and spaces where appropriate!


- You probably want paste(., sep=) above




graph-{par(bg=grey97, font=3,font.axis=3,bty=l,las=1, mar=c(8,6,4,2),
xpd=FALSE)
yrange-c(min(x,na.rm=TRUE), 1.05*max(x,na.rm=TRUE))
colori- c(Blue,Aquamarine1, Firebrick3, Chocolate4, BlueViolet,
Yellow3)

chart.TimeSeries(x, type=l,lwd=5, ylab=, xlab=, main=, date.format=%
Y, ylim=yrange, col=colori,
cex.axis=1.6, major.ticks=years, minor.ticks=FALSE, grid.color=gray50,
grid.lty=dotted)
legend(topleft,as.character(legenda$PAESE),bty=n,cex=1.7,lwd=5, ncol=2,
col=colori, horiz=F)


You want to write FALSE rather than F above.

I have not found the actual error, since your example is nopt 
reproducible and we do not know how your data look like.


Uwe Ligges




mtext(Fonte: Unctad, Pctas, side=1,line=5,adj=1,cex=1.8,col=grey20)
mtext(p, side=1,line=5,adj=0,cex=1.5,col=grey10)}}
dev.off()
rm(grafico)
})

The results is that I get the same graph for each element of my list.
Someone knows how to get one graph for each element of my list pasting the
names' list element  in the .png file??
Thanks for your attention!

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] What does class call mean? How do I make class formula into a call?



On Jun 24, 2011, at 6:12 PM, StellathePug wrote:


Hello R Users!
I have a list called tabs that I would like to have the same  
structure as
my list eqSystem. The two look like they have the same structure  
but they
are different because when I look at their attributes,  
class(eqSystem[[1]])
is call but class(tabs[[1]]) is formula. I want to have  
class(tabs[[1]])

as a call too.

So what does call mean?


An as yet unevaluated function invocation with first as the named  
function followed by quoted arguments is a call:


See the help(call) page:

 f - round
 A - 10.5
 (g - as.call(list(f, quote(A
.Primitive(round)(A)
 eval(g)
[1] 10

 call(mean, quote( c(1,2,3)))
mean(c(1, 2, 3))
 eval( call(mean, quote( c(1,2,3
[1] 2

It seems very unlikely that a formula object could be coerced into a  
valid call simply by altering its class. To convince us otherwise you  
need to provide more information than you have supplied to the  
present. The results of str() on these objects might be a first step.


--
David.


And how do I make an object of class formula be of class call?
Thank you so much!!!--Rita



class(tabs)

[1] list

class(tabs[1])

[1] list

class(tabs[[1]])

[1] formula class(eqSystem)
[1] list

class(eqSystem[1])

[1] list

class(eqSystem[[1]])

[1] call

Rita
=
If you think education is expensive, try ignorance.--Derek Bok

--
View this message in context: 
http://r.789695.n4.nabble.com/What-does-class-call-mean-How-do-I-make-class-formula-into-a-call-tp3623733p3623733.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


David Winsemius, MD
West Hartford, CT

__
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.

Re: [R] Installation of bigmemory fails

2011-06-25 Thread Jay Emerson

Premal,

Package authors generally welcome direct emails.

We've been away from this project since the release of 2.13.0 and I only just
noticed the build errors.  These generally occur because of some (usually
small and solvable) problem with compilers and the BOOST libraries.  We'll
look at it and see what we can do.  Please email us if you don't hear back
in the next week or so.

Thanks,

Jay


---
Hello All,
I tried to intall the bigmemory package from a CRAN mirror site and
received the following output while installing. Any idea what's going
on and how to fix it? The system details are provided below.

- begin error messages ---
* installing *source* package 'bigmemory' ...
 checking for Sun Studio compiler...no
 checking for Darwin...yes
** libs
g++45 -I/usr/local/lib/R/include -I../inst/include -fpic  -O2
-fno-strict-aliasing -pipe -Wl,-rpath=/usr/local/lib/gcc45 -c B\
igMatrix.cpp -o BigMatrix.o
g++45 -I/usr/local/lib/R/include -I../inst/include -fpic  -O2
-fno-strict-aliasing -pipe -Wl,-rpath=/usr/local/lib/gcc45 -c S\
haredCounter.cpp -o SharedCounter.o
g++45 -I/usr/local/lib/R/include -I../inst/include -fpic  -O2
-fno-strict-aliasing -pipe -Wl,-rpath=/usr/local/lib/gcc45 -c b\
igmemory.cpp -o bigmemory.o
bigmemory.cpp: In function 'bool TooManyRIndices(index_type)':
bigmemory.cpp:40:27: error: 'powl' was not declared in this scope
*** Error code 1

Stop in /tmp/Rtmpxwe3p4/R.INSTALL4f539336/bigmemory/src.
ERROR: compilation failed for package 'bigmemory'
* removing '/usr/local/lib/R/library/bigmemory'

The downloaded packages are in
   '/tmp/RtmpMZCOVp/downloaded_packages'
Updating HTML index of packages in '.Library'
Making packages.html  ... done
Warning message:
In install.packages(bigmemory) :
 installation of package 'bigmemory' had non-zero exit status
- end error messages -
It's a 64-bit FreeBSD 7.2 system running R version 2-13.0.
Thanks,
Premal

-- 
John W. Emerson (Jay)
Associate Professor of Statistics
Department of Statistics
Yale University
http://www.stat.yale.edu/~jay

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] AUTO: Chalk, Alan has a new email address

2011-06-25 Thread Alan Chalk



I am out of the office until 01/05/2012.

Please note that I have changed email address.  You can contact me at
alan.ch...@uk.rsagroup.com


Note: This is an automated response to your message  R-help Digest, Vol
100, Issue 26 [Virus checked] sent on 25/06/2011 11:00:11.

This is the only notification you will receive while this person is away.

Notice of Confidentiality

This transmission contains information that may be confidential and that may 
also be privileged. Unless you are the intended recipient of the message (or 
authorised to receive it for the intended recipient) you may not copy, forward, 
or otherwise use it, or disclose it or its contents to anyone else. If you have 
received this transmission in error please notify us immediately and delete it 
from your system.

RSA Insurance Group plc. Registered in England No. 2339826. The Registered 
Office is 9th Floor, One Plantation Place, 30 Fenchurch Street, London EC3M 3BD
[[alternative HTML version deleted]]

__
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.

Re: [R] texi2dvi runs but produces no output

2011-06-25 Thread David Hewitt

Christiaan,

Sorry I did not respond earlier. I have been away on vacation. With
all the changes in LyX 2.x to make Sweave stuff easier, I suspect this
problem should go away. I have not upgraded my system, but a couple
folks that have done so reported no problems with a setup like yours.
Probably best to send a request to the LyX users' list to get this
resolved, as LyX development is very interested in this aspect
nowadays.

http://www.lyx.org/MailingLists#toc4

- Dave

2011/6/17 Uwe Ligges lig...@statistik.tu-dortmund.de:

On 17.06.2011 09:24, christiaan pauw wrote:

Thanks for the advice. I tried to install the package as instructed.
Command
and results below:

install.packages(patchDVI, repos=http://R-Forge.R-project.org;)

Installing package(s) into ‘C:/Users/nova/Documents/R/win-library/2.13’
(as ‘lib’ is unspecified)
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘patchDVI’ is not available (for R version 2.13.0)

The problem is that the Windows binary of that package is really not
available on R-Forge.

You can install from sources if you ask R to:

install.packages(patchDVI, repos=http://R-Forge.R-project.org;,
type=source)

given you have the Rtools installed.

I then ran the tests in Rtools.

Which tests in Rtools???

I suspect the fact that I have I have
installed R in a path containing spaces may be the problem - maybe also
for

Paths with spaces generate problems for LaTeX and R tries to work around,
but may fail.

Not sure why you do the stuff below at all and why R cannot change the
working directory.

Uwe Ligges

the Sweave part. Is there any other remedy but to re-install R or can I
insert a link in a path without spaces ?

library(tools)
testInstalledBasic(both)

running strict specific tests
running code in ‘eval-etc.R’
unable to open output file
FAILED
[1] 1
Warning message:
running command 'C:/PROGRA~1/R/R-213~1.0/bin/i386/R CMD BATCH --vanilla
--no-timing eval-etc.R eval-etc.Rout' had status 2

testInstalledPackages(base)

Error in setwd(outDir) : cannot change working directory

testInstalledPackages(recommended)

Error in setwd(outDir) : cannot change working directory

On 16 June 2011 14:10, Duncan Murdochmurdoch.dun...@gmail.com wrote:

On 11-06-16 7:50 AM, christiaan pauw wrote:

Hi everybody.

Was the problem below ever solved? I have the same problem on Windows 7
with
R 2.13.0 and LyX 2 - everything freshly installed. My Rweave.bat and
MakeSweave.R files are similar to below (I followed
http://wiki.lyx.org/uploads/**LaTeX/SweaveR/lyx_with_r_and_**

sweave_instructions.pdfhttp://wiki.lyx.org/uploads/LaTeX/SweaveR/lyx_with_r_and_sweave_instructions.pdf
)

I don't use LyX or that batch file, I use some code I wrote that's in the
patchDVI package
(https://r-forge.r-project.**org/R/?group_id=233https://r-forge.r-project.org/R/?group_id=233)
that I wrote. You might want to try it.

The single line to run Sweave and pdflatex is

Rscript -e patchDVI::SweavePDF( '$1' )

where $1 is the name of the .Rnw file. If that doesn't work for you, I
might be able to help with debugging.

Duncan Murdoch

[[alternative HTML version deleted]]

__
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.

Re: [R] Need help on a R script part

2011-06-25 Thread Mike Miller

I'm curious about what would cause this (see below), if it isn't a joke. 
Is it possible that it didn't look ridiculous in the deleted HTML but the 
text looked bad?  It's almost unreadable.  I guess the HTML gets deleted 
because it is a waste of space, but I received a 14 MB message from this 
list the other day.


Mike


On Fri, 24 Jun 2011, Lusk Aris wrote:


Hi all,
I need all your help on this. I have the next part of 
code:e1=x1-mean(x1)e2=x2-mean(x2)n1=length(x1)n2=length(x2N=(n1 + 
n2)nu2=sum( c(  ( x1 -mean(x1) )^2 , ( x2-mean(x2) )^2  ) )/Nss=c(e1,e2) b3= 
N*sum(ss^4)/ (sum( ss^2)^2)what do lines 6-8 (mathematical 
notation)?Also the, what means part?for(j in 1:B){ ss11=sample(x1, 
n1, replace=TRUE) ss12=sample(x2, n2, replace=TRUE) 
}I would appreciate you could help on my inquiry, 
and I am awaiting for your soon answer Thx in advance, Lusk
[[alternative HTML version deleted]]


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] integration function

2011-06-25 Thread li li

Hi all,
   Can anyone please take a look at the following two functions.
The answer does not seem to be right.
   Thank you very much!

f1 - function(x)

{integrand - function (x, mu){

dnorm(x, mean=mu, sd=1)*dnorm(mu, mean=2, sd=1)

   }

integrate(integrand, -Inf, Inf,x)$val

}


f2 - function(x)

{integrand - function (x, mu){

dnorm(x, mean=mu, sd=1)*mu^2*dnorm(mu, mean=2, sd=1)

   }

integrate(integrand, -Inf, Inf,x)$val

}

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Vector with factors inside lists/tuples

Hi, this seems like a strange question, but in R is there a function that
can handle vectors containing factors inside lists/tuples? Or is there some
other approach/functions I can use?
Like for example

V1
{Harry,Brown)
{Brown,Harry)

I want to use these variables in a machine learning setting, And don't want
to convert these into multiple vectors, given share number of factors.

-- 
Håvard Wahl Kongsgård

http://havard.security-review.net/

[[alternative HTML version deleted]]

__
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.

Re: [R] integration function

2011-06-25 Thread Peter Ehlers


On 2011-06-25 08:48, li li wrote:

Hi all,
Can anyone please take a look at the following two functions.
The answer does not seem to be right.
Thank you very much!

f1- function(x)

 {integrand- function (x, mu){

 dnorm(x, mean=mu, sd=1)*dnorm(mu, mean=2, sd=1)

}

 integrate(integrand, -Inf, Inf,x)$val

 }


f2- function(x)

 {integrand- function (x, mu){

 dnorm(x, mean=mu, sd=1)*mu^2*dnorm(mu, mean=2, sd=1)

}

 integrate(integrand, -Inf, Inf,x)$val

 }


Your x and mu will get mightily confused.
The argument x in f1 is in fact used as the argument mu
in integrand() because, as the help page clearly indicates,
additional arguments follow the lower/upper limits in integrate().

A cleaner version of what you're doing is the following:

 f1 - function(mu){
   integrand - function (x, mu){
 dnorm(x, mean=mu, sd=1) * dnorm(mu, mean=2, sd=1)
   }
   integrate(integrand, -Inf, Inf, mu)[[value]]
 }

But then again, you could just evaluate dnorm(mu, 2, 1).
So I suspect that you want something different.

Ditto for f2.

Peter Ehlers



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Vector with factors inside lists/tuples

Well, when a think of it using an array would be a simple solution.
But to what extent are arrays supported by other R functions?

-Håvard

2011/6/25 Håvard Wahl Kongsgård haavard.kongsga...@gmail.com

 Hi, this seems like a strange question, but in R is there a function that
 can handle vectors containing factors inside lists/tuples? Or is there some
 other approach/functions I can use?
 Like for example

 V1
 {Harry,Brown)
 {Brown,Harry)

 I want to use these variables in a machine learning setting, And don't want
 to convert these into multiple vectors, given share number of factors.

 --
 Håvard Wahl Kongsgård

 http://havard.security-review.net/



[[alternative HTML version deleted]]

__
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.

Re: [R] Vector with factors inside lists/tuples



On Jun 25, 2011, at 12:49 PM, Håvard Wahl Kongsgård wrote:

Hi, this seems like a strange question, but in R is there a function  
that

can handle vectors containing factors inside lists/tuples?


Yes, A very strange question, indeed ... since dataframes are lists  
that commonly contain vectors of factors and you should have  
encountered them very early in your self-study of R. The number of  
functions that operate on dataframes is large. Are you very early in  
efforts at learning R? Have you read the Posting Guide? (You're still  
posting html format.)


?factor
?list
?dataframe


Or is there some
other approach/functions I can use?
Like for example

V1
{Harry,Brown)
{Brown,Harry)


Is that an example that would make sense in some other language?  
(Opening curly-brace and closing paren makes no sense in R or  for  
that matter in what small amount I know of set theory.) Since your  
example makes no sense, it remains possible that you're looking for  
set operations:


?union



I want to use these variables in a machine learning setting, And  
don't want

to convert these into multiple vectors, given share number of factors.


Lists (of which dataframes are one specific example) are the usual  
method of handling structures of arbitrary structure (including  
factors). 'lapply' is the usual choice for repetitive application of a  
function to elements of lists. The is also 'rapply' for recursive  
application


 lapply(list(factor(letters[1:10]), list(c(1:10), c(20:30) ),  
letters[10:20]), length)

[[1]]
[1] 10

[[2]]   # second element is a list with two members
[1] 2   # lapply() only works with the first 'level' of a list

[[3]]
[1] 11
 rapply(list(factor(letters[1:10]), list(c(1:10), c(20:30) ),  
letters[10:20]), length)

[1] 10 10 11 11
 lapply(list(factor(letters[1:10]), list(c(1:10), c(20:30) ),  
letters[10:20]), class)

[[1]]
[1] factor

[[2]]
[1] list

[[3]]
[1] character

--

David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] How to export to pdf in landscape orientation?

2011-06-25 Thread Juan Andres Hernandez

Does anybody know how to get a pdf file with landscape orientation?.

  pdf(file= 'my_file.pdf' ,onefile=T,paper='A4')
plot(sin, -pi, 2*pi)
   dev.off()

Thank's in advance

Juan A. Hernandez
Spain

[[alternative HTML version deleted]]

__
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.

Re: [R] Vector with factors inside lists/tuples



On Jun 25, 2011, at 1:33 PM, Håvard Wahl Kongsgård wrote:


Well, when a think of it using an array would be a simple solution.
But to what extent are arrays supported by other R functions?


Arrays are well supported by arithmetic, logical and accessor  
functions. Your questions seem very unfocussed. Arrays of factors  
might be a bit difficult since factors in R require preservation of  
attributes which arrays (and matrices) do not allow.




-Håvard

2011/6/25 Håvard Wahl Kongsgård haavard.kongsga...@gmail.com

Hi, this seems like a strange question, but in R is there a  
function that
can handle vectors containing factors inside lists/tuples? Or is  
there some

other approach/functions I can use?
Like for example

V1
{Harry,Brown)
{Brown,Harry)

I want to use these variables in a machine learning setting, And  
don't want
to convert these into multiple vectors, given share number of  
factors.


--
Håvard Wahl Kongsgård

http://havard.security-review.net/




[[alternative HTML version deleted]]


Still posting html format.


PLEASE do read the posting guide http://www.R-project.org/posting-guide.html

--

David Winsemius, MD
West Hartford, CT

__
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.

Re: [R] How to export to pdf in landscape orientation?

2011-06-25 Thread Rainer Schuermann

Tell PDF the size of your piece of paper - here is what works for me:

pdf( file = result.pdf, width = 28, height = 18 ) # numbers are cm
some( stuff )
dev.off()

Hope it helps,
Rainer


On Saturday 25 June 2011 18:46:28 Juan Andres Hernandez wrote:
 Does anybody know how to get a pdf file with landscape orientation?.
 
   pdf(file= 'my_file.pdf' ,onefile=T,paper='A4')
 plot(sin, -pi, 2*pi)
dev.off()
 
 Thank's in advance
 
 Juan A. Hernandez
 Spain
 
   [[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] How to export to pdf in landscape orientation?

2011-06-25 Thread Sarah Goslee

From the help for pdf:

  paper: the target paper size.  The choices are ‘a4’, ‘letter’,
  ‘legal’ (or ‘us’) and ‘executive’ (and these can be
  capitalized), or ‘a4r’ and ‘USr’ for rotated
  (‘landscape’).

So I'd use paper='a4r'. You can also set the width and height
directly.

Sarah

On Sat, Jun 25, 2011 at 1:46 PM, Juan Andres Hernandez
jhernandezcabr...@gmail.com wrote:
 Does anybody know how to get a pdf file with landscape orientation?.

  pdf(file= 'my_file.pdf' ,onefile=T,paper='A4')
    plot(sin, -pi, 2*pi)
   dev.off()

 Thank's in advance

 Juan A. Hernandez
 Spain



-- 
Sarah Goslee
http://www.functionaldiversity.org

__
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.

Re: [R] Vector with factors inside lists/tuples

Hi, sorry my question was not really clear

 |Are you very early in efforts at learning R?
No, have been a long term user of R, but only use R for the statistical stuff.

The heart of the issue is that I have list of keywords that I want to
analyse with a machine learning algorithm (20 000 keywords with a
response variables). It's much like micro array data, but in my case
it's not genes, but instead keywords. To get it to work in R, I
could create a data frame with multiple vectors containing different
factors.
That would look like this
V1, V2,
Harry, Kline
Brown, Larry

If I am not mistaken if I used V1 and V2 with the standard GLM
function the result would be like

glm( V0 ~ HARRY  + KLINE + Brown + Larry)

Or I could create a complex ordered array where keywords are
represented 1 and 0.
If I used that in GLM I would get the same result with glm?

But is there a better approach?

-Håvard

__
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.

Re: [R] Vector with factors inside lists/tuples



On Jun 25, 2011, at 2:13 PM, Håvard Wahl Kongsgård wrote:


Hi, sorry my question was not really clear

 |Are you very early in efforts at learning R?
No, have been a long term user of R, but only use R for the  
statistical stuff.


The heart of the issue is that I have list of keywords that I want to
analyse with a machine learning algorithm (20 000 keywords with a
response variables). It's much like micro array data, but in my case
it's not genes, but instead keywords. To get it to work in R, I
could create a data frame with multiple vectors containing different
factors.
That would look like this
V1, V2,
Harry, Kline
Brown, Larry

If I am not mistaken if I used V1 and V2 with the standard GLM
function the result would be like

glm( V0 ~ HARRY  + KLINE + Brown + Larry)


No. You are mistaken. Assuming that V0 is defined and has the same  
length as there are rows in that data.frame, then V1 and V2 would be  
the arguments in the formula and they would not be quoted.


?glm   # and work through the examples



Or I could create a complex ordered array where keywords are
represented 1 and 0.
If I used that in GLM I would get the same result with glm?

But is there a better approach?

-Håvard


David Winsemius, MD
West Hartford, CT

__
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.

Re: [R] Problems setting language in R-2.13.0 and opening RData

2011-06-25 Thread Prof Brian Ripley


Please see the rw-FAQ.

And your claims about 2.10.0 are simply not true.  There only ever has 
been an option to choose the language of the installer: see the 
rw-FAQ.


On Sat, 25 Jun 2011, Manabu Sakamoto wrote:


Dear list,

I just recently installed R-2.13.0 on my Windows7. I used to run R-2.10.0.

First of all, I used to be able to install R in English (in R-2.10.0)
during the installation procedure. My PC is in a Japanese environment
but I want R to be in English because I won't be able to interpret any
errors if they are in Japanese (I am Japanese so I can read them but I
won't be able to understand them). However, it seems that under
R-2.13.0, the option to install in English simply does not exist and I
have to associate LANGUAGE=en in the properties of all short cuts to
R.


You can set environment variables globally, which it seems is what you 
want.  Then any product using GNU gettext will give your messages in 
English.  (Windows may still give your Japanese messages.)



This leads to my second problem. I usually open a saved work space by
double clicking on a .RData file. I had no problems in R-2.10.0 but in
R-2.13.0, even though I associated R-2.13.0 with RData files during
installation, I had problems opening them by double-clicking (it
always came up with a RTerm window) but I found a R for Windows GUI
front-end that I can associate my RData with which enabled me to open
RData in the R GUI. However, this R window is in Japanese.

So my question is: is there a way to set R itself in English
(including this R for Windows GUI front-end) and not just the pathways
from short cuts? Any suggestions would be most appreciated.

many thanks in advance.
Manabu
--
Manabu Sakamoto, PhD
School of Earth Sciences
University of Bristol
manabu.sakam...@googlemail.com

__
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.



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  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

__
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.

Re: [R] Need help on a R script part

2011-06-25 Thread Duncan Murdoch


On 11-06-25 11:33 AM, Mike Miller wrote:

I'm curious about what would cause this (see below), if it isn't a joke.
Is it possible that it didn't look ridiculous in the deleted HTML but the
text looked bad?  It's almost unreadable.  I guess the HTML gets deleted
because it is a waste of space, but I received a 14 MB message from this
list the other day.


I imagine you need to contact the poster, and find out what they sent. 
It's hard to diagnose after it's been mangled.


Duncan Murdoch



Mike


On Fri, 24 Jun 2011, Lusk Aris wrote:


Hi all,
I need all your help on this. I have the next part of 
code:e1=x1-mean(x1)e2=x2-mean(x2)n1=length(x1)n2=length(x2N=(n1 + 
n2)nu2=sum( c(  ( x1 -mean(x1) )^2 , ( x2-mean(x2) )^2  ) )/Nss=c(e1,e2) b3= 
N*sum(ss^4)/ (sum( ss^2)^2)what do lines 6-8 (mathematical 
notation)?Also the, what means part?for(j in 1:B){ ss11=sample(x1, 
n1, replace=TRUE) ss12=sample(x2, n2, replace=TRUE) 
}I would appreciate you could help on my inquiry, 
and I am awaiting for your soon answer Thx in advance, Lusk
[[alternative HTML version deleted]]


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Access R functions from web

2011-06-25 Thread Tobias Verbeke


Hi Caveman,

On 06/25/2011 11:18 AM, Orvalho Augusto wrote:


I need a way to send R objects and call R functions from web. Is there any
project close or similar to that?

I want to be able to send an HTTP rquest from an existing application with
some data. And obtain a plot from R.


This is one of the typical integration scenarios
the R Service Bus is able to cope with.

http://www.openanalytics.eu/r-service-bus

The REST interface is documented here

http://rsb.doc.openanalytics.eu/
http://rsb.doc.openanalytics.eu/wsdocs/index.html

Best,
Tobias

__
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.

Re: [R] Competing-risks nomogram

2011-06-25 Thread Frank Harrell

Yes you use the linear predictor from your regression as the dependent
variable in the rms package's ols function.  You will get an R^2 of 1.0. 
You can depict the ols model with nomogram().  Note that there are so many
statistical issues in competing risks that doing this without a statistician
is risky.
Frank


-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context: 
http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3625011.html
Sent from the R help mailing list archive at Nabble.com.

__
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.

Re: [R] Vector with factors inside lists/tuples

 glm( V0 ~ HARRY  + KLINE + Brown + Larry)

 No. You are mistaken. Assuming that V0 is defined and has the same length as
 there are rows in that data.frame, then V1 and V2 would be the arguments in
 the formula and they would not be quoted.

 ?glm   # and work through the examples

With the example I meant that the factors in the vector V1 and V2
would be treated like individual binary/dummy variables.

Back to my real question; Is there no other way to do this in R???


2011/6/25 David Winsemius dwinsem...@comcast.net:

 On Jun 25, 2011, at 2:13 PM, Håvard Wahl Kongsgård wrote:

 Hi, sorry my question was not really clear

  |Are you very early in efforts at learning R?
 No, have been a long term user of R, but only use R for the statistical
 stuff.

 The heart of the issue is that I have list of keywords that I want to
 analyse with a machine learning algorithm (20 000 keywords with a
 response variables). It's much like micro array data, but in my case
 it's not genes, but instead keywords. To get it to work in R, I
 could create a data frame with multiple vectors containing different
 factors.
 That would look like this
 V1, V2,
 Harry, Kline
 Brown, Larry

 If I am not mistaken if I used V1 and V2 with the standard GLM
 function the result would be like

 glm( V0 ~ HARRY  + KLINE + Brown + Larry)

 No. You are mistaken. Assuming that V0 is defined and has the same length as
 there are rows in that data.frame, then V1 and V2 would be the arguments in
 the formula and they would not be quoted.

 ?glm   # and work through the examples


 Or I could create a complex ordered array where keywords are
 represented 1 and 0.
 If I used that in GLM I would get the same result with glm?

 But is there a better approach?

 -Håvard

 David Winsemius, MD
 West Hartford, CT





-- 
Håvard Wahl Kongsgård

http://havard.security-review.net/

__
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.

Re: [R] What does class call mean? How do I make class formula into a call?

2011-06-25 Thread peter dalgaard


On Jun 25, 2011, at 15:24 , David Winsemius wrote:

 
 On Jun 24, 2011, at 6:12 PM, StellathePug wrote:
 
 Hello R Users!
 I have a list called tabs that I would like to have the same structure as
 my list eqSystem. The two look like they have the same structure but they
 are different because when I look at their attributes, class(eqSystem[[1]])
 is call but class(tabs[[1]]) is formula. I want to have class(tabs[[1]])
 as a call too.
 
 So what does call mean?
 
 An as yet unevaluated function invocation with first as the named function 
 followed by quoted arguments is a call:
 
 See the help(call) page:
 
  f - round
  A - 10.5
  (g - as.call(list(f, quote(A
 .Primitive(round)(A)
  eval(g)
 [1] 10
 
  call(mean, quote( c(1,2,3)))
 mean(c(1, 2, 3))
  eval( call(mean, quote( c(1,2,3
 [1] 2
 
 It seems very unlikely that a formula object could be coerced into a valid 
 call simply by altering its class. To convince us otherwise you need to 
 provide more information than you have supplied to the present. The results 
 of str() on these objects might be a first step.

Actually, no. Any unevaluated expression in R is mode call, unless atomic or 
symbol. It will also be class call, unless expressedly overridden by an S3 
class assignment. Notice that operators are really function calls.
I.e. 

 mode(quote(x+y))
[1] call
 class(quote(x+y))
[1] call

But 

 class(quote(x))
[1] name
 class(quote(3.14159))
[1] numeric

(This is why the R docs keep talking about unevaluated expressions instead of 
call objects: They aren't always that.)

The ~ operator is also a function call. However, evaluating ~ returns an 
object which is the actual call assigned class formula (plus an environment 
attribute). 
 
 f - y ~ x
 class(f)
[1] formula
 unclass(f)
y ~ x
attr(,.Environment)
environment: R_GlobalEnv
 mode(f)
[1] call
 class(unclass(f))
[1] call

I.e., an unevaluated formulae expression (as in quote(y~x)) is class call, as 
is an unclassed formula object. So it is pretty easy to have objects of class 
formula very similar to objects of class call.

-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

__
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.

Re: [R] Vector with factors inside lists/tuples



On Jun 25, 2011, at 4:01 PM, Håvard Wahl Kongsgård wrote:


glm( V0 ~ HARRY  + KLINE + Brown + Larry)


No. You are mistaken. Assuming that V0 is defined and has the same  
length as
there are rows in that data.frame, then V1 and V2 would be the  
arguments in

the formula and they would not be quoted.

?glm   # and work through the examples


With the example I meant that the factors in the vector V1 and V2
would be treated like individual binary/dummy variables.


They would have been with the call I offered. I get the sense that the  
best advice might be to consult a local statistician.




Back to my real question; Is there no other way to do this in R???


Do this? You have offered no workable example and only the vaguest  
of descriptions of the task.


--
David.



2011/6/25 David Winsemius dwinsem...@comcast.net:


On Jun 25, 2011, at 2:13 PM, Håvard Wahl Kongsgård wrote:


Hi, sorry my question was not really clear

 |Are you very early in efforts at learning R?
No, have been a long term user of R, but only use R for the  
statistical

stuff.

The heart of the issue is that I have list of keywords that I want  
to

analyse with a machine learning algorithm (20 000 keywords with a
response variables). It's much like micro array data, but in my  
case

it's not genes, but instead keywords. To get it to work in R, I
could create a data frame with multiple vectors containing different
factors.
That would look like this
V1, V2,
Harry, Kline
Brown, Larry

If I am not mistaken if I used V1 and V2 with the standard GLM
function the result would be like

glm( V0 ~ HARRY  + KLINE + Brown + Larry)


No. You are mistaken. Assuming that V0 is defined and has the same  
length as
there are rows in that data.frame, then V1 and V2 would be the  
arguments in

the formula and they would not be quoted.

?glm   # and work through the examples



Or I could create a complex ordered array where keywords are
represented 1 and 0.
If I used that in GLM I would get the same result with glm?

But is there a better approach?

-Håvard


David Winsemius, MD
West Hartford, CT






--
Håvard Wahl Kongsgård

http://havard.security-review.net/


David Winsemius, MD
West Hartford, CT

__
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.

Re: [R] How to export to pdf in landscape orientation?

2011-06-25 Thread Berry Boessenkool



Hey Juan,

paper=a4r or USr for rotated (landscape))

i.e.

pdf(file='my_file.pdf', onefile=T, paper='A4r')
plot(sin, -pi, 2*pi)  ;  dev.off()


Greetings from Potsdam University, Germany,
Berry Boessenkool




 From: jhernandezcabr...@gmail.com
 Date: Sat, 25 Jun 2011 18:46:28 +0100
 To: r-help@r-project.org
 Subject: [R] How to export to pdf in landscape orientation?
 
 Does anybody know how to get a pdf file with landscape orientation?.
 
   pdf(file= 'my_file.pdf' ,onefile=T,paper='A4')
 plot(sin, -pi, 2*pi)
dev.off()
 
 Thank's in advance
 
 Juan A. Hernandez
 Spain
 
   [[alternative HTML version deleted]]
 
 __
 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.
  
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Moving average in a data table

2011-06-25 Thread Roman Naumenko


Hi,

I'm trying to figure out common approach on calculating MA on a dataset 
that contains column time.


After digging around, I believe functions rollmean and rollaply should 
be used.

However I don't quite understand the requirements for the underlying data.
Should it be zoo object type? Formatted in a special way?

As an example, I'm looking to get calculated avg=MA(variable) over 15 
sec period on time_sec column:


 date   variable   time_sec avg
 2011-05-17 132.55 11:29:59.579 132.55
 2011-05-17 132.65 11:29:59.946 132.60
 2011-05-17 132.5  11:29:59.946 132.57
 2011-05-17 132.5  11:29:59.946 132.55
 2011-05-17 132.55 11:29:59.946 132.55
 2011-05-17 132.6  11:29:59.946 132.56
 2011-05-17 132.55 11:29:59.946 132.56
 2011-05-17 132.65 11:29:59.947 132.57
 2011-05-17 132.85 11:30:00.45  132.60
 2011-05-17 132.9  11:30:00.45  132.63
 2011-05-17 133.05 11:30:00.45  132.67
 2011-05-17 132.2  11:30:00.45  132.63
 2011-05-17 132.5  11:30:00.45  132.62
 2011-05-17 132.7  11:30:00.50  132.63
 2011-05-17 132.75 11:30:00.57  132.63
 2011-05-17 132.55 11:30:00.70  132.63
 2011-05-17 132.25 11:30:00.70  132.61
 2011-05-17 132.25 11:30:00.71  132.59
 2011-05-17 132.35 11:30:00.173 132.57
 2011-05-17 132.45 11:30:00.173 132.57


Any help is really appreciated.

Thanks,
--Roman N.

__
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.

Re: [R] Competing-risks nomogram

2011-06-25 Thread Firas Abdollah

Many thanks

On Sat, Jun 25, 2011 at 10:00 PM, Frank Harrell [via R]
ml-node+3625011-8897305-247...@n4.nabble.com wrote:
 Yes you use the linear predictor from your regression as the dependent
 variable in the rms package's ols function. Â You will get an R^2 of 1.0.
 Â You can depict the ols model with nomogram(). Â Note that there are so many
 statistical issues in competing risks that doing this without a statistician
 is risky.
 Frank
 Frank Harrell
 Department of Biostatistics, Vanderbilt University

 
 If you reply to this email, your message will be added to the discussion
 below:
 http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3625011.html
 To unsubscribe from Competing-risks nomogram, click here.



-- 
Firas Abdollah, MD
Dept. of Urology
San Raffaele Hospital
Vita-Salute University,
Via Olgettina 60, 20132, Milan, Italy
Tel. +39 02 2643 7286
Fax. +39 02 2643 7298
E-mail: firas.abdol...@gmail.com


--
View this message in context: 
http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3625088.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] log-link function problem

2011-06-25 Thread pigpigmeow

y-gam(a~s(b),family=gaussian(link=log),data) 
y-gam(loga~s(b), family =gaussian (link=identity),data)
y-gam(loga~s(b),family=gaussian(link=log),data) 
what are the diffent these 3 equations?

--
View this message in context: 
http://r.789695.n4.nabble.com/log-link-function-problem-tp3625014p3625014.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Multivariate normal density in C for R

2011-06-25 Thread zerfetzen

Does anyone know of a package that uses C code to calculate a multivariate
normal density?

My goal is to find a faster way to calculate MVN densities and avoid R loops
or apply functions, such as when X and mu are N x K matrices, as opposed to
vectors, and in this particular case, speed really matters. I would like to
be able to use .C or .Call to pass X, mu, Sigma, and N to a C program and
have it return a vector of log densities to R.

I'm new to putting C in R, but am sure I'll figure it out. Thanks for any
suggestions.

--
View this message in context: 
http://r.789695.n4.nabble.com/Multivariate-normal-density-in-C-for-R-tp3624602p3624602.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] calling R from C

2011-06-25 Thread Desi Ap

I read R extensions on calling R within c code. I am on windows vista, cygwin 
and R-2.13.0.I can compile  link the c code with following commands$gcc 
-I/cygdrive/c/Progra~1/R/R-2.13.0/include -c -ggdb Rhello.c
gcc-L/cygdrive/c/Progra~1/R/R-2.13.0/bin/i386 -oRhello Rhello.o -lR
However I cant run the resulting .exe file with following command
LD_LIBRARY_PATH=/cygdrive/c/Progra~1/R/R-2.13.0/bin R_HOME=/cygdrive/c/Progra
~1/R/R-2.13.0 ./Rhello.exe
I get a pop up window and it just hangs when I try to run exe file. I assume 
calling R via c program on cygwin/windowsvista is known to be working.
if so, can some one comment on how to run above exe file.
thanks-kris

[[alternative HTML version deleted]]

__
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.

Re: [R] ggplot2 month and year boxplot x axis order problem

2011-06-25 Thread philipharrison

Hi,

Thanks, although I dont think it was the Date.Time variable that was the
problem because my x variable was Month.Year. 

I realise now that this month variable was a factor and I changed the order
of the factor using the following :

fish$MonthYr-factor(fish$MOYR,levels=c(05,2010,06,2010,07,2010,08,2010,09,2010,10,2010,11,2010,12,2010,01,2011,02,2011,03,2011,04,2011))

This seems to have ordered my x axis (factors)in the correct fashion.

Thanks again for your help

Phil

--
View this message in context: 
http://r.789695.n4.nabble.com/ggplot2-month-and-year-boxplot-x-axis-order-problem-tp3623029p3624680.html
Sent from the R help mailing list archive at Nabble.com.

__
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.

Re: [R] Moving average in a data table

2011-06-25 Thread Gabor Grothendieck

On Sat, Jun 25, 2011 at 3:15 PM, Roman Naumenko ro...@naumenko.ca wrote:
 Hi,

 I'm trying to figure out common approach on calculating MA on a dataset that
 contains column time.

 After digging around, I believe functions rollmean and rollaply should be
 used.
 However I don't quite understand the requirements for the underlying data.
 Should it be zoo object type? Formatted in a special way?

 As an example, I'm looking to get calculated avg=MA(variable) over 15 sec
 period on time_sec column:

  date           variable   time_sec         avg
  2011-05-17     132.55     11:29:59.579     132.55
  2011-05-17     132.65     11:29:59.946     132.60
  2011-05-17     132.5      11:29:59.946     132.57
  2011-05-17     132.5      11:29:59.946     132.55
  2011-05-17     132.55     11:29:59.946     132.55
  2011-05-17     132.6      11:29:59.946     132.56
  2011-05-17     132.55     11:29:59.946     132.56
  2011-05-17     132.65     11:29:59.947     132.57
  2011-05-17     132.85     11:30:00.45      132.60
  2011-05-17     132.9      11:30:00.45      132.63
  2011-05-17     133.05     11:30:00.45      132.67
  2011-05-17     132.2      11:30:00.45      132.63
  2011-05-17     132.5      11:30:00.45      132.62
  2011-05-17     132.7      11:30:00.50      132.63
  2011-05-17     132.75     11:30:00.57      132.63
  2011-05-17     132.55     11:30:00.70      132.63
  2011-05-17     132.25     11:30:00.70      132.61
  2011-05-17     132.25     11:30:00.71      132.59
  2011-05-17     132.35     11:30:00.173     132.57
  2011-05-17     132.45     11:30:00.173     132.57


rollapply and rollmean are for fixed offsets such as 5 rows before and
after.  For this problem modify the following depending on your
precise requirements:

Lines - date   variable   time_sec avg
 2011-05-17 132.55 11:29:59.579 132.55
 2011-05-17 132.65 11:29:59.946 132.60
 2011-05-17 132.5  11:29:59.946 132.57
 2011-05-17 132.5  11:29:59.946 132.55
 2011-05-17 132.55 11:29:59.946 132.55
 2011-05-17 132.6  11:29:59.946 132.56
 2011-05-17 132.55 11:29:59.946 132.56
 2011-05-17 132.65 11:29:59.947 132.57
 2011-05-17 132.85 11:30:00.45  132.60
 2011-05-17 132.9  11:30:00.45  132.63
 2011-05-17 133.05 11:30:00.45  132.67
 2011-05-17 132.2  11:30:00.45  132.63
 2011-05-17 132.5  11:30:00.45  132.62
 2011-05-17 132.7  11:30:00.50  132.63
 2011-05-17 132.75 11:30:00.57  132.63
 2011-05-17 132.55 11:30:00.70  132.63
 2011-05-17 132.25 11:30:00.70  132.61
 2011-05-17 132.25 11:30:00.71  132.59
 2011-05-17 132.35 11:30:00.173 132.57
 2011-05-17 132.45 11:30:00.173 132.57

DF - read.table(textConnection(Lines), header = TRUE)
DF - transform(DF, datetime = as.POSIXct(paste(date, time_sec)))

f - function(i) {
is.near - abs(as.numeric(DF$datetime[i] - DF$datetime))  7.5
mean(DF$variable[is.near])
}
sapply(1:nrow(DF), f)



-- 
Statistics  Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

__
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.

Re: [R] What does class call mean? How do I make class formula into a call?



On Jun 25, 2011, at 4:33 PM, peter dalgaard wrote:



On Jun 25, 2011, at 15:24 , David Winsemius wrote:



On Jun 24, 2011, at 6:12 PM, StellathePug wrote:


Hello R Users!
I have a list called tabs that I would like to have the same  
structure as
my list eqSystem. The two look like they have the same structure  
but they
are different because when I look at their attributes,  
class(eqSystem[[1]])
is call but class(tabs[[1]]) is formula. I want to have  
class(tabs[[1]])

as a call too.

So what does call mean?


An as yet unevaluated function invocation with first as the named  
function followed by quoted arguments is a call:


See the help(call) page:


f - round
A - 10.5
(g - as.call(list(f, quote(A

.Primitive(round)(A)

eval(g)

[1] 10


call(mean, quote( c(1,2,3)))

mean(c(1, 2, 3))

eval( call(mean, quote( c(1,2,3

[1] 2

It seems very unlikely that a formula object could be coerced into  
a valid call simply by altering its class. To convince us otherwise  
you need to provide more information than you have supplied to the  
present. The results of str() on these objects might be a first step.


Actually, no. Any unevaluated expression in R is mode call, unless  
atomic or symbol. It will also be class call, unless expressedly  
overridden by an S3 class assignment. Notice that operators are  
really function calls.

I.e.


mode(quote(x+y))

[1] call

class(quote(x+y))

[1] call

But


class(quote(x))

[1] name

class(quote(3.14159))

[1] numeric

(This is why the R docs keep talking about unevaluated expressions  
instead of call objects: They aren't always that.)


The ~ operator is also a function call. However, evaluating ~  
returns an object which is the actual call assigned class  
formula (plus an environment attribute).



f - y ~ x
class(f)

[1] formula

unclass(f)

y ~ x
attr(,.Environment)
environment: R_GlobalEnv

mode(f)

[1] call

class(unclass(f))

[1] call

I.e., an unevaluated formulae expression (as in quote(y~x)) is class  
call, as is an unclassed formula object. So it is pretty easy to  
have objects of class formula very similar to objects of class  
call.


Not the first time I have stumbled on such matters. Chamber's SfDA  
would be one obvious place to study. Do yu have any others that pop to  
mind?   The last example suggests that mode and class can each be  
call so that 'call' is somehow more primitive than function or  
formula.


And by way of directly addressing the OP's questions, it sounds as  
though applying unclass() to the formula objects might be attempted?






--

David Winsemius, MD
West Hartford, CT

__
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.

Re: [R] calling R from C