[R] Trouble compiling XML package
Dear Prof. Lang -
I am trying to install the XML library on a 64-bit SUSE linux system
(version info below) running 2.4.1.
I have gcc version 3.3.3, and libxml2 version 2.6.7. I know this is not
current, but I'm on a machine used and administered by others, and
updating libxml2 would require updating libc, and things get pretty
complicated from there.
Trying to install through R (1.9-0), I eventually get the error:
XMLTree.c: In function `xmlBufferWrite':
XMLTree.c:729: error: void value not ignored as it ought to be
make: *** [XMLTree.o] Error 1
I manually downloaded version 1.8-0 and got the same problem. I took a
look at that part of the code, but do not understand enough to start
tinkering with it. I was able to install an earlier version a couple of
years ago, and it was extremely useful (thanks!) but the relevant
machine has been decommissioned.
Can you make any suggestions about which component of my system this
might indicate needs to be changed? I checked the mailing list
archives, but didn't find anything. I'm hoping there's an alternative
to changing libxml2, with all the cascading requirements that would
bring (and no guarantee, with what I know now, that that's the problem).
Thanks,
Matt Wiener
version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
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Re: [R] Trouble compiling XML package [Broadcast]
Oops - I see I was unclear. I'm using R-2.4.1 to install; 1.9.0 is the
version of XML I was trying to load. I'll try your change - I'm really
using this for reading XML.
Thanks,
Matt
-Original Message-
From: Duncan Temple Lang [mailto:[EMAIL PROTECTED]
Sent: Friday, May 18, 2007 4:18 PM
To: Wiener, Matthew
Cc: R-help
Subject: Re: [R] Trouble compiling XML package [Broadcast]
Wiener, Matthew wrote:
Dear Prof. Lang -
I am trying to install the XML library on a 64-bit SUSE linux system
(version info below) running 2.4.1.
I have gcc version 3.3.3, and libxml2 version 2.6.7. I know this is
not
current, but I'm on a machine used and administered by others, and
updating libxml2 would require updating libc, and things get pretty
complicated from there.
Trying to install through R (1.9-0),
Wow, that's really old!
I eventually get the error:
XMLTree.c: In function `xmlBufferWrite':
XMLTree.c:729: error: void value not ignored as it ought to be
make: *** [XMLTree.o] Error 1
You might try changing the routine xmlBufferWrite to
static int
xmlBufferWrite (void * context, const char * buffer, int len) {
xmlBufferAdd((xmlBufferPtr) context, (const xmlChar *) buffer,len);
return(len);
}
That will work if there are no errors when adding to the buffer.
But this is used when generating XML in a particular way, i.e. using
internal nodes. So let's just hope that you don't invoke
this code and if you do, that there are no errors.
I manually downloaded version 1.8-0 and got the same problem. I took
a
look at that part of the code, but do not understand enough to start
tinkering with it. I was able to install an earlier version a couple
of
years ago, and it was extremely useful (thanks!) but the relevant
machine has been decommissioned.
Can you make any suggestions about which component of my system this
might indicate needs to be changed? I checked the mailing list
archives, but didn't find anything. I'm hoping there's an alternative
to changing libxml2, with all the cascading requirements that would
bring (and no guarantee, with what I know now, that that's the
problem).
Thanks,
Matt Wiener
version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
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Re: [R] count the # of appearances... [Broadcast]
Take a look at table.
Hope this helps,
Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of bunny ,
lautloscrew.com
Sent: Thursday, March 01, 2007 9:20 AM
To: r-help@stat.math.ethz.ch
Subject: [R] count the # of appearances... [Broadcast]
Hi there,
is there a possibility to count the number of appearances of an
element in a vector ?
i mean of any given element.. deliver all elements which are exactly
xtimes in this vector ?
thx in advance !!
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Re: [R] problem with throwing lines out of matrix [Broadcast]
You didn't' actually tell us what forfact is. You could try something like
(untested)
My.matrix - my.matrix[!(my.matrix[, 1] %in% remove.values), , drop = FALSE]
Also, reading some of the introductory R manuals you can find on CRAN in the
documentation section will really give you a leg up on some of these things.
Hope this helps.
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of bunny ,
lautloscrew.com
Sent: Thursday, March 01, 2007 2:09 PM
To: r-help@stat.math.ethz.ch
Subject: [R] problem with throwing lines out of matrix [Broadcast]
Dear all,
again i have a problem with special case of dropping lines out of a
matrix.
i tried the following, where throwout is a vector of length 18 with
simple id values that should be compared to any
for (k in 1:length(throwout))
{
mymatrix=matrix(mymatrix[-(forfact[k]),],ncol=4)
}
this didnt work and i tried the following to find the error:
mymatrix[,1][mymatrix[,1]==throwout[7]]
this returned me a nice value - everything fine...
but other same other values for throwout didnt work - because the
throwout value simply is not in this matrix.
but i need the same throwout vector for different matrices - so i
need to use it.
does anybody have an idea how i can throw out all lines in every of
my 5 matrices that contain values of the throwout in their first
column ?
and how to deal with the problem that not every matrix contains all
throwout values in its first column...
maybe this might help:
in the end all matrices should have the same number of lines.
thx in advance, i´ll keep on trying ;)
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Re: [R] count sequence of integers [Broadcast]
The function rle will give you what you are looking for.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Martin Becker
Sent: Thursday, February 15, 2007 5:52 AM
To: Samuel Kemp
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] count sequence of integers [Broadcast]
Samuel Kemp wrote:
Hi,
I would like to be able to count a sequence of numbers. For example,
given a
vector of the following integers
(1,1,1,2,2,2,2,3,3,3,3,3,3,1,1,1,1, 3,3)
the function would return
(3, 4, 6, 4,2)
Does anyone have any cool ideas to solve this?
Maybe not the most efficient way, but
count - function (x) diff(c(0,which(diff(x)!=0),length(x)))
should work (for integer sequences!):
x-c(1,1,1,2,2,2,2,3,3,3,3,3,3,1,1,1,1,3,3)
count(x)
[1] 3 4 6 4 2
Regards,
Martin
Any help appreciated.
Regards,
Sam.
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Re: [R] legend in lattice densityplot [Broadcast]
From the documentation for xyplot (referred to from densityplot): The position of the key can be controlled in either of two possible ways. If a component called space is present, the key is positioned outside the plot region, in one of the four sides, determined by the value of space, which can be one of top, bottom, left and right. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Albert Vilella Sent: Wednesday, February 14, 2007 8:46 AM To: R-help@stat.math.ethz.ch Subject: Re: [R] legend in lattice densityplot [Broadcast] How can I place the legend to the left or right of the densityplot? By default, it goes at the top, and as it is a rather long list, the density plot only uses half the space of the whole graphic... On 11/30/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: Me too on Windows XP. Its probably just a bug or unimplemented feature in the SVG driver. Write to the maintainer of that package For a workaround generate fig output and then convert it to svg using whatever fig editor or converter you have. (On my windows system I use the free fig2dev converter although it inserted a DOCTYPE statement into the generated SVG file that IE7 did not recognize but once I manually deleted that it displayed ok in IE7.) # after producing file01.fig run # fig2dev -L svg file01.fig file01.svg # or use some other fig to svg converter or editor xfig(file = /file01.fig, onefile = TRUE) library(lattice) set.seed(1) DF - data.frame(x = c(rnorm(100,1,2),rnorm(100,2,4),rnorm(100,3,6)), f = sample(c(A,B,C,D,E),300,replace=TRUE)) densityplot(~ x, DF, groups = f, auto.key = TRUE, plot.points = FALSE, par.settings = list(superpose.line = list(col = c(1,1,2,2), lty = 1:2, lwd = c(1,1,1,1,2 dev.off() On 11/30/06, Albert Vilella [EMAIL PROTECTED] wrote: Should it be a problem to print this dashed line plots as svgs? library(RSvgDevice) devSVG(file = /home/avilella/file01.svg, width = 20, height = 16, bg = white, fg = black, onefile=TRUE, xmlHeader=TRUE) densityplot(...) dev.off() I am getting all the lines as continuous, not dashed... On 11/30/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: Yes by using the lty suboption of superpose.line. Here is a modification of the prior example to illustrate: We also use lwd as well in this example. set.seed(1) DF - data.frame(x = c(rnorm(100,1,2),rnorm(100,2,4),rnorm(100,3,6)), f = sample(c(A,B,C,D,E),300,replace=TRUE)) library(lattice) densityplot(~ x, DF, groups = f, auto.key = TRUE, plot.points = FALSE, par.settings = list(superpose.line = list(col = c(1,1,2,2), lty = 1:2, lwd = c(1,1,1,1,2 On 11/30/06, Albert Vilella [EMAIL PROTECTED] wrote: Can I combine colors and line types? For example, would it be possible to have 5 colors per 2 types of lines (continuous and dashed)? On 11/29/06, Chuck Cleland [EMAIL PROTECTED] wrote: Albert Vilella wrote: Are this legend colors correlated to the plot? They are if you rely on the colors in trellis.par.get(superpose.line)$col If you want different colors you might use trellis.par.set() to temporarily change the colors: x - c(rnorm(100,-2,1),rnorm(100,0,1),rnorm(100,2,1)) f - rep(c(A,B,C), each=100) df - data.frame(x,f) library(lattice) oldpar - trellis.par.get(superpose.line)$col trellis.par.set(superpose.line = list(col = heat.colors(3))) densityplot(~ x, groups = f, data = df, plot.points=FALSE, auto.key=TRUE) trellis.par.set(superpose.line = list(col = oldpar)) If you don't require points or lines in the key, you also could do something like this: densityplot(~ x, groups = f, data = df, plot.points=FALSE, key = simpleKey(levels(df$f), lines=FALSE, points=FALSE, col=heat.colors(3)), col=heat.colors(3)) To use your own colors without changing the trellis settings and to get lines or points in the key, you probably need at least to use key = simpleKey() rather than the auto.key argument, and you may need to look into draw.key(). Other people on the list might know simpler approaches for using your own colors in this situation. If I do a: densityplot(~x, groups=f, plot.points=FALSE, auto.key=TRUE,col=heat.colors(5)) I get different colors in the legend than the plot... On 11/29/06, Chuck Cleland [EMAIL PROTECTED] wrote: Albert Vilella wrote: Hi, I have a densityplot like this: x = c(rnorm(100,1,2),rnorm(100,2,4),rnorm(100,3,6))
Re: [R] matlab style plotting in R [Broadcast]
In traditional R graphics, you can take a look at matplot.
You might also want to look at the lattice package.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Maria
Vatapitakapha
Sent: Tuesday, February 13, 2007 12:20 PM
To: r-help@stat.math.ethz.ch
Subject: [R] matlab style plotting in R [Broadcast]
Hello
I was wondering how I can achieve matlab style plotting in R,
in the sense that matlab allows you to plot multiple sets of variables
within the same
x-y axes. plot in R does not seem to cater for this. I tried 'overplot'
from
the gplots package but this assumes different y axes for the variables.
any suggestions would be very appreciated
Maria
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Re: [R] R [Broadcast]
Hi. The package you are looking for is not a standard package (that is,
one that gets installed automatically with R).
There is documentation available, though. From cran
(http://cran.r-project.org), go to manuals, look at R Installation and
Administration, particularly Section 6, which talks about installing
packages.
Briefly:
Install.packages(KernGPLM) might work (in unix or windows). And on
Windows, you can also download a zip file from cran and use Install
package from local zip file in the menu.
Hope this helps.
Regards,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of magda haggag
Sent: Thursday, February 08, 2007 2:55 PM
To: r-help@stat.math.ethz.ch
Subject: [R] R [Broadcast]
Dear Professor,
I am preparing for a Ph.D in semiparametric regression at Cairo
university in Egypt. Referring to R package KernGPLM, I obtained R
version 2.4.1 but I did not find package KernGPLM. Please, help me how
can I obtain this package. Thanks in advance.
Name: Magda Haggag
E-mail: [EMAIL PROTECTED]
Address: 27, Notrdam Desion st., Gleem, Alexandria, Egypt.
-
8:00? 8:25? 8:40? Find a flick in no time
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Re: [R] help on determining operating system [Broadcast]
You can indeed compile and run R directly through the unix layer in Mac
OS (or at least you could about 2 years ago, which was the last time I
tried).
Regards,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold
Sent: Tuesday, December 12, 2006 2:47 PM
To: Kenneth Benoit; LU YING
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] help on determining operating system [Broadcast]
BTW, Mac OS sits on the Darwin unix system. So, you have all the
benefits of Mac and can access unix via the terminal (Steve Jobs is
brilliant). Things like emacs are waiting for you to use on the Mac. I
haven't explored whether one can install R on the Mac and use it via the
unix interface (or whether there is any reason to do so).
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Kenneth Benoit
Sent: Tuesday, December 12, 2006 2:39 PM
To: LU YING
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] help on determining operating system
Hi - I don't want to ignite any holy wars, but for 10 years
until last year I used Linux, I occasionally use a Windows
machine at home, and last year switched to Mac OS. Of all
the GUIs for R out there, the mac is the best by far IMHO.
And R on my macbook is faster than on a pentium 4 3.2GHz
running either linux or win xp.
Ken
LU YING wrote:
Dear list,
I am an R user and I also write my own package in
R(sometime i need to
write in C), and right now i am thinking about buying a new
workstation--and i am trying to decide if i should get
a mac with OS X or a linux machine (for example Dell).
I have experience using R on linux (but i have been just a
user and never
been a admin) but i am hesitating of managing a linux
system on my own
(btw I would like to have my new workstation to be used as
a server), so
right now I am leaning toward of buying a Mac Pro. But from
the website,
it sounds like R doesnt work quite well with Mac operating system
yet...so I was wondering if anybody here have any experiences of
using/developing R package on a Mac machine? Is it smooth enough?
(oh by the way, i am not a Mac user yet, Windows has been
the primary
operating system that i used, but after hearing many good things
of OS X, I am really interested in switching over.)
any suggestions are appreciated!
Ying
Ying Lu
Assistant Professor
Dept. Sociology
U-Colorado at Boulder
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--
Kenneth Benoit
Associate Professor of Political Science
Department of Political Science, Trinity College
Dublin 2, Ireland
http://benoit.tcd.ie
Tel: 353-1-608-2491
Fax: 353-1-677-0546
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Re: [R] Accessing R from Java [Broadcast]
I've had good luck with Rserve. http://stats.math.uni-augsburg.de/Rserve/
Hope this helps,
Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of fuad
Sent: Tuesday, October 10, 2006 9:58 PM
To: R-help@stat.math.ethz.ch
Subject: [R] Accessing R from Java [Broadcast]
Hello All,
I am Fuad from Indonesia. I am doing a research using R. I need to access R
from Java.
Here are my computer specifications :
1. Windows XP
2. Java 1.4.0
3. R 2.2.1
4. rJava_0.4.3.zip ; I download the binary from CRAN
5. Rserve_0.4 ; I download the exe from Rosuda
6. JRI_0.3.5.tar.gz from Rosuda too
I have successfully install and try a little code in R.
I have install packages rJava from RGUI and it was successful.
But when I try to load packages using library(rJava) I have error : unable
to load shared library rJava.dll. There is no Jvm.dll.
So I copied jvm.dll from JAVA_HOME\bin to R_HOME\bin, and it seems done well
until I try to wake up Java Virtual Machine using .jinit() I received error
: cannot create JVM.
Is there anyway I can call R inside Java code ?
Please help me. Thank you
Best regards,
Fuad
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Re: [R] postcript file / xyplot function [Broadcast]
This is FAQ 7.22. Lattice functions produce graphic objects, which are not
displayed by default. If you print your graph, you should be fine. Also,
take a look at the documentation for panel.xyplot. Using type = c(p, r)
should make things simpler.
Regards,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Tuesday, October 03, 2006 8:00 AM
To: R-help@stat.math.ethz.ch
Subject: [R] postcript file / xyplot function [Broadcast]
Hi,
I would like save a curve in a postscript file.
It when I use a common plot function (plot)
postscript(file=file.eps)
plot(x,y)
dev.off()
It's not working with the xyplot function (lattice package).
postscript(file=Z,height=8,width=8,horizontal=FALSE)
xyplot(data[,3]~data[,2]|data[,1],panel=function(x,y){panel.xyplot(x,y)
COEFF-coef(lm(log(y)~x))
panel.curve(exp(COEFF[1]+COEFF[2]*x))
dev.off()
Do anyone know how to use the postscript function with a xyplot function ?
Thanks by advance
Jessica Gervais
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Re: [R] java R interface [Broadcast]
We have successfully used Rserve: http://stats.math.uni-augsburg.de/Rserve/
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Lu Yuefeng
Sent: Thursday, August 31, 2006 1:24 PM
To: r-help@stat.math.ethz.ch
Subject: [R] java R interface [Broadcast]
Hello all,
I am wondering if you have experience or information about calling R
routines within JAVA? Is it feasible and how to pass the data/results? TXIA!
Yuefeng
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Re: [R] Plot y ~ x under condition of variable a and b [Broadcast ]
It's the |source in your formula that tells lattice to separate them.
If you drop that, you'll get all points without S and P distinguished at
all. If you add a groups argument, you should get them presented with
different colors/symbols/etc. depending on your trellis settings (warning:
untested code):
par.plot(lnvol~lnden, groups = source,data=dat,sub=as.factor(plotid),col=T)
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of jennystadt
Sent: Friday, August 25, 2006 11:28 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Plot y ~ x under condition of variable a and b [Broadcast]
Hi All,
I want to plot y~ x under the condition of variable a and b. Followed is the
dataset:
plotid lndenlnvol source
369 9037.0 10.419002 -4.101039226 S
370 9037.0 9.840548 -2.432385723 S
371 9037.0 8.973351 -1.374842169 S
372 9037.0 8.242756 -0.813800113 S
373 9037.0 8.006368 -0.366743413 S
374 9037.0 7.396335 -0.041375532 S
375 9037.0 6.194405 0.744573249 S
376 9038.0 10.417209 -2.938129138 S
377 9038.0 9.709296 -1.906228589 S
378 9038.0 8.581107 -1.187441385 S
379 9038.0 7.539027 -0.748873856 S
380 9038.0 6.866933 -0.228547521 S
381 9038.0 6.672033 0.222818889 S
382 9038.0 6.380123 0.863026089 S
11003.1 7.281089 5.563470357 P
21003.1 7.165854 5.587837467 P
31003.1 7.126938 5.604757978 P
41003.1 6.833951 5.709078555 P
560 3.1 6.634462 5.678818058 P
610 3.2 7.052830 5.534234273 P
710 3.2 6.905777 5.559511276 P
810 3.2 6.885776 5.590614404 P
910 3.2 6.685106 5.716040812 P
10103.2 6.495349 5.631784504 P
11103.3 6.697376 5.414815010 P
12103.3 6.553336 5.441823472 P
13103.3 6.581116 5.455788329 P
14103.3 6.279641 5.543868038 P
15103.3 6.119298 5.528003301 P
16103.4 7.035589 5.783924732 P
17103.4 6.875624 5.798852319 P
18103.4 6.812445 5.807787244 P
I used par.plot(lnvol~lnden|source,data=dat,sub=as.factor(plotid),col=T);
It gave good plots, but it put the different data sources to separated
graphs, i.e. S and P. What I want is to plot them on the same graph. If
anyone has the experience in doing plotting like this, please kindly give me
some hints. Thanks!
Jen.
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Re: [R] using split.screen? [Broadcast]
This means that the margins for 10 screens would take up more room than you have - essentially the plot area is being squeezed to nothing. You can try reducing your margins using par. Also, it looks like you're trying to split into 20 screens there. Hope this helps, Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bill Shipley Sent: Tuesday, July 18, 2006 10:02 AM To: R help list Subject: [R] using split.screen? [Broadcast] Hello. I am having trouble understanding the use of split.screen. I want to divide the device surface first into 4 equal screens: split.screen(figs=c(2,2)) This works. I next want to subdivide each of these 4 screens into 10 subscreens. I do, for the first of these 4 screens: screen(1,new=T) and then: split.screen(figs=c(10,2)) My understanding is that this should split screen 1 (i.e. top right) into 10 screens within its area. However, this does not work and I get the following error message: Error in plot.new() : figure margins too large Does anyone know what I am doing wrong? Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Handshake exception in Rserve [Broadcast]
We had something similar, and as far as I recall the problem turned out to
be that we had not set the config file to allow remote connections.
This would probably be better put on the Rosuda mailing list:
http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of jaydeep chovatia
Sent: Monday, July 17, 2006 12:52 AM
To: r-help@stat.math.ethz.ch
Cc: [EMAIL PROTECTED]
Subject: [R] Handshake exception in Rserve [Broadcast]
Hello,
We are facing some problem while calling a Rserve API from our Java client.
The details are as below:
1) We have installed Rserve on linux machine Nagarajan(Port: 6311) and
related modules.
2) We have started the Rserve in daemon mode perfectly by executing the
comman R CMD Rserve on the linux machine.
But when the Java client executes the statement: Rconnection c = new
Rconnection (Nagrajan, 6311), we are getting an exception: handshake
exception: expected 32 bytes received -1 byte.
It would be really great if you could help us out to resolve the issue or
provide a probable root cause of the problem.
Thank you,
Jaydeep
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Re: [R] superimposing histograms con't [Broadcast]
I wrote some code to do this. It only works with 2 groups (that's all I
needed), but could probably be generalized. It got my graph made, and I
haven't needed a graph like this one again, so I never went back to really
clean it up.
It works by first plotting both sets of rectangles, then going back over the
ones that had the first bar totally covered by the second.
Hope this helps,
Matt Wiener
f.back.front.hist -
function(breaks, x1, x2, col1 = gray50, col2 = white,
lwd = diff(range(mids))/20,
xlab = , ylab = ,
leg.text = NULL, ...){
if(length(x1) != length(x2))
stop(x1 and x2 must have same length)
if(length(x1) != length(breaks) - 1)
stop(length of breaks must be 1 more than length of x1 and x2)
plot.lim - c(0, max(c(x1, x2)))
mids - 0.5 * (breaks[-1] + breaks[-length(breaks)])
plot(mids, pmax(x1, x2), col = par()$bg, lwd = lwd,
ylim = plot.lim, xlab = xlab, ylab = ylab,
cex.axis = 1.5, font.axis = 2, cex.lab = 1.5, font.lab = 2, ...)
rect(breaks[-length(breaks)], 0, breaks[-1], x1, col = col1)
rect(breaks[-length(breaks)], 0, breaks[-1], x2, col = col2)
ind - x1 x2
rect(breaks[-length(breaks)][ind], 0,
breaks[-1][ind], x1[ind] ,col = col1)
if(!is.null(leg.text))
legend(mids[1], plot.lim[2], leg.text,
fill = c(col1, col2), cex = 1.5)
}
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jeff Miller
Sent: Wednesday, June 28, 2006 4:21 PM
To: 'Bill Shipley'; 'R help list'
Subject: Re: [R] superimposing histograms con't [Broadcast]
I was just thinking about this last night.
I would like to do the same but WITH overlapping.
For example, I graph 2 sets of count data. Say the bars for the 1`s
overlap...I would like to show that with a different shading for the group
that has the higher frequency. For example, it could be black up to a
frequency of 5 followed by diagonal-dashes from 5-7 representing the higher
frequency of a second group.
Thank you,
Jeff Miller
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bill Shipley
Sent: Wednesday, June 28, 2006 3:54 PM
To: R help list
Subject: [R] superimposing histograms con't
Earlier, I posted the following question:
I want to superimpose histograms from three populations onto the same graph,
changing the shading of the bars for each population. After consulting the
help files and the archives I cannot find out how to do this (seemly)
simple graph. To be clear, I want
- a single x axis (from -3 to 18)
- three groups of bars forming the histograms of each population (they
will not overlap much, but this is a detail)
- the bars from each histogram having different shadings or other visually
distinguishing features.
Gabor Grothendieck [EMAIL PROTECTED] pointed to some code to to this
but I have found another way that works even easier.
hist(x[sel1],xlim=c(a,b),ylim=c(A,B)) - this plots the histogram for the
first group (indexed by sel1) but with an x axis and a y axis that spans the
entire range.
par(new=T) - to keep on the same graph
hist(x[sel2],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the second
histogram
par(new=T) - to keep on the same graph
hist(x[sel3],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the third
histogram
Bill Shipley
North American Editor, Annals of Botany
Editor, Population and Community Biology series, Springer Publishing
Dipartement de biologie, Universiti de Sherbrooke,
Sherbrooke (Quibec) J1K 2R1 CANADA
[EMAIL PROTECTED]
http://callisto.si.usherb.ca:8080/bshipley/
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Re: [R] strange matrix behaviour: is there a matrix with one row?
Use drop = FALSE in your subscripting calls. That will retain matrixness. For example: y - matrix(1:8, ncol = 2) is.matrix(y[-c(1,2,3),,drop = FALSE] More info is on the help page for [. You can type: ?[ to get it from the command line. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, April 07, 2006 9:16 AM To: Gabor Grothendieck Cc: Brian Quinif; r-help@stat.math.ethz.ch; [EMAIL PROTECTED] Subject: [R] strange matrix behaviour: is there a matrix with one row? Consider this: y - matrix(1:8, ncol=2) is.matrix(y[-c(1,2),]) [1] TRUE is.matrix(y[-c(1,2,3),]) [1] FALSE is.matrix(y[-c(1,2,3,4),]) [1] TRUE It seems like an inconsistent behaviour: - with 2 or more rows we have a matrix - with 1 row we do not have a matrix and - with 0 rows we have a matrix again I just stumbled on this behaviour, because I had a problem with my program in which I have assumed that matrix with some rows removed is still a matrix, which seems to be mostly true, but it is not true if only one row is left. Comments? Suggestions? How to work around this problem - without to many if statements? Best regards, Ryszard __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to change the trellis graph background color
Take a look at trellis.par.set(). For example, trellis.par.set(theme = col.whitebg()) changes things to look more or less like the default from the standard R graphics functions. But you can change one option at a time too. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Lisa Wang Sent: Friday, March 31, 2006 4:23 PM To: R-Help Subject: [R] how to change the trellis graph background color Hello there, Please shed some light on how to change the background color of trellis graphic background. Thanks a lot lisa Wang Toronto, Ca __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Impaired boxplot functionality - mean instead of median
interaction(A, B) will create a single factor made up of the combinations of the two factors A and B. Perhaps that would let you use plotmeans. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Evgeniy Kachalin Sent: Thursday, December 01, 2005 3:37 PM To: r-help@stat.math.ethz.ch Subject: Re: [R] Impaired boxplot functionality - mean instead of median Marc Schwartz (via MN) пишет: Marc Schwartz (via MN) пишет: So plotmeans is incapable of: boxplot(numerical~fact1+fact2). Is there any way further? I think that somehow we are talking past each other here. plotmeans() does what it is designed to do, which is to simplify the process of plotting group-wise point estimates and user defined error bars/intervals around the point estimates. In your case, these intervals would be standard deviations around each of the group means as you have indicated. Review the examples in ?plotmeans. As Martin and others have pointed out, you need to remove boxplots from the equation here, as they were not designed to plot means and standard deviations. Again, what I'm talking about: plotmeans is incapable of analyzing the formula. For example, I have two factors: A - a, b, c, and B - d, e, f. If i plot: boxplot(num~A+B) what do I get? Eight boxes: ad, ae, af, ba, be, bf, cd, ce, cf. If I plot: plotmeans(num~A+B) - what do I get? Nothing. Because plotmeans cannot combine two factors in various combination. Is there a simple way to do it? Anyway... That's wrong way, all what is neccessary is to have a boxplot with mean istead of median. Is there simple way to do it? Statistical software like Statistica 7.0 offers any possible combination of what Boxplot could mean. Is it possible to have only one modification to R's boxplot? Thank you for kind answers. Also please tell me, where should I send replies: to conference adress or to those who answer me directly. -- Evgeniy __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Combine related plots
You can also look at xyplot in the lattice package. You will have to set up your data slightly differently than for the standard graphics package, but it may well be worth learning to do so. The lattice package has enormous flexibility for combining multiple sets of data in one panel or plotting them in separate panels. Hope this helps, Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Vivien W. Chen Sent: Wednesday, November 16, 2005 8:49 AM To: r-help@stat.math.ethz.ch Subject: [R] Combine related plots Dear R users, If I have to combine plots which have the same independent and dependent variables in one graph. Which command should I use? Any example? Can I use panel? Your help will be deeply appreciated. Thanks! -Vivien Chen- [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Scale of plots
See xlim and ylim in the documentation on the plot command. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Miller Sent: Monday, November 07, 2005 10:12 AM To: r-help@stat.math.ethz.ch Subject: [R] Scale of plots I would like to know how I can change the axis to run from 0 to 50 say, instead of the 0 to 200 it gives me. Many thanks Mark Miller __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Random Forest with R
It's randomForest. Searching (simple text find) on the packages web page of CRAN using either random or forest would find you this. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Louis Ferre Sent: Tuesday, September 27, 2005 8:45 AM To: r-help@stat.math.ethz.ch Subject: [R] Random Forest with R Hi, what is the name of the package that provides Random Forest with R. Sincerely Louis Ferré http://www.univ-tlse2.fr/grimm/smash/ferre/index.html Equipe GRIMM-2254 Département de Math-Info 5 allées Antonio Machado 31058 Toulouse Cedex Tel: 0561504608 0561503982 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R , Java DCOM
This is not a direct answer to your question. But Rserve (http://stats.math.uni-augsburg.de/Rserve/) provides another possible approach. We've had good success with it. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Rajarshi Guha Sent: Wednesday, September 21, 2005 10:00 AM To: R Subject: [R] R , Java DCOM Hi, I am working on a Java project that will run primarily on Windows. As part of the project I would like to use the R engine. However, from what I have seen on this list the SJava list, installing SJava on Windows can be troublesome. As a result I was wondering if anybody had used DCOM to access R from a Java program on Windows (if it is all possible). Any pointers to documents and/or examples would be appreciated. Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Gravity brings me down. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] *** saving files ***
Depending on the size of your objects, you may be able to just keep them in
a list, especially as you say you will need them in the same order later.
If because of memory constraints or for some other reason you really need to
have a separate file for each round, you can generate object and file names
using paste, assign the object to the name with assign, and save the file:
(warning: untested code)
for(i in 1:n){
obj.name - paste(base.obj.name, i, sep = .)
file.name - paste(obj.name, rda, sep = .) # or whatever other
file name you want
this.obj - my.fn.that.creates.object(my.arguments)
assign(obj.name, this.obj)
save(list = obj.name, file = file.name)
}
When retrieving the files, you can use a similar loop, but instead of using
assign, you can use get to retrieve the value and assign it to another
variable. Or, in interactive use, you know the name so you can refer to the
variable.
Hope this helps,
Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Shahrokh Keiwani
Sent: Wednesday, September 14, 2005 9:43 AM
To: r-help@stat.math.ethz.ch
Subject: [R] *** saving files ***
Hi,
I need help :o(
I want that my function saves result files in a for()-loop while it runs
automatically.
the filenames must be saved like:
file_1 - for 1. result
file_2 - for 2. result
file_3 - for 3. result
and
.
.
.
file_n - for n. result
the file names are the same identified by _1, _2 , _3, ... , _n
these files will loaded by a second function later in the same sequence
(_1 to _n).
how can I do that ...
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Re: [R] adding text to the corner of a lattice plot
I think this message from the help archives might address your question (found using the query lattice mtext on R site search: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/51605.html. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of RINNER Heinrich Sent: Friday, September 09, 2005 4:16 AM To: r-help@stat.math.ethz.ch Subject: [R] adding text to the corner of a lattice plot Dear R community, I am using R 2.1.1 on Windows XP, package lattice Version 0.12-5, and want to add text (sort of a dat-stamp actually) to the lower left corner of a lattice plot, prefarably _after_ the plot has been created. Here is a simple example what I do in base graphics: # base graphics: plot(rnorm(100), rnorm(100)) mtext(as.character(Sys.Date()), side = 1,line = -2, outer = T, adj = 0, font = 1, cex = 0.7) How can I get the same using lattice? # lattice: require(lattice) xyplot(rnorm(100) ~ rnorm(100)) ??? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] label *on the side* in conditional lattice plots?
I think you might be able to use the horizontal argument to lattice to rotate all your plots and squish them in the other dimension. (Though I don't know whether you consider that a good outcome ...) Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Maciej Kalisiak Sent: Wednesday, August 31, 2005 4:21 PM To: r-help@stat.math.ethz.ch Subject: [R] label *on the side* in conditional lattice plots? I'm doing bwplot(x ~ y | z, ...) with lattice, but would like the z-labels to appear to the *side* of each bwplot, rather than on top... is this possible? The main reason is that my bwplots are horizontal, and as such can be nicely squished in the vertical axis (big space-saver when including in papers), but the labels get in the way, look too large in comparison, while I have all this empty space to the side of the plots which is being wasted instead... -- Maciej Kalisiak [EMAIL PROTECTED] http://www.dgp.toronto.edu/~mac __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] heatmap color distribution
You can use the breaks argument in image to do this. (You don't specify a function you're using, but other heatmap functions probably have a similar parameter.) Look across all your data, figure out the ranges you want to have different colors, and specify the appropriate break points in each call to image. Then you're using the same color set in each one. You run the risk, of course, that some of your images will have a very narrow color range, which might obscure interesting features. But nothing stops you from making more than one plot. Hope this helps. Regards, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Michaelson Sent: Thursday, July 21, 2005 9:26 AM To: r-help@stat.math.ethz.ch Subject: [R] heatmap color distribution Hi all, I've got a set of gene expression data, and I'm plotting several heatmaps for subsets of the whole set. I'd like the heatmaps to have the same color distribution, so that comparisons may be made (roughly) across heatmaps; this would require that the color distribution and distance functions be based on the entire dataset, rather than on individual subsets. Does anyone know how to do this? Thanks in advance, Jake __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] heatmap color distribution
Breaks affects the binning into colors. Try this. Assume that temp is one
of your data sets. It's values are restricted to 0.25 - 0.75, and we'll
assume that the full data set goes from 0 to 1.
temp - matrix(runif(60, 0.25, 0.75), nc = 6)
breaks - seq(from = 0, to = 1, length = 11)
image(temp2, col = heat.colors(10)) # full range of
color
image(temp2, col = heat.colors(10), breaks = breaks)# muted colors
The second image is told about all the colors, and about the full range of
data through breaks, and only uses the colors in the middle.
Is that what you mean?
HTH,
Matt
-Original Message-
From: Jake Michaelson [mailto:[EMAIL PROTECTED]
Sent: Thursday, July 21, 2005 10:45 AM
To: Wiener, Matthew
Cc: R-help@stat.math.ethz.ch
Subject: Re: [R] heatmap color distribution
Thanks for the reply. As I understand it, breaks only controls the
binning. The problem I'm having is that each subset heatmap has
slightly different min and max log2 intensities. I'd like the colors
to be based on the overall (complete set) max and min, not the subsets'
max and min -- I could be wrong, but I don't think breaks will help
me there. And you're right - this might obscure some of the
trends/features, but we'll also plot the default heatmaps.
Also (I should have specified) I'm using heatmap.2.
Thanks,
Jake
On Jul 21, 2005, at 8:09 AM, Wiener, Matthew wrote:
You can use the breaks argument in image to do this. (You don't
specify a
function you're using, but other heatmap functions probably have a
similar
parameter.) Look across all your data, figure out the ranges you want
to
have different colors, and specify the appropriate break points in
each call
to image. Then you're using the same color set in each one. You run
the
risk, of course, that some of your images will have a very narrow color
range, which might obscure interesting features. But nothing stops
you from
making more than one plot.
Hope this helps.
Regards,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jacob Michaelson
Sent: Thursday, July 21, 2005 9:26 AM
To: r-help@stat.math.ethz.ch
Subject: [R] heatmap color distribution
Hi all,
I've got a set of gene expression data, and I'm plotting several
heatmaps for subsets of the whole set. I'd like the heatmaps to have
the same color distribution, so that comparisons may be made
(roughly) across heatmaps; this would require that the color
distribution and distance functions be based on the entire dataset,
rather than on individual subsets. Does anyone know how to do this?
Thanks in advance,
Jake
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Re: [R] unable to call R t-test from Java
This does not address the question of how to do this the way you're trying
to do it, using Omegahat. But I've had good results using Simon Urbanek's
program Rserve: http://stats.math.uni-augsburg.de/Rserve/
Hope this helps,
Matthew Wiener
Applied Computer Science Mathematics
Merck Research Laboratories
Rahway, NJ 07065
732-594-5303
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of O'Brien, Laura
Sent: Wednesday, July 20, 2005 10:42 AM
To: r-help@stat.math.ethz.ch
Subject: [R] unable to call R t-test from Java
Hello,
My colleague and I would like to write Java code that invokes R to do a
simple TTest. I've included my sample java code below. I tried various
alternatives and am unable to pass a vector to the TTest method. In my
investigation, I tried to call other R methods that take vectors and also
ran into various degrees of failure. Any insight you can provide or other
Web references you can point me to would be appreciated.
Thank you,
Laura O'Brien
Application Architect
--- code --
package org.omegahat.R.Java.Examples;
import org.omegahat.R.Java.ROmegahatInterpreter;
import org.omegahat.R.Java.REvaluator;
public class JavaRCall2
{
/**
* want to see if I can eval a t.test command like what I would run in
the
* R command line
*/
static public void runTTestByEval_cores(REvaluator e,
ROmegahatInterpreter interp)
{
/* produces a core */
System.err.println(eval a t.test);
Object value = e.eval(t.test (c(1,2,3), c(4,5,6)));
if (value != null)
interp.show(value);
}
/**
* want to see if I can eval anything that takes a vector, e.g. mean,
* like what I would run in the R command line
*/
static public void runMeanByEval_works(REvaluator e,
ROmegahatInterpreter interp)
{
System.err.println(\r\n evaluation string mean command);
Object value = e.eval(mean(c(1,2,3)));
if(value != null)
{
interp.show(value );
System.err.println(\r\n);
}
}
/**
* if I pass mean a org.omegahat.Environment.DataStructures.numeric what do
I get? NaN
*/
static public void runMeanByNumericList_nan(REvaluator e,
ROmegahatInterpreter interp)
{
Object[] funArgs = new Object[1];
// given argument is not numeric or logical
org.omegahat.Environment.DataStructures.numeric rList1 = new
org.omegahat.Environment.DataStructures.numeric(3);
double[] dList = new double[3];
dList[0] = (double) 1.1;
dList[1] = (double) 2.2;
dList[2] = (double) 3.3;
rList1.setData(dList, true);
System.err.println(rList1.toString());
funArgs[0] = rList1 ;
System.err.println(\r\n Calling mean and passing an omegahat
vector);
Object value = e.call(mean, funArgs);
if(value != null)
{
interp.show(value );
System.err.println(\r\n);
}
}
/**
* let's run some tests on the vector passed in and see what R thinks
I'm handing it
*
* it returns
* isnumeric: false
* mode: list
* length:2
*/
public static void runTestsOnOmegahatNumeric(REvaluator e,
ROmegahatInterpreter interp)
{
Object[] funArgs = new Object[1];
// given argument is not numeric or logical
org.omegahat.Environment.DataStructures.numeric rList1 = new
org.omegahat.Environment.DataStructures.numeric(3);
double[] dList = new double[3];
dList[0] = (double) 1.1;
dList[1] = (double) 2.2;
dList[2] = (double) 3.3;
rList1.setData(dList, true);
System.err.println(rList1.toString());
funArgs[0] = rList1 ;
System.err.println(\r\n Calling isnumeric and passing an omegahat
vector);
Object value = e.call(is.numeric, funArgs);
if(value != null)
{
interp.show(value );
System.err.println(\r\n);
}
// mode is list
System.err.println(\r\n Calling mode and passing an omegahat
vector);
value = e.call(mode, funArgs);
if(value != null)
{
interp.show(value );
System.err.println(\r\n);
}
System.err.println(\r\n Calling length and passing an omegahat
vector);
System.err.println(\r\n);
System.err.println(INTERESTING: thinks the length is 2!);
value = e.call(length, funArgs);
if(value != null)
{
interp.show(value );
System.err.println(\r\n);
}
}
/**
* run the mean on a java array. Does it also return NAN?
* It returns a different value than the mean -- 2.1... instead of
2.2
*/
Re: [R] Another simple q - removing negative values
To leave x with only the non-negative elements, you can use x[x = 0]. Also see the function subset. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Michael Hopkins Sent: Friday, July 15, 2005 8:00 AM To: r-help@stat.math.ethz.ch Subject: [R] Another simple q - removing negative values Sorry folks but again I have failed in my understanding of how to do a very simple thing. I've read the various texts and searched the help archives but no positive result so far. I want to remove all the rows in a data frame where one of the variables has negative values. In approx Stata pseudocode: drop _all, if( x 0 ) Please either point me to relevant sections of the docs or supply me with solution - I'm sure it's very simple. Michael __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vectorisation suggestion
Federico -
match will give you the (first) index of each element of its first
argument in its second argument. So match(vector.1, vector.2) tells you
where each element of vector.1 appears in vector.2. So if you use table
on that vector, you'll see how many times each element of vector.2 appears.
Something like:
first.occur - match(vector.1, vector.2)
table(factor(vector.2[first.occur], levels = sort(unique(vector.2)))
(changing it into a factor means you won't lose values of vector.2 that
never appear in vector.1.)
An example:
vec1 - sample(1:10, 500, replace = TRUE)
table(vec1)
vec1
1 2 3 4 5 6 7 8 9 10
61 37 43 47 49 59 51 48 53 52
vec2 - 0:11
vec3 - match(vec1, vec2)
table(factor(vec2[vec3], levels = sort(unique(vec2
0 1 2 3 4 5 6 7 8 9 10 11
0 61 37 43 47 49 59 51 48 53 52 0
This also works if one of the members of vec1 is not in vec2 -- that member
simply gets ignored. (As you can see if add, say, a 20 at the end of
vec1.)
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Federico Calboli
Sent: Monday, June 20, 2005 4:16 PM
To: r-help
Subject: [R] vectorisation suggestion
Hi All,
I am counting the number of occurrences of the terms listed in one
vector in another vector.
My code runs:
for( i in 1:length(vector3)){
vector3[i] = sum(1*is.element(vector2, vector1[i]))
}
where
vector1 = vector containing the terms whose occurrences I want to count
vector2 = made up of a number of repetitions of all the elements of
vector1
vector3 = a vector of NAs that is meant to get the result of the
counting
My problem is that vector1 is about 6 terms, and vector2 is
62... can anyone suggest a faster code than the one I wrote?
Cheers,
Federico Calboli
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 75941602 Fax +44 (0)20 75943193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
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RE: [R] a more elegant approach to getting the majority level
The which.max solution is fine as long as the maximum is always unique. Otherwise, which.max will give you the first maximum. So using the x == max(x) version will have an advantage if there can be ties. Regards, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Uwe Ligges Sent: Thursday, May 26, 2005 10:57 AM To: [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] a more elegant approach to getting the majority level Rajarshi Guha wrote: Hi, I have a factor and I would like to find the most frequent level. I think my current approach is a bit long winded and I was wondering if there was a more elegant way to do it: x - factor(sample(1:0, 5,replace=TRUE)) levels(x)[ which( as.logical((table(x) == max(table(x == TRUE ) ] (== TRUE) can ALWAYS be omitted, see also: library(fortunes) fortune(TRUE) x == max(x) should be replaced by which.max(x) as.logical() is superfluous Hence we get: names(which.max(table(x))) Uwe Ligges (The length of x will always be an odd number, so I wont get a tie in max()) Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Alcohol, an alternative to your self - 'Alcohol' by the Bare Naked Ladies __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Plot range resizing when adding additiona lines
In traditional, or base graphics, see matplot, which does exactly what
you describe.
You can also look at lattice graphics, which will give you flexibility to
plot in a single panel or multiple panels.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Hikel, Jerry
Sent: Tuesday, May 24, 2005 4:41 PM
To: R-help@stat.math.ethz.ch
Subject: [R] Plot range resizing when adding additiona lines
Hi -- I have searched the documentation and archives on graphing
capabilities in R for the past couple of hours, but I haven't been able
to find anything directly related to my problem.
I want to create a plot with several lines displayed on it. I want each
line to be displayed in a different color, so it seems the only way to
do this is to create a plot and then use the lines() function. However,
once i create the original plot, when I add new lines to the plot, the
axes range stays the same, and the new lines often extend beyond the
range of the original axes, cutting off the data of the added lines.
Is there any way to force the plot to resize it's axes range when new
lines are added, or is there some other optional way of implementing
this? Thanks.
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RE: [R] R annoyances
(a) If what you're trying to do is just apply exp, or any other element-wise function, you can just say exp(mtx). You avoid both apply and the transpose, and save time in the bargain. If your actual function really does depend on multiple elements, it may be a little more complicated. You could conceivably write a myapply function to do the apply followed by the transpose, but then of course you still need to keep track of which way you're going. (b) You want to look into the drop = FALSE option: Sub.mtx - mtx[,1,drop = FALSE] Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chalasani, Prasad Sent: Thursday, May 19, 2005 10:37 AM To: r-help@stat.math.ethz.ch Subject: [R] R annoyances Dear R Folks, I'm a big fan of R, but there are a couple of things that repeatedly annoy me, and I wondered if anyone has neat ways to deal with them. (a) When using apply row-wise to a matrix, it returns the results column-wise, and to preserve the original orientation, I've to do a transpose. E.g. I've to keep doing a transpose, which I consider to be quite annoying. transformed.mtx - t(apply( mtx, 1, exp)) (b) When extracting 2 or more columns of a matrix, R returns the result as a matrix, BUT when extracting just one column, it returns a vector/array, rather than a matrix, so I've to keep doing as.matrix, which is annoying. sub.mtx - as.matrix(mtx[,1]) Of course I could write a suitable function cols - function(mtx,range) as.matrix(mtx[, range]) but then I lose the syntactic sugar of being able to say [,1]. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] apply vs sapply vs loop - lm() call appl(y)ied on array
Christoph --
There was just a thread on this earlier this week. You can search in the
archives for the title: refitting lm() with same x, different y.
(Actually, it doesn't turn up in the R site search yet, at least for me.
But if you just go to the archive of recent messages, available through
CRAN, you can search on refitting and find it. The original post was from
William Valdar, on April 19.)
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Christoph Lehmann
Sent: Thursday, April 21, 2005 9:24 AM
To: R-help@stat.math.ethz.ch
Subject: [R] apply vs sapply vs loop - lm() call appl(y)ied on array
Dear useRs
(Code of the now mentioned small example is below)
I have 7 * 8 * 9 = 504 series of data (each length 5). For each of
theses series I want to compute a lm(), where the designmatrx X is the
same for all these computations.
The 504 series are in an array of dimension d.dim - c(5, 7, 8, 9)
means, the first dimension holds the data-series.
The lm computation needs performance optimization, since in fact the
dimensions are much larger. I compared the following approaches:
using a for-loop. using apply, and using sapply. All of these require
roughly the same time of computation. I was astonished since I expected
at least sapply to outperfomr the for-loop.
Do you have me another solution, which is faster? many thanks
here is the code
## --
t.length - 5
d.dim - c(t.length,7,8,9) # dimesions: time, x, y, z
Y - array( rep(1:t.length, prod(d.dim)) + rnorm(prod(d.dim), 0, 0.1),
d.dim)
X - c(1,3,2,4,5)
## performance tests
## using for loop
date()
z - rep(0, prod(d.dim[2:4]))
l - 0
for (i in 1:dim(Y)[4])
for (j in 1:dim(Y)[3])
for (k in 1:dim(Y)[2]) {
l - l + 1
z[l] - unlist(summary(lm(Y[,k, j, i] ~ X)))$r.squared
}
date()
## using apply
date()
z - apply(Y, 2:4, function(x) unlist(summary(lm(x ~ X)))$r.squared)
date()
## using sapply
date()
fac - rep(1:prod(d.dim[2:4]), rep(t.length, prod(d.dim[2:4])))
z - sapply(split(as.vector(Y), fac), FUN = function(x)
unlist(summary(lm(x ~ X)))$r.squared)
dim(z) - d.dim[2:4]
date()
## --
--
Christoph LehmannPhone: ++41 31 930 93 83
Department of Psychiatric NeurophysiologyMobile: ++41 76 570 28 00
University Hospital of Clinical Psychiatry Fax:++41 31 930 99 61
Waldau[EMAIL PROTECTED]
CH-3000 Bern 60 http://www.puk.unibe.ch/cl/pn_ni_cv_cl_04.html
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RE: [R] Question for layout function
Shawn --
You can do this by re-using numbers in the layout matrix. The examples in
the help for layout have several examples of this.
For this particular example, I think that layout(cbind(c(1,1), c(2,3)))
would probably do it (untested).
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Shawn Lee
Sent: Thursday, April 21, 2005 9:23 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Question for layout function
Dear people,
Is there a way to generate three graphs having 2x2 layout, but left half
is merged ?
Like below.
-
|||
|||
|||
|||
-
Two times of layout function with par(new=FALSE) do not accept it.
Shawn Lee
--
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RE: [R] Keeping factors with zero occurrences in table output
Ravi -- If you use table on a factor, you'll get 0's if appropriate: table(sample(1:5, 10, replace = TRUE)) #no 2's, by chance 1 3 4 5 3 1 2 4 table(sample(1:5, 20, replace = TRUE)) # no 6's here, so 6 doesn't show up 1 2 3 4 5 3 5 2 5 5 ## now make it a factor, and you get 0 3's and 0 6's table(factor(sample(1:5, 20, replace = TRUE), levels = 1:6)) 1 2 3 4 5 6 5 4 0 1 10 0 ## just happened to get no 3's in previous sample; it doesn't happen every time: table(factor(sample(1:5, 20, replace = TRUE), levels = 1:6)) 1 2 3 4 5 6 7 3 3 5 2 0 You can probably create the factor you want with interaction on participants and ranks. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ravi Varadhan Sent: Wednesday, April 20, 2005 11:38 AM To: r-help@stat.math.ethz.ch Subject: [R] Keeping factors with zero occurrences in table output Dear R group, I have a data frame which contains data on preferences on 7 items (ranks 1 through 7) listed by each participant. I would like to tabulate this in a 7x7 table where the rows would be the items and the columns would be the number of times that item received a particular rank. I tried doing this by creating a matrix by rbinding each vector obtained using table on each item. This, however, does not work because there are some items which didn't receive some of the ranks, so table does not list that item. Is there a way to force it to list the item and give a 0 to it? Or, is there a simpler way to solve this problem? Thanks for any help, Ravi. -- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] -- [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Storing vectors as vectors and iterating through them
Ken -- try using lists:
vec.list - list(1:5, 2:4, 3:8)
vec.list - c(vec.list, list(7:9))
vec.list
[[1]]
[1] 1 2 3 4 5
[[2]]
[1] 2 3 4
[[3]]
[1] 3 4 5 6 7 8
[[4]]
[1] 7 8 9
Then you can use lapply or sapply, or just a for loop, to iterate over
the list, applying your function to each element.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ken Termiso
Sent: Monday, April 18, 2005 1:09 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Storing vectors as vectors and iterating through them
Hi all,
I have a bunch of int vectors. Each vector holds a bunch of ints that
correspond to row numbers of an existing matrix. I use the int vectors to
pull out rows of data from a matrix, i.e.
data - my_matrix[int_vector,]
I would like to store these int vectors in some sort of data structure that
will preserve them as-is and allow iteration. I guess what I'm looking for
would be something analogous to the java Vector class, as in this java-like
pseudocode :
Vector V = new Vector;
V.add(a,b,c) // where a,b,c are lists
for(int i = 0; iV.size; i++)
{
List L = (List)Vector.get(i);
plot(L);
}
The point is to iterate through the data structure containing the int
vectors, and, for each int vector, do some clustering and plotting, but what
I cannot find is a data structure in R that would support this.. trying
c(a,b,c) does not preserve each int vector, but instead merges all the ints
into one vector. I need to keep them separate (so I can create a separate
plot for each vector).
Thanks in advance,
Ken
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RE: [R] ks.test for conditional distribution Y|x
Couldn't you do this by subtracting 0.5 + x from your y values and checking for normality with mean 0 and sd = 1 (using ks.test or another test of normality). If you fail, you'll have to do additional work to find out whether pairs with some particular x value (or range of x values) is causing the problem, but I think this fits the question as stated. Of course, if you have discrete x values, and enough data at each one, you could just run the check for each x. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Vicky Landsman Sent: Thursday, April 07, 2005 3:16 PM To: R-help list Subject: [R] ks.test for conditional distribution Y|x Dear experts, Is it possible to use ks.test function to check the goodness of fit of the conditional distribution Y|X=x? For example, I would like to check that my data (Y,X) come from Norm(0.5+x,1) using KS. Thank you in advance, Victoria Landsman. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R FAQ 2.8
I have used the R statistical computing environment. No-one has ever asked me to change it, but maybe someone else has something better. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robin Hankin Sent: Friday, April 01, 2005 8:30 AM To: R-help@stat.math.ethz.ch Subject: [R] R FAQ 2.8 Hi [thanks to everyone for advice on Recall() and sapply()] The R FAQ section 2.8 discusses how to cite R in publications, but does not (AFAICS) tell me how to describe R in a sentence. To wit, in my latest paper (destined for Rnews) one sentence reads: The R programming language (3) has been applied . . . where reference (3) is R Core 2004. Now, the referee has pointed out that the expression R computer language is not to be encouraged, as R is an implementation of the S language. How would the List rephrase my sentence above? I also use the phrase R code, which the referee flags for rewording (on similar grounds to the above). Any suggestions for this? -- Robin Hankin Uncertainty Analyst Southampton Oceanography Centre European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Non-linear minimization
I have had my best luck by re-parametrizing so that I no longer needed restrictions. For example, if parameters must be positive, then I optimize over parameters in log space, taking the exponential within my function. This requires small changes to the function I'm optimizing (and the gradient, if supplied), but, for me at least, has worked better than trying to enforce box constraints as in L-BFGS-B. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sébastien Ballesteros Sent: Tuesday, March 08, 2005 8:24 AM To: r-help@stat.math.ethz.ch Subject: [R] Non-linear minimization hello, I have got some trouble with R functions nlm(), nls() or optim() : I would like to fit 3 parameters which must stay in a precise interval. For exemple with nlm() : fn-function(p) sum((dN-estdata(p[1],p[2],p[3]))^2) out-nlm(fn, p=c(4, 17, 5), hessian=TRUE,print.level=2) with estdata() a function which returns value to fit with dN (observed data vactor) My problem is that only optim() allows me to set parameters interval with L-BFGS-B method but this one doesn't work in my case. I have heard about nls2 package (www.inra.fr/bia) but it doesn't work on Windows. Do you know any solutions Thank's a lot for reading my post Best regards Sebastien INA P-G ecology dpt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Creating a correlation Matrix
From the help for cor (from the stats package): If x and y are matrices then the covariances (or correlations) between the columns of x and the columns of y are computed. So if you make a matrix with each column corresponding to one of your variables, you can get what you're after. For future reference, help.search(correlation) turns up the proper page as the first suggestion. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jessica Higgs Sent: Monday, February 07, 2005 10:58 AM To: R-help@stat.math.ethz.ch Subject: [R] Creating a correlation Matrix Hi all: I have a question on how to go about creating a correlation matrix. I have a huge amount of data21 variables for 3471 times. I want to see how each of the variables correlate to each other. Any help would be appreciated, including which package and which functions I should use to do this. Thanks, Jessica Higgs Masters Student Department of Meteorology Penn State University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Creating a correlation Matrix
It looks like you have missing observations. With the use argument, you can specify complete observations or pairwise-complete observations. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jessica Higgs Sent: Monday, February 07, 2005 12:54 PM To: Spencer Graves; R-help@stat.math.ethz.ch Subject: Re: [R] Creating a correlation Matrix I've tried using cor() by the following sequence: C - cor(x, y = NULL, use = all.obs, method = c(pearson)) where x is my matrix of 21 columns and 3471 rows. and I get this error: Error in cor(x, y = NULL, use = all.obs, method = c(pearson)) : missing observations in cov/cor any suggestions? At 08:32 AM 2/7/2005 -0800, Spencer Graves wrote: Have you considered cor? The command 'help.search(correlation)' suggests among other functions var(stats), the documentation for which also includes cor. If this is not adequate, PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html . It may help you get more useful replies in the future. spencer graves Jessica Higgs wrote: Hi all: I have a question on how to go about creating a correlation matrix. I have a huge amount of data21 variables for 3471 times. I want to see how each of the variables correlate to each other. Any help would be appreciated, including which package and which functions I should use to do this. Thanks, Jessica Higgs Masters Student Department of Meteorology Penn State University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] two issues (black and white trellis graphics)
On the first issue, there's a recent post you can find in the archives. It's from Deepayan Sarkar on January 2 this year. It would probably pop up on a search for black white lattice or something similar. The key part of his answer: I'd do something like this as part of the initialization: ... library(lattice) ltheme - canonical.theme(color = FALSE) ## in-built BW theme ltheme$strip.background$col - transparent ## change strip bg lattice.options(default.theme = ltheme) ## set as default Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dean Sonneborn Sent: Thursday, February 03, 2005 2:53 PM To: R-help@stat.math.ethz.ch Subject: [R] two issues I'm working on a graphic but have run into a road block about two issues. I don't have a color printer so I want to produce the graphic in black and white. I'm currently using this statement trellis.device(bg=white) but the body of the graphic contains color. What is the code to create the whole thing in black and white. The other issue might be a bit more tricky. I'm using this statement: auto.key=TRUE and in the body of the graphic I'm getting two different symbols and on the screen I see two symbols in the key but when I print it the key only contains one symbol for both! here's the whole R code statement: dotplot(chemical~adjlogmle| convert*tdnew, data=allrisk , group=rodentx, main=Interspecies Conversion, pch=1:2, auto.key=TRUE, scales = list(tick.number=10), fontfamily = HersheySans) Thanks, Dean Sonneborn M.S. Public Health Sciences * University of California, Davis 916 734-6656 * formerly Epidemiology Preventive Medicine [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] how to use do.call(rbind, get(list(mlist)))
Roger -- First, if you have the data frames in a list already, you can just use those; no need to bother with the names. If the data frames are all separate, but you have the names, you can first create a list of the data frames themselves: do.call(rbind, lapply(mlist, get)) # assumes they're in the workspace An example: temp1 - matrix(runif(10), 5, 2) temp2 - matrix(-runif(10), 5, 2) (for easy identifiability) temp3 - do.call(rbind, lapply(c(temp1, temp2), get)) temp3 - do.call(rbind, list(temp1, temp2)) (same as above) Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of roger bos Sent: Friday, January 21, 2005 12:07 PM To: r-help@stat.math.ethz.ch Subject: [R] how to use do.call(rbind, get(list(mlist))) I have around 200 data frames I want to rbind in a vectorized way. The object names are: m302 m303 ... m500 So I tried: mlist - paste(m,302:500,sep=) dat - do.call(rbind, get(list(mlist))) and I get Error in get(x, envir, mode, inherits) : invalid first argument I know rbind is valid because dat - rbind(m302, m303, m304, m305) works, I am just too lazy to type it out to m500. I also tried it without the get() portion, but then dat ends up being a column with just the names of the objects, not the objects themselves. Thanks in advance for showing me the errors in my attempts. Roger __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Calculating a table of symbol frequencies
Kurt --
If you create a vector of alignment positions, you should be able to do
alignment.pos - rep(1:236, each = 72)
table(data.frame(as.vector(align1), alignment.pos))
You may want to coerce align1 to a factor with appropriate levels, in case
you are missing some amino acids. Otherwise there's an automatic coercion,
I believe, and you will use only the levels actually present in your data.
Here's an example using the first 10 letters of the alphabet instead of the
amino acid set:
align1 - matrix(sample(LETTERS[1:10], 200, replace = TRUE), nr = 5, nc =
40)
alignment.pos - rep(1:40, each = 5)
table(data.frame(as.vector(align1), alignment.pos))
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Wollenberg, Kurt R
Sent: Thursday, January 06, 2005 11:36 AM
To: 'r-help@stat.math.ethz.ch'
Subject: [R] Calculating a table of symbol frequencies
Hello all:
I have a protein sequence alignment in a data frame (align1, 72 x 236),
where each row is a protein and each column a site in the alignment. AA is
vector of amino acid symbols plus - (gap). I can calculate amino acid
frequencies at each site by:
align1.F - matrix(0,nrow=22,ncol=236,dimnames=list(AA,seq(1:236)))
for(i in 1:236)
align1.F[names(summary(align1[[i]])),i] -
(summary(align1[[i]])/length(align1[[i]]))
Is there a more efficient (i.e., without a loop) way to do this? Is there
some way to use table or ftable to create an 22 x 236 table of amino acid
frequencies from align1 and AA in one fell swoop?
Thanks,
Kurt Wollenberg, PhD
Tufts Center for Vision Research
New England Medical Center
750 Washington St, Box 450
Boston, MA, USA
[EMAIL PROTECTED]
617-636-8945 (Fax)
617-636-9028 (Lab)
The most exciting phrase to hear in science, the one that heralds new
discoveries, is not Eureka! (I found it!) but That's funny ...
--Isaac Asimov
**
Confidentiality Notice\ **\ The inf...{{dropped}}
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RE: [R] Replacing all NA values in a matrix
Michael -- is.na works on the full matrix. The commands below construct a matrix, insert some NA's, and then convert them all to 0. temp1 - matrix(runif(25), 5, 5) temp1[temp1 0.1] - NA temp1[is.na(temp1)] - 0 Hope this helps. Regards, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of michael watson (IAH-C) Sent: Wednesday, January 05, 2005 9:26 AM To: R-help@stat.math.ethz.ch Subject: [R] Replacing all NA values in a matrix OK, dumb question, and it is probably in the docs somewhere, but after 12 months working with R and quite a while looking at the docs, I still don't know (or have forgotten) how to replace all NA values in a matrix at once with some other value. I can do it column by column using is.na(), but I can't figure out how to do it for the whole matrix. My apologies, I am ashamed ;-) Michael Watson Head of Informatics Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire RG20 7NN UK Phone : +44 (0)1635 578411 ext. 2535 Mobile: +44 (0)7990 827831 E-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Massive clustering job?
It sounds like clara in package cluster might help. Regards, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dan Bolser Sent: Wednesday, December 15, 2004 6:37 AM To: R mailing list Subject: [R] Massive clustering job? Hi, I have ~40,000 rows in a database, each of which contains an id column and 20 additional columns of count data. I want to cluster the rows based on these count vectors. Their are ~1.6 billion possible 'distances' between pairs of vectors (cells in my distance matrix), so I need to do something smart. Can R somehow handle this? My first thought was to index the database with something that makes nearest neighbour lookup more efficient, and then use single linkage clustering. Is this kind of index implemented in R (by default when using single linkage)? Also 'grouping' identical vectors is very easy. I tried making groups more fuzzy by using a hashing function over the count vectors, but my hash was too crude. Any way to do fuzzy grouping in R which scales well? For example, removing identical vectors gives me ~30,000 rows (and ~900 million pairs of distances). As an example of how fast I can group, the above query took 0.13 seconds in mysql (using an index over every element in the vector). However, if I tried to calculate a distance between every pair of non identical vectors (lets say I can calculate ~1000 eutlidian distances per second) it would take me ~10 days just to calculate the distance matrix. Sorry for all the information. Any suggestions on how to cluster such a huge dataset (using R) would be appreciated. Cheers, Dan. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Logical and
Alexander -- a[!(a %in% b)] should do the trick. setdiff could also probably be used. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Alexander Sokol Sent: Thursday, November 11, 2004 8:34 AM To: [EMAIL PROTECTED] Subject: [R] Logical and Hello, I have the following very simple problem: Say I have two vectors, a-c(1,7,4,5,9,11) b-c(7,4,9) I would like to create a vector containing the elements in a which are not in b. Obviously, this is possible by writing a[a!=b[1] a!=b[2] a!=b[3]] But I would like a solution which is applicable to the situation where the number of elements in b is unknown. I have looked in the R manuals, the FAQ and the mailing lists, but have been unable to find a solution. Thank you for your replies, Alexander __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Quick data-manipulation question
Sean --
You want do.call(rbind, your.list.of.data.frames). do.call is helpful in
a lot of situations when you want to construct a list of arguments and then
apply a function.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sean Davis
Sent: Thursday, October 28, 2004 9:30 AM
To: r-help
Subject: [R] Quick data-manipulation question
I have a list of data frames and I want to concatenate them into a
single data frame, basically appending all of the data frames to each
other (they are all the same shape, in terms of columns). I'm looking
for a nice way to do that. I can of course just consecutively rbind
them to a master dataframe, but I have 22,000 such data frames, each
with a few hundred rows, so this process takes a good while. Should be
simple, I imagine
Here is a toy data structure.
j - list()
for (i in letters[1:26]) {j[[i]] -
data.frame(rep(i,25),matrix(rnorm(250),nrow=25))}
Thanks.
Sean
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RE: [R] graph question
Dean -- I believe just setting log = y in your plot command should do this. For example: plot(runif(100, 1, 100), runif(100, 1, 100), log = xy) gives me tick marks at 2, 5, 10, 20, 50, and 100. (YMMV because of the random numbers.) Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dean Sonneborn Sent: Tuesday, October 12, 2004 2:02 PM To: [EMAIL PROTECTED] Subject: [R] graph question I would like to produce a graph which plots a log scale variable on the y-axis but have the tick marks on the y-axis be the non log transformed values that are round like .5, 1, 2, 3, 4 etc. Has anyone done something like this in the past? How did you implement it in the code? Thanks, Dean __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R-(wiki)-pedia?
When you think there should be new links, or can offer an example you think would be clearer, it might be worth submitting a documentation modification proposal (through the bug tracking link on the R home page, for example). That would improve the basic documentation, which is what most people will see first. Regards, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dan Bolser Sent: Thursday, October 07, 2004 1:30 PM To: Gabor Grothendieck Cc: [EMAIL PROTECTED] Subject: Re: [R] R-(wiki)-pedia? On Wed, 6 Oct 2004, Gabor Grothendieck wrote: Dan Bolser dmb at mrc-dunn.cam.ac.uk writes: : : Is there an R wiki? : : Looking at the huge amount of traffic on this list, I think wiki could be : an exelet outlet for all the constructive enthusiasm here. : : I don't think it would be too hard to port the existing R documentation : (the stuff you get with the ?) onto a wiki system, then users could add : their own examples and comments. : : Having distinct web page style organization would be easier to navigate : than the mailing list archives. I like the online version of the R-docs, : but I miss 'user comments' and I miss being able to fix trivial things. : : The user contributed links could supply the best statistical online : resources to supplement the R-documentation, with links to the relevant : FAQ's and Tutorials supplementing the whole thing. : : Now I have said it this sounds too good to not exist already... Anyone : dumped the R-documentation onto a wiki system? : : Given the capability of R to be integrated into web pages, this could be : really really great. : : Cheers, : Dan. There is one at http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl?RwikiHome Unfortunately, no one seems to use it. I just added some pages... I think it would be great if people could get motivated to contribute to something like this. Its one of those cases of just getting the ball rolling... Do you think you can dump the existing R-docs into this wiki as a framework to get things going? So often I read the docks and think, now if only this linked here, and if only this example were more clear etc... After I solve my problem I want to fix the docs. Wiki would let me do that. How about you host a 'best diff in 30 days' competition each month, and winning contributors could be announced on the list? Can we integrate R-embedded web pages into the wiki? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] a little question about R
letters[1;4] LETTERS[1:4] for capitals. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, September 07, 2004 8:42 PM To: [EMAIL PROTECTED] Subject: [R] a little question about R Hello,sir: Here's a little question about R which needs your help.Thanks in advance. If I wanna make a sequence just like a,b,c,d (In other words,a vector consists of 4 characters :a,b,c,d ).How can I do it in a shortcut manner? Yes,I can do it as following: c(a,b,c,d) and the result is:[1] a b c d. But I remember there's a shortcut manner to do the same thing,something like c(a:d).But the system said:Error in a:d : NA/NaN argument So I wonder the correct method to do it(I remember the expression is very similar with c(a:d)). Thanks from the bottom of my heart. My best regards! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] for (i in ...) { df[[i]]- .....}
Take a look at do.call.
In your case, 'do.call(cbind, cc)' should work.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Luis Rideau Cruz
Sent: Friday, August 27, 2004 9:12 AM
To: [EMAIL PROTECTED]
Subject: [R] for (i in ...) { df[[i]]- .}
R-help,
In the following loop :
for(i in 1:8)
{
cc[[i]]-tapply(test[,i+6],list(puntar=test$puntar),sum)/tapply(test[,5],lis
t(puntar=test$puntar),sum)
cbind.data.frame(cc[[1]],cc[[2]],cc[[3]],cc[[4]],
cc[[5]],c[[6]],cc[[7]],cc[[8]])
}
Is there anyway I can 'cbind.data.frame' the objects cc[[ i ]] without
actually writing every single element??
In this case there are 8 but what if it is a large number??
Thank you
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RE: [R] Welch-JM-Test or Brown-Forsythe-Test in R?
Does oneway.test do what you want? Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sven Hartenstein Sent: Monday, June 21, 2004 3:23 PM To: [EMAIL PROTECTED] Subject: [R] Welch-JM-Test or Brown-Forsythe-Test in R? Hi, I want to test mean differences of 2 groups with heterogenous variances and wonder whether Welch-JM-Test and/or Brown-Forsythe-Test are available in R. (These two are the ones I found in the literature and SPSS provides, I'm open for alternatives.) Any help apreciated! Sven __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Sloppy argument checking for named arguments
Christian --
This is not a bug, but a feature, and the dot is not the issue here. R uses
partial argument matching on function arguments.
So:
f - function(foobar = 0){print(foobar)}
f
function(foobar = 0){print(foobar)}
f(fo=1)
[1] 1
f(foo=1)
[1] 1
f(foob=1)
[1] 1
f(fooba=1)
[1] 1
f(foon=1)
Error in f(foon = 1) : unused argument(s) (foon ...)
f(foobar2=1)
Error in f(foobar2 = 1) : unused argument(s) (foobar2 ...)
This is mentioned in Venables Ripley, MASS 4th edition on p. 55. I can't
find it right now in the Introduction to R that is linked to on the main
html help index page. However, it is discussed in the R Language
Definition you can get to from the same page.
It seems like there must be an easier path to the information that I haven't
thought of.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Thursday, June 03, 2004 12:20 AM
To: [EMAIL PROTECTED]
Subject: [R] Sloppy argument checking for named arguments
Dear R Gurus,
i recently noticed that R does sloppy argument checking for named
arguments, if the argument contains a dot.
Example:
f - function(foo.bar=0) { print(foo.bar) }
f(foo=1)
[1] 1
I guess, this should be considered as a bug.
Anyway, the consequence is that bugs caused by typing errors
of this kind may are *very* hard to discover in complex progams.
Christian
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RE: [R] type checking --- just a thought
Ivo --
The stopifnot statement can be used to do this sort of check. For
example, if you need to check that one of your arguments is a vector with
length = N, you can add
stopifnot(is.vector(myarg))
stopifnot(length(myarg) = N)
To the beginning of your function. This will throw an error if one of the
conditions is not met. The rest of your conditions can be checked
similarly.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of ivo welch
Sent: Friday, May 14, 2004 10:23 AM
To: [EMAIL PROTECTED]
Subject: [R] type checking --- just a thought
hi: would it be useful to build into R an optional mechanism that
typechecks arguments? for example,
sum.across - function ( inpmatrix : matrixtype( dim[1]1, dim[2]3
) ) : vector { }
# this would define a sum.across function that can take matrices
or data sets, but not vectors,
# and which indicates that it will return a vector.
xsum - sum.across( 1:10 ); # error
repeat - function( series : vector( dim0 ), times : scalar(
value0 ) ) : vector;
similarly, a common input error condition may be calling a function with
a NULL vector, or with a vector with fewer than N observations. many
statistical functions have such hard-wired limits. I know that if
statements can do this, but this might make for a nice standardized
language feature. on the other hand, the effort and complexity may not
be worth the extra functionality.
and one beg to the language maintainers for something that I hope is simple:
in R 1.8.2, please add to the source function information where
(file:linenumber) dies or ends.
regards,
/ivo
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[R] FW: Aligning different trellis plots
All --
I am trying to combine trellis plots and having a couple of small problems.
I'm trying to combine two trellis plots that display data of different
kinds. Each has a single row of plots, and I'd like to display them over
one another. So I use
print(plot1, split = c(1,1,2,1), more = TRUE)
print(plot2, split = c(1,2,1,2))
I end up with two minor issues. First, I'd like to have the top of the
bottom plot touch the bottom of the top plot, so it all looks like one plot
(I'd turn off the strip in the bottom one). I've turned off the x labels
and bottom axes for the top plot, but there still ends up being some space
between them. The effect I'm looking for is like setting various components
of mar to 0 in base graphics, but I can't figure out how to do it.
The second issue has to do with axes. My two plots have the same number of
panels across, and I would like them to line up vertically. However, my
y-axis labels, on the left of each plot, are slightly different size, and
this means that the panels are of slightly different sizes in the two plots.
Here's a toy example that shows my two problems.
df.1 - data.frame(x = rep(1:10, 5),
y = runif(50, 0, 10),
group = rep(1:5, each = 10))
df.2 - data.frame(x = rep(1:10, 5),
y = runif(50, -1, 1),
group = rep(1:5, each = 10))
plot.1 - xyplot(y ~ x | group, data = df.1,
scales = list(x = list(alternating = 0),
y = list(alternating= 1)),
xlab = , ## same results with
xlab = NULL
layout = c(5,1,1))
plot.2 - xyplot(y ~ x | group, data = df.2,
scales = list(alternating = 1),
layout = c(5,1,1))
print(plot.1, split = c(1,1,1,2), more = TRUE)
print(plot.2, split = c(1,2,1,2))
I realize that it could be the xlab = that is giving me trouble -- it may
still be reserving space. But xlab = NULL does the same thing, and I
haven't been able to find anything else to try.
One moderately ugly way to solve the problem is to use position instead of
split in the print statement for the trellis plots, and use overlapping
ranges to force the bottom of the top plot to line up with the top of the
bottom plot. But it would be nice to have something a little more
automatic.
Or is there some better way to do this altogether -- perhaps that would
force a single plot to contain two kinds of panels? That seems to really go
against the principle of lattice graphics, though.
Thanks for any help.
Regards,
Matt Wiener
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RE: [R] Readbin and file position
The seek command will allow you to skip to a particular byte position in
the file. You can define the position you want relative to your current
position, or to the start of the file.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jonathan Greenberg
Sent: Thursday, February 12, 2004 9:51 PM
To: R-help
Subject: [R] Readbin and file position
I have a binary file which is an image with multiple bands, arranged in BSQ
format such that R, B and G are all N x M sized matrices (corresponding to
Red, Blue and Green colors respectively). The BSQ file arranges the data as
[R, B, G], so to access the B matrix, I have to read forward N x M + 1
number of samples. Is there a fast way to define a variable as the B matrix
exclusively (e.g. Can I use readbin to fast forward N x M + 1 samples to
the beginning of the B matrix, and then read/define the B matrix
exclusively, or do I have to read the entire file into memory, then subset
out the B matrix?)
Thanks!
--j
--
Jonathan Greenberg
Graduate Group in Ecology, U.C. Davis
http://www.cstars.ucdavis.edu/~jongreen
http://www.cstars.ucdavis.edu
AIM: jgrn307 or jgrn3007
MSN: [EMAIL PROTECTED] or [EMAIL PROTECTED]
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RE: [R] Error in randomForest.default(m, y, ...) : negative lengt h vectors are not allowed
Christian -- You don't provide enough information (like a call) to answer this. I suspect, though, that you may be subsetting in a way that passes randomForest no data. I'm not aware offhand of an easy way to get this error from randomForest. I tried creating some data superficially similar to yours to see whether something would break if there were only a single value in the variable to be explained, but everything worked fine (though it does give a reasonable warning). test.dat - data.frame(a = rep(0, 1000), b = runif(1000), c = sample(0:1, 1000, replace = TRUE, p = c(.8, .2)) t8 - randomForest(a ~ b + c, data = test.dat) Warning message: The response has five or fewer unique values. Are you sure you want to do regression? in: randomForest.default(m, y, ...) test.dat[sample(1:1000, 100),a] - runif(100, 1, 200) t8 - randomForest(a ~ b + c, data = test.dat) Some other generated data might come up with the error, but I'd bet on the subsetting problem. Hope this helps, -Matt Matthew Wiener RY84-202 Applied Computer Science Mathematics Dept. Merck Research Labs 126 E. Lincoln Ave. Rahway, NJ 07065 732-594-5303 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Christian Schulz Sent: Wednesday, December 03, 2003 9:42 AM To: [EMAIL PROTECTED] Subject: [R] Error in randomForest.default(m, y, ...) : negative length vectors are not allowed Hi, what i'm doing wrong? I'm using a data.frame with ~ 90.000 instances and 7 attributes, 5 are binary recoded 1 independend variable are a real one and the target is a real one,too. The distributions are not very skewed in the dummy variables ,but in the real variables are ~ 60.000 zero values instances, but zero means no money is payed and is a important value! Many thanks for help suggestions, regards,christian __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] add a point to regression line and cook's distance
If you know that the line should pass through (0,0), would it make sense to do a regression without an intercept? You can do that by putting -1 in the formula, like: lm(y ~ x - 1). Hope this helps, Matt Matthew Wiener RY84-202 Applied Computer Science Mathematics Dept. Merck Research Labs 126 E. Lincoln Ave. Rahway, NJ 07065 732-594-5303 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Spencer Graves Sent: Wednesday, December 03, 2003 5:51 PM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Subject: Re: [R] add a point to regression line and cook's distance What is the context? What do the outliers represent? If you think carefully about the context, you may find the answer. hope this helps. spencer graves p.s. I know statisticians who worked for HP before the split and who still work for either HP or Agilent, I'm not certain which. If you want to contact me off-line, I can give you a couple of names if that might help. [EMAIL PROTECTED] wrote: Hi, This is more a statistics question rather than R question. But I thought people on this list may have some pointers. MY question is like the following: I would like to have a robust regression line. The data I have are mostly clustered around a small range. So the regression line tend to be influenced strongly by outlier points (with large cook's distance). From the application 's background, I know that the line should pass (0,0), which is far away from the data cloud. I would like to add this point to have a more robust line. The question is: does it make sense to do this? what are the negative impacts if any? thanks, jonathan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Questions on Random Forest
It looks like image_and_label has only 2 columns, so when you take img_and_label[,2] you have a vector left. Even if that weren't the case, you're going to need to pass in both the gray scale points and labels, presumably in a data frame. You've created a character matrix below, so you're just passing in a character vector of labels. You'll probably want something like rf - randomForest(label~image,data=image_and_label,importance=TRUE, proximity=TRUE), assuming that image_and_label is a data frame with elements image and label. For the second question, see the documentation for the predict method for random forests; for the third, the answer is yes, random forests can be used with multiple variables. There is an introduction to the random forests package in volume 2, issue 3 of the R newsletter (available in the documentation section of cran). Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Fucang Jia Sent: Monday, November 24, 2003 10:31 AM To: [EMAIL PROTECTED] Subject: [R] Questions on Random Forest Hi, everyone, I am a newbie on R. Now I want to do image pixel classification by random forest. But I has not a clear understanding on random forest. Here is some question: As for an image, for example its size is 512x512 and has only one variable -- gray level. The histogram of the image looks like mixture Gaussian Model, say Gauss distribution (u1,sigma1), (u2,sigma2),(u3,sigma3). And a image classified by K-means or EM algorithm, so the class label image is also 512x512 and has 0, 1, 2 value. I read the binary image data as follows: datafile - file(bone.img,rb) img - readBin(datafile,size=2,what=integer,n=512*512,signed=FALSE) img - as.matrix(img) close(datafile) labelfile - file(label.img,rb) label - readBin(labelfile,size=2,what=integer,n=512*512,signed=FALSE) label - as.matrix(label) close(labelfile) img_and_label - c(img,label) // binds the image data and class label img_and_label - as.matrix(img_and_label) img_and_label - array(img_and_label, dim=c(262144,2)) Random Forest need a class label like Species in the iris. I do not know how to set a class label like Species to the img. So I run the command as follows: set.seed(166) rf - randomForest(img_and_label[,2],data=image_and_label,importance=TRUE, proximity=TRUE) which outputs: Error in if (n == 0) stop(data (x) has 0 rows) : argument is of length zero Could anyone tell what is wrong and how can do the RF? Secondly, if there is an new image , say img3 (dimension is 512x512,too), how can I use the former result to classifify the new image? Thirdly, whether or not random forest be used well if there is only one variable, say pixel gray level, or three variables, such as red, green, blue color component to an true color image? Thank you very much! Best, Fucang Fucang Jia, Ph.D student Institute of Computing Technology, Chinese Academy of Sciences Post.Box 2704 Beijing, 100080 P.R.China E-mail:[EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] 64-bit R on AIX?
R-helpers -- Has anyone gotten R to compile as a 64-bit application on AIX 5L (or any other version)? (I don't have the details of the errors here, as I'm not the person actually doing the compiling. I might be able to get them if someone wants to see them in particular.) Thanks for any help. Matthew Wiener RY84-202 Applied Computer Science Mathematics Dept. Merck Research Labs 126 E. Lincoln Ave. Rahway, NJ 07065 732-594-5303 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] newby problem - concatenate lists
c(x,y) will do it. Hope this helps -Matt -Original Message- From: Axel Benz [mailto:[EMAIL PROTECTED] Sent: Friday, September 19, 2003 8:57 AM To: [EMAIL PROTECTED] Subject: [R] newby problem - concatenate lists Hi, a very basic question: What ist the easiest way in R to concatenate two lists of vectors? E.g, I have x-list(c(1,2)) y-list(c(3,4)) and I want to receive list(c(1,2),c(3,4)) thank you! Axel Fraunhofer Institut fuer Arbeitswirtschaft und Organisation (IAO) Dipl. Inf. Axel Benz Nobelstr. 12 D-70569 Stuttgart Germany Tel. +49(0)7119702289 Fax. +49(0)7119702192 mail: mailto:[EMAIL PROTECTED] www: http://www.vis.iao.fhg.de [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Getting 2 kinds of quotes inside a pasted string
Hi, all.
I would like to use pipe to run a file through an awk program before
scanning (to reduce the amount of data I'll be taking in). I would like to
construct the awk program in R, and also to be able to set the awk variable
FS, to accommodate different field separators in different files.
My problem is that I keep getting the quotes escaped in the string that
comes out, and that sets the field separator to something different.
What I'd like to end up with is something like:
awk 'BEGIN{FS=;}'
If I can get this, I can put the rest of the awk program together. What I
actually keep getting is
awk 'BEGIN{FS=\;\}'.
That is, the quote characters are escaped.
I can print this with quote = FALSE, and get the string I'm looking for.
But when I paste that into the larger awk program, the quotes are
nonetheless escaped (presumably because the print, quote = FALSE affects
only display and not the internal structure).
I've also tried sprintf, but run into the same problem. I'd very much
appreciate it if someone could show me how to create the string I'm looking
for, or tell me a better way to go about filtering the file in the first
place. I'd prefer not to scan in everything and do the subsetting in R; the
files I'm using are very large, and the whole point is not to have to load
the whole file into memory.
Thanks very much,
Matthew Wiener
RY84-202
Applied Computer Science Mathematics Dept.
Merck Research Labs
126 E. Lincoln Ave.
Rahway, NJ 07065
732-594-5303
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RE: [R] Variance Computing- - HELP!!!!!!!!!!!!!!!!!!
Hi.
There is no reason the variance of a normal should decrease as you take
larger samples. Indeed, in your call itself, you say that you want a sample
from a normal with a standard deviation of 3, and so a variance of 9. As
expected, both of your estimates of variance are close to 9.
What should decrease is the variance of the estimate of the mean, which is
the variance of the sample divided by the number of elements in your sample.
That will indeed decrease as n increases.
Also, a couple of R programming points raised by your example:
You can populate your entire matrix of random numbers with a single call,
with good time savings. (That probably doesn't matter much in this toy
example, but might if you do larger simulations for some problem.)
For example: matrix(rnorm(10, 0, 3), nr = 100, nc = 1000) gets you your
matrix small.
Similarly, your loop over the rows for taking variance can be replaced by
yy - apply(small, 1, var)
Which may not be faster, but is certainly easier to read. And of course
you'd want to replace the call to var with a function that calculates
standard error.
Hope this helps,
Matt Wiener
-Original Message-
From: Padmanabhan, Sudharsha [mailto:[EMAIL PROTECTED]
Sent: Tuesday, August 19, 2003 1:43 PM
To: [EMAIL PROTECTED]
Subject: [R] Variance Computing- - HELP!!
Hello,
I am running a few simulations for clinical trial anlysis. I want some help
regarding the following.
We know trhat as the sample size increases, the variance should decrease,
but
I am getting some unexpected results. SO I ran a code (shown below) to check
the validity of this.
large-array(1,c(1000,1000))
small-array(1,c(100,1000))
for(i in 1:1000){large[i,]-rnorm(1000,0,3)}
for(i in 1:1000){small[i,]-rnorm(100,0,3)}}
yy-array(1,100)
for(i in 1:100){yy[i]-var(small[i,])}
y1y-array(1,1000)
for(i in 1:1000){y1y[i]-var(large[i,])}
mean(yy);mean(y1y);
[1] 8.944
[1] 9.098
This shows that on an average,for 1000 such samples of 1000 Normal numbers,
the variance is higher than that of a 100 samples of 1000 random numbers.
Why is this so?
Can someone please help me out
Thanks.
Regards
~S.
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RE: [R] exporting help
Perhaps you should read one of the introductory manuals in the Contributed
Documentation section of cran.us.r-project.org. This will introduce many
of the basic commands, and save you time and frustration.
You will probably end up wanting to use either read.table or scan to get
your data into R.
Hope this helps,
Matt Wiener
-Original Message-
From: Ashley Minor [mailto:[EMAIL PROTECTED]
Sent: Tuesday, July 08, 2003 4:17 PM
To: [EMAIL PROTECTED]
Subject: [R] exporting help
i need step by step directions on how to export a text file into the r
file
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RE: [R] cumulative frequency distribution plot
You can also take a look at ecdf in the stepfun package.
Hope this helps,
Matt
-Original Message-
From: Spencer Graves [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 24, 2003 2:39 PM
To: Tommy E. Cathey
Cc: [EMAIL PROTECTED]
Subject: Re: [R] cumulative frequency distribution plot
It depends on what you mean by that. Consider the following:
x - rnorm(100)
plot(x, pnorm(x))
This plot is a cdf of pseudo-normal data.
I've seen many people make these things, and I've never understoon
what they see in these plots that they can't see better in a normal
probability plot:
qqnorm(x, datax=T)
What can you see in the first type plot that is not so easily seen
in
the second?
Spencer Graves
Tommy E. Cathey wrote:
Does R do cumulative frequency distribution plots?
--
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High Performance Computing Scientific Visualization
SAIC, Supporting the EPA
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RE: [R] Combining the components of a character vector
The collapse argument does what you want:
x - c(Bob, loves, Sally)
paste(c, collapse = )
Hope this helps,
Matt Wiener
-Original Message-
From: John Miyamoto [mailto:[EMAIL PROTECTED]
Sent: Wednesday, April 02, 2003 6:54 PM
To: R discussion group
Subject: [R] Combining the components of a character vector
Dear Help,
Suppose I have a character vector.
x - c(Bob, loves, Sally)
I want to combine it into a single string: Bob loves Sally .
paste(x) yields:
paste(x)
[1] Bob loves Sally
The following function combines the character vector into a string in the
way that I want, but it seems somewhat inelegant.
paste.vector - function(x, ...) {
output - NULL
for (i in 1:length(x)) output - paste(output, x[i], ...)
output } #end of function definition
paste.vector(x)
[1] Bob loves Sally
Is there a more natural (no loop) way to do this in R?
John Miyamoto
John Miyamoto, Dept. of Psychology, Box 351525
University of Washington, Seattle, WA 98195-1525
Phone 206-543-0805, Fax 206-685-3157, Email [EMAIL PROTECTED]
Homepage http://faculty.washington.edu/jmiyamot/
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RE: [R] cdf function: inverse to quantile?
Take a look at ecdf in package stepfun. -Original Message- From: DED (David George Edwards) [mailto:[EMAIL PROTECTED] Sent: Thursday, April 03, 2003 6:20 AM To: '[EMAIL PROTECTED]' Subject: [R] cdf function: inverse to quantile? Is there a function in R for calculating empirical cumulative distribution functions, i.e. the inverse of the quantile function? Perhaps in some library? I'd hate to have to re-invent the wheel. David Edwards, Biostatistics, Novo Nordisk A/S, Bagsværd, Denmark. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Tlf: +45 44 42 62 35. Fax: +45 44 42 14 80 [[alternate HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] a statistic question about chisq.test()
One other option. I usually find that when I do the chisq.test with exact p-value calculation, I find the p-values are nearly identical to the results when I use the approximation and get the warnings (I'm usually dealing with just a few bins with less than 5, and many bins with more than 5). So frequently, when I'm using chisq.test in a program, and expect to do it many times, I'll sometimes eliminate the warnings this way: old.warn - options()$warn options(warn = -1) do the chisq.test here options(warn = old.warn) This will suppress the warning messages. Hope this helps. Matt Wiener -Original Message- From: Uwe Ligges [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 26, 2003 4:24 PM To: aprilsun Cc: [EMAIL PROTECTED] Subject: Re: [R] a statistic question about chisq.test() aprilsun wrote: Hi, In the chisq.test(), if the expected frequency for some categories is 5, there will be a warning message which says Warning message: Chi-squared approximation may be incorrect in: chisq.test(x, p = probs) It's a warning message, not an error. It point's you to the problem that a number 5 is not large, whereas in theory large numbers are assumed when running this test. I am wondering whether there are some methods to get rid of this mistake... Seems the ?chisq.test() doesn't provide more options to solve this problem. Or, the only choice is to preprocess the data to avoid this situation? It depends on the problem. Fisher's exact test (or it's extended version) might be an alternative, see ?fisher.test and an appropriate statistics textbook. Uwe Ligges Thanks a lot! aprilsun __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] manipulating ... inside a function
As Brian Ripley pointed out in a recent post, you can just give g() its own
... argument.
Regards,
Matt Wiener
-Original Message-
From: Liaw, Andy [mailto:[EMAIL PROTECTED]
Sent: Friday, March 21, 2003 3:37 PM
To: '[EMAIL PROTECTED]'
Subject: [R] manipulating ... inside a function
Dear R-help,
Can some one tell me how to do the following (if it's possible)?
Suppose I have a function like this:
f - function(x, y, ...) {
## some code
g(x, y, ...)
## some more code
}
The problem is that g() may not understand everything that comes through in
Is there a way to delete some component of ... and then pass it to
g()?
Here's the description of the real problem: f() is a panel.something
function, and g() is a model fitting function. Lattice passes
panel.number as part of ... to f(), and g() complains about unused
argument panel.number.
I'd be very grateful for any help!
Cheers,
Andy
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RE: [R] r-help using random generating
You can save some time by generating all your samples at one time: t1 - matrix(rnorm(5 * n, 100, 10), nc = n) apply(t1, 2, mean) (Or use colVars and colMeans to save even more time) Hope this helps, Matt Wiener -Original Message- From: Cheryl H. [mailto:[EMAIL PROTECTED] Sent: Tuesday, March 18, 2003 11:26 PM To: [EMAIL PROTECTED] Subject: [R] r-help using random generating To whom it may concern: Given that my sample size is n, my mean is 100, and my sd is 10, I need to use a random number generator (which I believe is the function rnorm(5,100,10)), but I need to repeat it a large number of times, and then plot the sampling distributions of the sample means, sd's, and variances of those generated sets. I'm having a real hard time trying to figure out how to do this easily. Please help if possible! Thanks, Cheryl __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] multidimensional function fitting
Take a look at package mgcv. Hope this helps. --Matt -Original Message- From: RenE J.V. Bertin [mailto:[EMAIL PROTECTED] Sent: Thursday, February 27, 2003 1:39 PM To: [EMAIL PROTECTED] Subject: [R] multidimensional function fitting Hello, I have been looking around for how to perform a multidimensional, arbitrary function fit (in any case non-linear; more below), but haven't found anything yet on how to accomplish this. I found some references to the funfits package (that apparently is now called fields), but as far as I have understood it, it does not do what I need. Basically, I have a set of data that describe some measured, dependent variable as a function of a number of controlled variables, in casu z=f(x,y). What I need is to obtain some f that reliably describes my data on the range of controlled variables. (This is for inverse-filtering in a visual stimulus programme, so I don't really care about the form of f as long as it is reasonably simple to implement -- i.e. a spline surface would not be ideal in the context ;^). ) Clearly, something like fit-lm(z~x+y+x*y+x*x+y*y, data) does not give the result I want. Is there a package somewhere that allows to do this sort of operation? Like a multidimensional version of polyreg()? Thanks in advance, RenE Bertin __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] help on cut?
cut returns a factor. Try something like t1 - cut(data.vector, breaks = my.breaks, labels = my.label) as.numeric(as.character(t1)) This is an issue that comes up frequently with factor. Take a look at the help page for factor for some warnings. Hope this helps, Matt Wiener -Original Message- From: Nina Wawro [mailto:[EMAIL PROTECTED]] Sent: Wednesday, January 29, 2003 11:39 AM To: R-help Subject: [R] help on cut? Dear R-users, I'm trying to recode a variable. After using cut(data.vector,breaks=my.breaks,labels=my.label) I need the data.vector to have the same values as the labels. To make it clear: x-runif(10) y-cut(x,breaks=c(0,0.3,0.7,0.9,1),labels=c(3,6,7,9)) as.numeric(y) returns something like a vector 1 3 3 2 2 1 4 2 3 4 . I need something like 3 7 7 6 6 3 7 9 6 7 9 for further use. I might be using the wrong function but a loop seems to be inefficient as I need to do it about 60 times with varying length of labels Is there a quick solution? Thanks for any help in advance! Nina Wawro R.1.6.0 on Windows2000 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
