date:20110921


Dear users,

I have already sent this email last week, but haven't received an 
answer. So here is my second try.


By running the script below, R crashes systematically at the last 
command, namely dev.off(), on Windows 7, but not on Windows XP.
I therefore don't provide a reproducible example and do not really 
extract the relevant parts of the script because it has most likely 
nothing to do with the script itself. I can do it though if you think it 
might be relevant.


R crashes on Windows 7, sessionInfo():
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] splines   stats graphics  grDevices utils datasets  methods
[8] base
other attached packages:
[1] doBy_4.4.0 MASS_7.3-13snow_0.3-7 
lme4_0.999375-41
[5] Matrix_0.9996875-3 lattice_0.19-30multcomp_1.2-7 
mvtnorm_0.9-9991

[9] R2HTML_2.2 survival_2.36-9RSvgDevice_0.6.4.1 R.utils_1.7.8
[13] R.oo_1.8.1 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] grid_2.13.1   nlme_3.1-101  stats4_2.13.1


But it works perfectly on Windows XP, sessionInfo():
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] splines   stats graphics  grDevices utils datasets  methods
[8] base
other attached packages:
[1] doBy_4.4.0 MASS_7.3-14snow_0.3-6 
lme4_0.999375-41
[5] Matrix_0.9996875-3 lattice_0.19-33multcomp_1.2-7 
mvtnorm_0.9-9991

[9] R2HTML_2.2 survival_2.36-9RSvgDevice_0.6.4.1 R.utils_1.7.8
[13] R.oo_1.8.1 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] grid_2.13.1   nlme_3.1-102  stats4_2.13.1

Except the locale, I don't see any difference and I don't really 
understand how that would make R crash by running dev.off(). I would 
guess that the problem comes from RSvgDevice on Windows 7. Can someone 
help me to solve this issue?


Thank you for your help,
Ivan



 script -
library(R.utils)
library(RSvgDevice)
library(doBy)
primate_med - loadObject(primate_med.Rbin)

select - primate_med
seq.yvar - c(5,12,8,9)
ind.xvar - 4

filename - paste(regression, names(datobj)[ind.xvar], 
paste(names(datobj)[seq.yvar],collapse=_), 
paste(selvarstr,collapse=_), sep=_) filename - gsub(.median, , 
filename)


select_mean - 
summaryBy(as.formula(paste(.~,names(select)[ind.xvar])), data=select, 
FUN=mean)


devSVG(file=paste(filename, .svg, sep=))
par(mfrow=c(2,2))
diff_len - length(select)-length(select_mean)

for (i in seq_along(seq.yvar)){
  k - seq.yvar[i]
  plot(select[[k]]~select[[ind.xvar]], type=p, pch=1, 
xlab=names(select)[ind.xvar], ylab=names(select)[k], las=1)
  points(select_mean[[ind.xvar-diff_len]], select_mean[[k-diff_len]], 
pch=18, cex=2)

  two_reg(dat=select, xvar=ind.xvar, yvar=k)
}

dev.off()
-

--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php

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Re: [R] tcltk freezes R

2011-09-21 Thread Prof Brian Ripley


On Tue, 20 Sep 2011, tm wrote:


Hi there,

I have the following problem on my macbook air with mac os x lion on it.
when any program tries to load the tcltk library the R GUI or R command line
freezes. also happens if I just use library(tcltk)

changing versions of tcltk and/or R doesn't help. currently I have the
following:
R version 2.13.2 beta (2011-09-19 r57030)


Pre-built or built youself?


tcltk 8.5.10

any suggestions?


Use the recommended version of Tcl/Tk at 
http://cran.r-project.org/bin/macosx/tools/
(which is 8.5.5: and uses X11 not Aqua: I use Aqua Tcl/Tk with 
command-line R).


And please do as you were asked and use r-sig-mac for OS X-specific 
questions.




thanks a lot already,
t.

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

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Re: [R] ARIMA - Skipping intermediate lags

2011-09-21 Thread Prof Brian Ripley


On Tue, 20 Sep 2011, leighton155 wrote:


Hello,

I am a new R user.  I am trying to use the arima command, but I have a
question on intermediate lags.  I want to run in R the equivalent Stata
command of ARIMA d.yyy, AR(5) MA(5 7).  This would tell the program I am
interested in AR lag 5, MA lag 5, and MA lag 7, all while skipping the
intermediate lags of AR 1-4, and MA 1-4, 6.  Is there any way to do this in
R?  Thank you.


Yes.  See the 'fixed' argument on the help page.  Note that this is 
not recommended in general 




--
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__
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and provide commented, minimal, self-contained, reproducible code.



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

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[R] Problem with predict and lines in plotting binomial glm

2011-09-21 Thread Heystek, A, Me 15418...@sun.ac.za

Problems with predict and lines in plotting binomial glm
Dear R-helpers

I have found quite a lot of tips on how to work with glm through this mailing 
list, but still have a problem that I can't solve.
I have got a data set of which the x-variable is count data and the y-variable 
is proportional data, and I want to know what the relationship between the 
variables are.
The data was overdispersed (the residual deviance is much larger than the 
residual degrees of freedom) therefore I am using the quasibinomial family, 
thus the y-variable is a matrix of successes and failures (20 trials for every 
sample, thus each y-variable row counts up to 20).

x - c(1200, 1200, 1200, 1200, 1200, 1200, 1200, 1200, 1800, 1800, 1800, 1800, 
1800, 1800, 1800, 1800, 1800, 2400, 2400, 2400, 2400, 2400, 2400, 2400, 3000, 
3000, 3600, 3600, 3600, 3600, 4200, 4200, 4800, 4800, 5400, 6600, 6600, 7200, 
7800, 7800, 8400, 8400, 8400, 9000, 9600, 10200, 13200, 18000, 20400, 24000, 
25200, 36600)
successes - c(6, 16, 11, 14, 11, 16, 13, 13, 14, 16, 12, 12, 11, 15, 12, 9, 7, 
7, 17, 15, 13, 9, 9, 12, 14, 8, 9, 16, 7, 9, 14, 11, 8, 8, 13, 6, 16, 11, 9, 7, 
9, 8, 4, 14, 7, 3, 3, 9, 12, 8, 4, 6)
failures - c(14, 4, 9, 6, 9, 4, 7, 7, 6, 4, 8, 8, 9, 5, 8, 11, 13, 13, 3, 5, 
7, 11, 11, 8, 6, 12, 11, 4, 13, 11, 6, 9, 12, 12, 7, 14, 4, 9, 11, 13, 11, 12, 
16, 6, 13, 17, 17, 11, 8, 12, 16, 14)
y - cbind(successes, failures)
data - data.frame(y, x)

glm1 - glm(y ~ x, family= quasibinomial, data= data)
glm2 - glm(y ~ log(x), family=quasibinomial, data= data) # residual 
deviance is lower with log transformed x-value
plot(x, successes)
lines(x, predict(glm1, type= response), lwd=2)




Firstly, because of the skewed distribution of the x variable I am not sure 
whether it should be log transformed or not.  When I do log transform it, the 
residual deviance and the p-value for the slope is lower.
Either way, the lines command does not plot any line and neither does it give 
any error messages.  On some of my other data it plots a line way below all the 
data points.  From what I can gather, the predict function as it is now uses 
the fitted values because no newdata argument is specified. I want the line to 
be predicted from the same x-values.  I tried two ways of adding the newdata 
argument:

## a data.frame using the original x-values
lines(x, predict(glm2, type= response, newdata= as.data.frame(x)))
##  or a data.frame with values (the same length as y) from the range of x 
values
newdf - data.frame(seq(min(x), max(x), length=52))
lines(x, predict(glm2, type=response, newdata= newdf))

Only the second option plotted a line once, but then I could never get it to do 
the same again on a new plot even though I used the same variables and same 
code.


Thank you very much for your time and patient
Anina Heystek

BSc Honours student
Department of Botany and Zoology
University of Stellenbosch, Stellenbosch, South Africa
15418...@sun.ac.za



[[alternative HTML version deleted]]

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Re: [R] R crash

2011-09-21 Thread Barry Rowlingson

On Wed, Sep 21, 2011 at 8:57 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de wrote:
 Dear users,

 I therefore don't provide a reproducible example and do not really extract
 the relevant parts of the script because it has most likely nothing to do
 with the script itself. I can do it though if you think it might be
 relevant.

 In which case you could reduce your code to something we can all try
- does this crash for you:

library(RSvgDevice)
devSVG(file=foo.svg)
plot(1:10)
dev.off()

 - if not then something I've taken from your script is causing the
problem. Add bits back until it crashes.

 - if it does still crash then its likely a fundamental devSVG
problem, and you've now got something that hundreds of people reading
this can just cut n paste and go 'me too' or 'crashes for me'.

Barry

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[R] R CMD build and vignettes

2011-09-21 Thread Ashim Kapoor

Dear R-helpers,

www.statistik.lmu.de/~*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf

says that  R CMD build creates the pdf from a .Rnw file. But when I do R CMD
build followed by R CMD check it gives me a warning that there is a vignette
without a PDF. My query is : when
R CMD build works it creates a pdf in the doc subdirectory of the directory
returned by system.file(package = mypackage) and not in the inst/doc
directory of the package that we are creating. Do we have to Sweave and
create the pdf in the inst/doc subdirectory on our own ? Please clarify.

Regards,
Ashim

[[alternative HTML version deleted]]

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Re: [R] R crash


Dear Barry,

Thanks for your input, that is indeed a very good idea (shame on me not 
to have thought about it...).


As expected, it works fine on Windows XP, but crashes on Windows 7 at 
dev.off (which means that the svg file is correctly created, but R 
crashes every time, a bit annoying). This is therefore a devSVG problem 
on Windows 7.


Now, does anyone know how to fix this?

TIA,
Ivan

Le 9/21/2011 10:34, Barry Rowlingson a écrit :

On Wed, Sep 21, 2011 at 8:57 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de  wrote:

Dear users,
I therefore don't provide a reproducible example and do not really extract
the relevant parts of the script because it has most likely nothing to do
with the script itself. I can do it though if you think it might be
relevant.

  In which case you could reduce your code to something we can all try
- does this crash for you:

library(RSvgDevice)
devSVG(file=foo.svg)
plot(1:10)
dev.off()

  - if not then something I've taken from your script is causing the
problem. Add bits back until it crashes.

  - if it does still crash then its likely a fundamental devSVG
problem, and you've now got something that hundreds of people reading
this can just cut n paste and go 'me too' or 'crashes for me'.

Barry



--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php

__
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Re: [R] Problem with predict and lines in plotting binomial glm

2011-09-21 Thread Eik Vettorazzi

Hi Anina,
predict.glm returns predicted probabilities, when used with
type=response, so you have to either scale the probs to the number of
trials for any x or you plot probs from start:

par(mfcol=c(1,2))
plot(x, successes)
lines(x, (successes+failures)*predict(glm1, type= response), lwd=2)
plot(x, successes/(successes+failures))
lines(x, predict(glm1, type= response), lwd=2)

If you use predict with new data, please name the rows accordingly, when
you actually want to use them:

newdf - data.frame(seq(min(x), max(x), length=20))
#you would expect 20 predictions, but *surprise* you get
length(predict(glm2, type=response, newdata= newdf)) #52!
newdf - data.frame(x=seq(min(x), max(x), length=20))
length(predict(glm2, type=response, newdata= newdf)) #ok

And you should use the appropriate x in lines as well:

plot(x,successes/(successes+failures))
lines(newdf$x, predict(glm2, type=response, newdata= newdf),col=red)

Cheers

Am 21.09.2011 09:55, schrieb Heystek, A, Me 15418...@sun.ac.za:
 Problems with predict and lines in plotting binomial glm
 Dear R-helpers
 
 I have found quite a lot of tips on how to work with glm through this mailing 
 list, but still have a problem that I can't solve.
 I have got a data set of which the x-variable is count data and the 
 y-variable is proportional data, and I want to know what the relationship 
 between the variables are.
 The data was overdispersed (the residual deviance is much larger than the 
 residual degrees of freedom) therefore I am using the quasibinomial family, 
 thus the y-variable is a matrix of successes and failures (20 trials for 
 every sample, thus each y-variable row counts up to 20).
 
 x - c(1200, 1200, 1200, 1200, 1200, 1200, 1200, 1200, 1800, 1800, 1800, 
 1800, 1800, 1800, 1800, 1800, 1800, 2400, 2400, 2400, 2400, 2400, 2400, 2400, 
 3000, 3000, 3600, 3600, 3600, 3600, 4200, 4200, 4800, 4800, 5400, 6600, 6600, 
 7200, 7800, 7800, 8400, 8400, 8400, 9000, 9600, 10200, 13200, 18000, 20400, 
 24000, 25200, 36600)
 successes - c(6, 16, 11, 14, 11, 16, 13, 13, 14, 16, 12, 12, 11, 15, 12, 9, 
 7, 7, 17, 15, 13, 9, 9, 12, 14, 8, 9, 16, 7, 9, 14, 11, 8, 8, 13, 6, 16, 11, 
 9, 7, 9, 8, 4, 14, 7, 3, 3, 9, 12, 8, 4, 6)
 failures - c(14, 4, 9, 6, 9, 4, 7, 7, 6, 4, 8, 8, 9, 5, 8, 11, 13, 13, 3, 5, 
 7, 11, 11, 8, 6, 12, 11, 4, 13, 11, 6, 9, 12, 12, 7, 14, 4, 9, 11, 13, 11, 
 12, 16, 6, 13, 17, 17, 11, 8, 12, 16, 14)
 y - cbind(successes, failures)
 data - data.frame(y, x)
 
 glm1 - glm(y ~ x, family= quasibinomial, data= data)
 glm2 - glm(y ~ log(x), family=quasibinomial, data= data) # residual 
 deviance is lower with log transformed x-value
 plot(x, successes)
 lines(x, predict(glm1, type= response), lwd=2)
 
 
 
 
 Firstly, because of the skewed distribution of the x variable I am not sure 
 whether it should be log transformed or not.  When I do log transform it, the 
 residual deviance and the p-value for the slope is lower.
 Either way, the lines command does not plot any line and neither does it give 
 any error messages.  On some of my other data it plots a line way below all 
 the data points.  From what I can gather, the predict function as it is now 
 uses the fitted values because no newdata argument is specified. I want the 
 line to be predicted from the same x-values.  I tried two ways of adding the 
 newdata argument:
 
 ## a data.frame using the original x-values
 lines(x, predict(glm2, type= response, newdata= as.data.frame(x)))
 ##  or a data.frame with values (the same length as y) from the range of x 
 values
 newdf - data.frame(seq(min(x), max(x), length=52))
 lines(x, predict(glm2, type=response, newdata= newdf))
 
 Only the second option plotted a line once, but then I could never get it to 
 do the same again on a new plot even though I used the same variables and 
 same code.
 
 
 Thank you very much for your time and patient
 Anina Heystek
 
 BSc Honours student
 Department of Botany and Zoology
 University of Stellenbosch, Stellenbosch, South Africa
 15418...@sun.ac.za
 
 
 
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Department of Medical Biometry and Epidemiology
University Medical Center Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/7410-58243
F ++49/40/7410-57790

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Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 

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[R] Poisson-Gamma computation (parameters and likelihood)

2011-09-21 Thread Sebastiano Putoto

Good afternoon/morning readers. This is the first time I am trying to run
some Bayesian computation in R, and am experiencing a few problems.

I am working on a Poisson model for cancer rates which has a conjugate Gamma
prior.

1) The first question is precisely how I work out the parameters.

#Suppose I assign values to theta with seq()
theta-seq(0,1,len=500)

#Then I try out the parameters that seem to fit with a certain prior idea on
theta (see next)
a=182
b=3530
gaprior-dgamma(theta,a,b)

It should work by trial-and-error (according to Bayesian Computation with
R) , but how can I check the parameters turned out well: should I just look
at the plot, or evaluate it through the 1 - pgamma(x,a,b) function, having
knowledge of the 5th percentile (data from US Cancer Statistics)?

2) Then, the next problem I have regards the likelihood distribution.

#Having the react table, I name the columns (with y=deaths, and x=exposures)
react
x  y
1   6 15
2   5 16
3   3 12
4   4  6
5  27 77
6   7 17
7   4 11
8   5 10
9  23 63
10 11 29

yr - react[,2]
xr - react[,1]



#I then compute the likelihood
poislike=dpois(yr, theta*xr)

#And this is what I come up with, which I really don't understand.
poislike
[1] 0 0 0 0 0 0 0 0 0 0

The values shouldn't be all null, otherwise my posterior cannot be computed
properly. Does anyone have any idea on where I could possibly have messed it
up?

Thank you very much for your attention.

Regards,

Sebastiano Putoto (University of Pavia, Italy)

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[R] problem with function Truncate in package distr

2011-09-21 Thread Duarte Viana

Hello all,

Can someone tell me why the following mixture of two log-normal
distributions does not get truncated? What puzzles me is that the
function works almost always, but for certain combinations (like the
one below), it does not.

# R code example
library(distr)
mix-UnivarMixingDistribution(Lnorm(3.2,0.5),Lnorm(5.4,0.6),mixCoeff=c(0.3,0.7))
mix.trunc-Truncate(mix,lower=0.001,upper=3000)
distr.sample-r(mix.trunc)(100)
range(distr.sample)

Why do I get values over 3000 (which was the defoned upper limit)?

Some help would be greatly appreciated.

Duarte Viana

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[R] Cannot allocate vector of size x

2011-09-21 Thread Michael Haenlein

Dear all,

I am running a simulation in which I randomly generate a series of vectors
to test whether they fulfill a certain condition. In most cases, there is no
problem. But from time to time, the (randomly) generated vectors are too
large for my system and I get the error message: Cannot allocate vector of
size x.

The problem is that in those cases my simulation stops and I have to start
it again manually. What I would like to do is to simply ignore that the
error happened (or probably report that it did) and then continue with
another (randomly) generated vector.

So my question: Is there a way to avoid that R stops in such a case and just
restarts the program from the beginning as if nothing happened?
I hope I'm making myself clear here ...

Thanks,

Michael

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Re: [R] Cannot allocate vector of size x

2011-09-21 Thread Rubén Roa

Check one of the examples in

?try

It has this heading:

## run a simulation, keep only the results that worked.

If your system is Windows, you can also try to increase the memory available 
for one application, in order to avoid the problem.
Do a search for 3GB switch

HTH

Dr. Ruben H. Roa-Ureta
Senior Researcher, AZTI Tecnalia,
Marine Research Division,
Txatxarramendi Ugartea z/g, 48395, Sukarrieta,
Bizkaia, Spain

-Mensaje original-
De: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] En 
nombre de Michael Haenlein
Enviado el: miércoles, 21 de septiembre de 2011 11:54
Para: r-help@r-project.org
Asunto: [R] Cannot allocate vector of size x

Dear all,

I am running a simulation in which I randomly generate a series of vectors to 
test whether they fulfill a certain condition. In most cases, there is no 
problem. But from time to time, the (randomly) generated vectors are too large 
for my system and I get the error message: Cannot allocate vector of size x.

The problem is that in those cases my simulation stops and I have to start it 
again manually. What I would like to do is to simply ignore that the error 
happened (or probably report that it did) and then continue with another 
(randomly) generated vector.

So my question: Is there a way to avoid that R stops in such a case and just 
restarts the program from the beginning as if nothing happened?
I hope I'm making myself clear here ...

Thanks,

Michael

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Cannot allocate vector of size x

2011-09-21 Thread Jim Holtman

how much memory do you have on your system? How large are the vectors you are 
creating? How many other large vectors do you have in memory?  Remove all 
unused objects and do gc() to reclaim some of the memory. Remember all objects 
are in memory and you have to understand how large they are and how many you 
have. Ther is more information you have to provide and some more inspection you 
have to do.

Sent from my iPad

On Sep 21, 2011, at 5:53, Michael Haenlein haenl...@escpeurope.eu wrote:

 Dear all,
 
 I am running a simulation in which I randomly generate a series of vectors
 to test whether they fulfill a certain condition. In most cases, there is no
 problem. But from time to time, the (randomly) generated vectors are too
 large for my system and I get the error message: Cannot allocate vector of
 size x.
 
 The problem is that in those cases my simulation stops and I have to start
 it again manually. What I would like to do is to simply ignore that the
 error happened (or probably report that it did) and then continue with
 another (randomly) generated vector.
 
 So my question: Is there a way to avoid that R stops in such a case and just
 restarts the program from the beginning as if nothing happened?
 I hope I'm making myself clear here ...
 
 Thanks,
 
 Michael
 
[[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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[R] Statmath-R-Forge: Request denied

2011-09-21 Thread Vikram Bahure

Dear All,

I want to subscribe for Statmath-R-Forge mailing list. But I am getting the
following reply and I am unable to subscribe.

Any insight on this would be appreciated.

Regards
Vikram Bahure

__

Your request to the Statmath-R-Forge mailing list

   Subscription request

has been rejected by the list moderator.  The moderator gave the
following reason for rejecting your request:

This list is not public. Please register trackers and forums
instead.

Any questions or comments should be directed to the list administrator
at:

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[R] Strucchange gbreakpoints

2011-09-21 Thread Vikram Bahure

Hi,

I am  a new user to R.

I am using strucchange to generate breakpoints:
--
 res - gbreakpoints(GDP.new ~ 1,data=a,h=2,breaks=5)
 print(res)

 Optimal 6-segment partition for `lm' fit:

Call:
gbreakpoints(formula = GDP.new ~ 1, data = a, h = 2, breaks = 5)

Breakpoints at observation number:
10 19 25 38 48

Corresponding to breakdates:
1960 1969 1975 1988 1998
--
I want to access the breakdates.

I can access the breakpoints by: res[[1]]

I wish to access breakpoints dates but still struggling. I hope get some
help.

Thanks in advance.

Regards
Vikram

[[alternative HTML version deleted]]

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

Re: [R] R CMD build and vignettes

2011-09-21 Thread Enrico Schumann



Hi Ashim,

after 'R CMD build' the vignettes are in the pkg*.tar.gz file, not in 
your package directory. So if you run 'R CMD build pkg' and then 'R 
CMD check pkg*.tar.gz', you should not get that warning.


For such questions you may get better answers on R-devel; see, eg,  this 
thread here


https://stat.ethz.ch/pipermail/r-devel/2011-May/060775.html

Regards,
Enrico

Am 21.09.2011 11:01, schrieb Ashim Kapoor:

Dear R-helpers,

www.statistik.lmu.de/~*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf

says that  R CMD build creates the pdf from a .Rnw file. But when I do R CMD
build followed by R CMD check it gives me a warning that there is a vignette
without a PDF. My query is : when
R CMD build works it creates a pdf in the doc subdirectory of the directory
returned by system.file(package = mypackage) and not in the inst/doc
directory of the package that we are creating. Do we have to Sweave and
create the pdf in the inst/doc subdirectory on our own ? Please clarify.

Regards,
Ashim

[[alternative HTML version deleted]]

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



--
Enrico Schumann
Lucerne, Switzerland
http://nmof.net/

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

Re: [R] Cannot allocate vector of size x

2011-09-21 Thread Rubén Roa

Yes, on a recent heavy-duty job -profile likelihood of Tweedie power parameter 
for a relatively complex glm with hundreds of thousands rows dataframe- I had 
the cannot allocate vector ... error, then I just closed-saved the main 
workspace, full of large objects, then I did the profiling on a fresh and 
almost empty (with strictly necessary objects) workspace, and it run 
successfully. Then I just loaded the two workspaces to one session,  and 
continued happily to the end of the job. :-)

Dr. Ruben H. Roa-Ureta
Senior Researcher, AZTI Tecnalia,
Marine Research Division,
Txatxarramendi Ugartea z/g, 48395, Sukarrieta,
Bizkaia, Spain

-Mensaje original-
De: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] En 
nombre de Jim Holtman
Enviado el: miércoles, 21 de septiembre de 2011 12:11
Para: Michael Haenlein
CC: r-help@r-project.org
Asunto: Re: [R] Cannot allocate vector of size x

how much memory do you have on your system? How large are the vectors you are 
creating? How many other large vectors do you have in memory?  Remove all 
unused objects and do gc() to reclaim some of the memory. Remember all objects 
are in memory and you have to understand how large they are and how many you 
have. Ther is more information you have to provide and some more inspection you 
have to do.

Sent from my iPad

On Sep 21, 2011, at 5:53, Michael Haenlein haenl...@escpeurope.eu wrote:

 Dear all,
 
 I am running a simulation in which I randomly generate a series of 
 vectors to test whether they fulfill a certain condition. In most 
 cases, there is no problem. But from time to time, the (randomly) 
 generated vectors are too large for my system and I get the error 
 message: Cannot allocate vector of size x.
 
 The problem is that in those cases my simulation stops and I have to 
 start it again manually. What I would like to do is to simply ignore 
 that the error happened (or probably report that it did) and then 
 continue with another (randomly) generated vector.
 
 So my question: Is there a way to avoid that R stops in such a case 
 and just restarts the program from the beginning as if nothing happened?
 I hope I'm making myself clear here ...
 
 Thanks,
 
 Michael
 
[[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide 
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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

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

Re: [R] R CMD build and vignettes

2011-09-21 Thread Ashim Kapoor

Dear Enrico,

Many thanks for your reply.I was doing R CMD check pkg ( where pkg is the
directory name and NOT the tar ball  ). May I ask another query or should
this goto R-devel ? Once I do a R CMD build the vignette PDF's are inside
the tar ball ,how will I put the PDF for the vignette in the pkg/inst/doc/
of my svn folder so I can commit it and other people can see no bugs when
the check the directory.  Perhaps I am misunderstanding something much more
basic.

Best Regards,
Ashim

On Wed, Sep 21, 2011 at 3:53 PM, Enrico Schumann enricoschum...@yahoo.dewrote:


 Hi Ashim,

 after 'R CMD build' the vignettes are in the pkg*.tar.gz file, not in
 your package directory. So if you run 'R CMD build pkg' and then 'R CMD
 check pkg*.tar.gz', you should not get that warning.

 For such questions you may get better answers on R-devel; see, eg,  this
 thread here

 https://stat.ethz.ch/**pipermail/r-devel/2011-May/**060775.htmlhttps://stat.ethz.ch/pipermail/r-devel/2011-May/060775.html

 Regards,
 Enrico

 Am 21.09.2011 11:01, schrieb Ashim Kapoor:

 Dear R-helpers,

 www.statistik.lmu.de/~*leisch***/*Sweave*/*Sweave*-Rnews-2003-**2.pdfhttp://www.statistik.lmu.de/%7E*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf

 says that  R CMD build creates the pdf from a .Rnw file. But when I do R
 CMD
 build followed by R CMD check it gives me a warning that there is a
 vignette
 without a PDF. My query is : when
 R CMD build works it creates a pdf in the doc subdirectory of the
 directory
 returned by system.file(package = mypackage) and not in the inst/doc
 directory of the package that we are creating. Do we have to Sweave and
 create the pdf in the inst/doc subdirectory on our own ? Please clarify.

 Regards,
 Ashim

[[alternative HTML version deleted]]

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


 --
 Enrico Schumann
 Lucerne, Switzerland
 http://nmof.net/


[[alternative HTML version deleted]]

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

Re: [R] Strucchange gbreakpoints

2011-09-21 Thread Achim Zeileis


On Wed, 21 Sep 2011, Vikram Bahure wrote:


Hi,

I am  a new user to R.

I am using strucchange to generate breakpoints:


The answer is still the same as last week:
https://stat.ethz.ch/pipermail/r-help/2011-September/289944.html


--

res - gbreakpoints(GDP.new ~ 1,data=a,h=2,breaks=5)
print(res)


Optimal 6-segment partition for `lm' fit:

Call:
gbreakpoints(formula = GDP.new ~ 1, data = a, h = 2, breaks = 5)

Breakpoints at observation number:
10 19 25 38 48

Corresponding to breakdates:
1960 1969 1975 1988 1998
--
I want to access the breakdates.

I can access the breakpoints by: res[[1]]

I wish to access breakpoints dates but still struggling. I hope get some
help.

Thanks in advance.

Regards
Vikram

[[alternative HTML version deleted]]

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



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

Re: [R] R crash

2011-09-21 Thread Barry Rowlingson

On Wed, Sep 21, 2011 at 10:12 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de wrote:
 Dear Barry,

 Thanks for your input, that is indeed a very good idea (shame on me not to
 have thought about it...).

 As expected, it works fine on Windows XP, but crashes on Windows 7 at
 dev.off (which means that the svg file is correctly created, but R crashes
 every time, a bit annoying). This is therefore a devSVG problem on Windows
 7.

 Now, does anyone know how to fix this?

 Why are you using that svg device when there's a perfectly good one
included in R? See help(svg).

Barry

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

Re: [R] R CMD build and vignettes

2011-09-21 Thread Enrico Schumann

There are various options, and it depends on your work flow and the
people that you expect to use the code. If they get a working copy of
the directory (with only the Rnw-files*) and then build/install the
package, they get the pdfs; so you do not need to add the pdfs. (If they
don't build the package, you could also distribute the tarball.)

You can also build the vignettes through 'Sweave' (in the utils package;
or use 'R CMD Sweave'). Or, after you ran 'R CMD check', go to the
'pkg.Rcheck' directory it created: there you will also find the pdfs
(under /pkg/doc). Or simply extract the pdfs from the *.tar.gz.

As I said, it depends on your work flow and the work flow of your
coworkers. If you need to provide the pdfs, you can decide on one way
and then write some batch-file that automates the procedure.

Regards,
Enrico

* and other required files like bib-files

Am 21.09.2011 12:38, schrieb Ashim Kapoor:

Dear Enrico,

Many thanks for your reply.I was doing R CMD check pkg ( where pkg is the
directory name and NOT the tar ball ). May I ask another query or should
this goto R-devel ? Once I do a R CMD build the vignette PDF's are inside
the tar ball ,how will I put the PDF for the vignette in the pkg/inst/doc/
of my svn folder so I can commit it and other people can see no bugs when
the check the directory. Perhaps I am misunderstanding something much more
basic.

Best Regards,
Ashim

On Wed, Sep 21, 2011 at 3:53 PM, Enrico Schumannenricoschum...@yahoo.dewrote:

Hi Ashim,

after 'R CMD build' the vignettes are in thepkg*.tar.gz file, not in
your package directory. So if you run 'R CMD buildpkg' and then 'R CMD
checkpkg*.tar.gz', you should not get that warning.

For such questions you may get better answers on R-devel; see, eg, this
thread here

https://stat.ethz.ch/**pipermail/r-devel/2011-May/**060775.htmlhttps://stat.ethz.ch/pipermail/r-devel/2011-May/060775.html

Regards,
Enrico

Am 21.09.2011 11:01, schrieb Ashim Kapoor:

Dear R-helpers,

www.statistik.lmu.de/~*leisch***/*Sweave*/*Sweave*-Rnews-2003-**2.pdfhttp://www.statistik.lmu.de/%7E*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf

says that R CMD build creates the pdf from a .Rnw file. But when I do R
CMD
build followed by R CMD check it gives me a warning that there is a
vignette
without a PDF. My query is : when
R CMD build works it creates a pdf in the doc subdirectory of the
directory
returned by system.file(package = mypackage) and not in the inst/doc
directory of the package that we are creating. Do we have to Sweave and
create the pdf in the inst/doc subdirectory on our own ? Please clarify.

Regards,
Ashim

[[alternative HTML version deleted]]

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

--
Enrico Schumann
Lucerne, Switzerland
http://nmof.net/

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

Re: [R] R crash

2011-09-21 Thread Duncan Murdoch


On 11-09-21 5:12 AM, Ivan Calandra wrote:

Dear Barry,

Thanks for your input, that is indeed a very good idea (shame on me not
to have thought about it...).

As expected, it works fine on Windows XP, but crashes on Windows 7 at
dev.off (which means that the svg file is correctly created, but R
crashes every time, a bit annoying). This is therefore a devSVG problem
on Windows 7.

Now, does anyone know how to fix this?


RSvgDevice is a contributed package; you should contact the maintainer 
of it.  There's also an svg() device in the upcoming R 2.14.0 on Windows 
(it has been on Unix-alikes for longer, I think); perhaps it will do 
what you need.


Duncan Murdoch



TIA,
Ivan

Le 9/21/2011 10:34, Barry Rowlingson a écrit :

On Wed, Sep 21, 2011 at 8:57 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de   wrote:

Dear users,
I therefore don't provide a reproducible example and do not really extract
the relevant parts of the script because it has most likely nothing to do
with the script itself. I can do it though if you think it might be
relevant.

   In which case you could reduce your code to something we can all try
- does this crash for you:

library(RSvgDevice)
devSVG(file=foo.svg)
plot(1:10)
dev.off()

   - if not then something I've taken from your script is causing the
problem. Add bits back until it crashes.

   - if it does still crash then its likely a fundamental devSVG
problem, and you've now got something that hundreds of people reading
this can just cut n paste and go 'me too' or 'crashes for me'.

Barry





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

Re: [R] R CMD build and vignettes

2011-09-21 Thread Ashim Kapoor

On Wed, Sep 21, 2011 at 5:15 PM, Enrico Schumann enricoschum...@yahoo.dewrote:

There are various options, and it depends on your work flow and the people
that you expect to use the code. If they get a working copy of the directory
(with only the Rnw-files*) and then build/install the package, they get the
pdfs; so you do not need to add the pdfs. (If they don't build the package,
you could also distribute the tarball.)

You can also build the vignettes through 'Sweave' (in the utils package; or
use 'R CMD Sweave'). Or, after you ran 'R CMD check', go to the
'pkg.Rcheck' directory it created: there you will also find the pdfs
(under /pkg/doc). Or simply extract the pdfs from the *.tar.gz.

As I said, it depends on your work flow and the work flow of your
coworkers. If you need to provide the pdfs, you can decide on one way and
then write some batch-file that automates the procedure.

Thank you Enrico that was very interesting to hear.
Regards,
Ashim

Am 21.09.2011 12:38, schrieb Ashim Kapoor:

Dear Enrico,

Best Regards,
Ashim

On Wed, Sep 21, 2011 at 3:53 PM, Enrico Schumannenricoschumann@yahoo.**
de enricoschum...@yahoo.dewrote:

Hi Ashim,

after 'R CMD build' the vignettes are in thepkg*.tar.gz file, not in
your package directory. So if you run 'R CMD buildpkg' and then 'R CMD
checkpkg*.tar.gz', you should not get that warning.

For such questions you may get better answers on R-devel; see, eg, this
thread here

https://stat.ethz.ch/pipermail/r-devel/2011-May/060775.htmlhttps://stat.ethz.ch/**pipermail/r-devel/2011-May/**060775.html
https://stat.ethz.**ch/pipermail/r-devel/2011-May/**060775.htmlhttps://stat.ethz.ch/pipermail/r-devel/2011-May/060775.html

Regards,
Enrico

Am 21.09.2011 11:01, schrieb Ashim Kapoor:

Dear R-helpers,

www.statistik.lmu.de/~*leisch*/*Sweave*/*Sweave*-Rnews-**
2003-**2.pdfhttp://www.statistik.lmu.de/%7E*leisch***/*Sweave*/*Sweave*-Rnews-2003-**2.pdf
http://www.**statistik.lmu.de/%7E*leisch*/***
Sweave*/*Sweave*-Rnews-2003-2.**pdfhttp://www.statistik.lmu.de/%7E*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf

Regards,
Ashim

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-helphttps://stat.ethz.ch/mailman/**listinfo/r-help
https://stat.**ethz.ch/mailman/listinfo/r-**helphttps://stat.ethz.ch/mailman/listinfo/r-help

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

and provide commented, minimal, self-contained, reproducible code.

--
Enrico Schumann
Lucerne, Switzerland
http://nmof.net/

[[alternative HTML version deleted]]

Re: [R] R crash

I think Duncan answered it: because there is no svg() in R2.13.1 for 
Windows.

Thank you for your help
Ivan

Le 9/21/2011 13:40, Barry Rowlingson a écrit :

On Wed, Sep 21, 2011 at 10:12 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de  wrote:

Dear Barry,

Thanks for your input, that is indeed a very good idea (shame on me not to
have thought about it...).

As expected, it works fine on Windows XP, but crashes on Windows 7 at
dev.off (which means that the svg file is correctly created, but R crashes
every time, a bit annoying). This is therefore a devSVG problem on Windows
7.

Now, does anyone know how to fix this?

  Why are you using that svg device when there's a perfectly good one
included in R? See help(svg).

Barry



--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php

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

Re: [R] R crash

2011-09-21 Thread R. Michael Weylandt michael.weyla...@gmail.com


Dear Duncan,

Thanks for the info. I'll be waiting for it then.
I once tried to contact the maintainer of this package, but never got an 
answer; so I haven't tried this time. I'll try again.


Ivan

Le 9/21/2011 13:45, Duncan Murdoch a écrit :

On 11-09-21 5:12 AM, Ivan Calandra wrote:

Dear Barry,

Thanks for your input, that is indeed a very good idea (shame on me not
to have thought about it...).

As expected, it works fine on Windows XP, but crashes on Windows 7 at
dev.off (which means that the svg file is correctly created, but R
crashes every time, a bit annoying). This is therefore a devSVG problem
on Windows 7.

Now, does anyone know how to fix this?


RSvgDevice is a contributed package; you should contact the maintainer 
of it.  There's also an svg() device in the upcoming R 2.14.0 on 
Windows (it has been on Unix-alikes for longer, I think); perhaps it 
will do what you need.


Duncan Murdoch



TIA,
Ivan

Le 9/21/2011 10:34, Barry Rowlingson a écrit :

On Wed, Sep 21, 2011 at 8:57 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de   wrote:

Dear users,
I therefore don't provide a reproducible example and do not really 
extract
the relevant parts of the script because it has most likely nothing 
to do

with the script itself. I can do it though if you think it might be
relevant.

   In which case you could reduce your code to something we can all try
- does this crash for you:

library(RSvgDevice)
devSVG(file=foo.svg)
plot(1:10)
dev.off()

   - if not then something I've taken from your script is causing the
problem. Add bits back until it crashes.

   - if it does still crash then its likely a fundamental devSVG
problem, and you've now got something that hundreds of people reading
this can just cut n paste and go 'me too' or 'crashes for me'.

Barry








--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php

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Re: [R] help in interpreting paired t-test

2011-09-21 Thread Jean V Adams

Ted Harding wrote on 09/20/2011 05:26:58 PM:
 
 Further to the plot suggested below, the plot
 
   plot(log(A),log(B/A),pch=+,col=blue)
 
 reveals an interesting structure to the data. Distinct curved
 sequences are clearly visible. While their curved form is a
 consequence of the fact that, for large A, A/B is close to 1
 and so they tend to approach 1 asymptotically (hence the
 curving over towards flatness), what is really interesting
 is the appearance of distinct curves, as if there were at least
 7 (or at least 8) distinct subsets to the data, each subset
 following a different curve. Perhaps these are related to
 observed variables?
 
 Ted.


The distinct curves that you observed are a side effect of the data being 
rounded to the nearest thousandth.  They disappear if noise is added to 
the data.

a - A + runif(length(A), -0.0005, 0.0005)
b - B + runif(length(B), -0.0005, 0.0005)
plot(a, b/a, log=xy)

Jean


 On 20-Sep-11 18:15:50, Ted Harding wrote:
  As can be seen by plotting as follows:
  
plot(A,B,pch=+,col=blue)   ## The raw data
  
plot(A,B-A,pch=+,col=blue) ## The differences versus A
lines(c(0,0.7),c(0,0))
  
  Ted.
  
  On 20-Sep-11 17:54:15, Timothy Bates wrote:
  Yes, in over 3/4s of the data points A is  B? which suggests the A
  measure is reading higher than the B measuring system.
  
  length(A[AB])/length(A)
  
  
  On 20 Sep 2011, at 6:46 PM, Pedro Mardones wrote:
  
  Dear all;
  
  A very basic question. I have the following data:
  
  
**
  *
  *
  
  A - 1/1000*c(347,328,129,122,18,57,105,188,57,257,53,108,336,163,
  62,112,334,249,45,244,211,175,174,26,375,346,153,32,
  89,32,358,202,123,131,88,36,30,67,96,135,219,122,
  89,117,86,169,179,54,48,40,54,568,664,277,91,290,
  116,80,107,401,225,517,90,133,36,50,174,103,192,150,
  225,29,80,199,55,258,97,109,137,90,236,109,204,160,
  95,54,50,78,98,141,508,144,434,100,37,22,304,175,
  72,71,111,60,212,73,50,92,70,148,28,63,46,85,
  111,67,234,65,92,59,118,202,21,17,95,86,296,45,
  139,32,21,70,185,172,151,129,42,14,13,75,303,119,
  128,106,224,241,112,395,78,89,247,122,212,61,165,30,
  65,261,415,159,316,182,141,184,124,223,39,141,103,149,
  104,71,259,86,85,214,96,246,306,11,129)
  
  B - 1/1000*c(351,313,130,119,17,50,105,181,58,255,51,98,335,162,
  60,108,325,240,44,242,208,168,170,27,356,341,150,31,
  85,29,363,185,124,131,85,35,27,63,92,147,217,117,
  87,119,81,161,178,53,45,38,50,581,661,254,87,281,
  110,76,100,401,220,507,94,123,36,47,154,99,184,146,
  232,26,77,193,53,264,94,110,128,87,231,110,195,156,
  95,51,50,75,93,134,519,139,435,96,37,21,293,169,
  70,80,104,64,210,70,48,88,67,140,26,52,45,90,
  106,63,219,62,91,56,113,187,18,14,95,86,284,39,
  132,31,22,69,181,167,150,117,42,14,11,73,303,109,
  129,106,227,249,111,409,71,88,256,120,200,60,159,27,
  63,268,389,150,311,175,136,171,116,220,30,145,95,148,
  102,70,251,88,83,199,94,245,305,9,129)
  
  
**
  *
  *
  
  plot(A,B)
  abline(0,1)
  
  At a glance, the data look very similar. Data A and B are two
  measurements of the same variable but using different devices (on a
  same set of subjects). Thus, I thought that a paired t-test could be
  appropriate to check if the diff between measurement devices = 0.
  
  t.test(A-B)
  
  
**
  *
  *
  
  One Sample t-test
  
  data:  A - B
  t = 7.6276, df = 178, p-value = 1.387e-12
  alternative hypothesis: true mean is not equal to 0
  95 percent confidence interval:
  0.002451622 0.004162903
  sample estimates:
   mean of x
  0.003307263
  
  
**
  *
  *
  The mean diff is 0.0033 but the p-value indicates a strong evidence
  to
  reject H0.
  
  I was expecting to find no differences so I'm wondering whether the
  t-test is the appropriate test to use. I'll appreciate any comments
  or
  suggestions.
  
  
  E-Mail: (Ted Harding) ted.hard...@wlandres.net
  Fax-to-email: +44 (0)870 094 0861
  Date: 20-Sep-11   Time: 19:15:47
 
 
 E-Mail: (Ted Harding) ted.hard...@wlandres.net
 Fax-to-email: +44 (0)870 094 0861
 Date: 20-Sep-11   Time: 23:26:53

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Re: [R] Statmath-R-Forge: Request denied

2011-09-21 Thread Paul Hiemstra

 On 09/21/2011 10:11 AM, Vikram Bahure wrote:
 Dear All,

 I want to subscribe for Statmath-R-Forge mailing list. But I am getting the
 following reply and I am unable to subscribe.

 Any insight on this would be appreciated.

 Regards
 Vikram Bahure

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 Your request to the Statmath-R-Forge mailing list

Subscription request

 has been rejected by the list moderator.  The moderator gave the
 following reason for rejecting your request:

 This list is not public. Please register trackers and forums
 instead.

 Any questions or comments should be directed to the list administrator
 at:

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I think your problem is that:

This list is not public

Just my 2ct...and Any questions or comments should be directed to the
list administrator...

Paul

-- 
Paul Hiemstra, Ph.D.
Global Climate Division
Royal Netherlands Meteorological Institute (KNMI)
Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39
P.O. Box 201 | 3730 AE | De Bilt
tel: +31 30 2206 494

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Re: [R] R-help Digest, Vol 103, Issue 20

2011-09-21 Thread mihalicza . peter

Szeptember 12-től 26-ig irodán kívül vagyok, és az emailjeimet nem érem el.

Sürgős esetben kérem forduljon Kárpáti Edithez (karpati.e...@gyemszi.hu).

Üdvözlettel,
Mihalicza Péter


I will be out of the office from 12 till 26 September with no access to my 
emails.

In urgent cases please contact Ms. Edit Kárpáti (karpati.e...@gyemszi.hu).

With regards,
Peter Mihalicza

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[R] Problem with caret + foreach + M5 combination

2011-09-21 Thread Antoine Stevens

Hello,

I often use the caret package to develop regression models and compare
their performance. The foreach package is integrated in caret and can be
used to speed up the process through parallel computations.
Since caret version 5.01-001, one just need to register the cores with one
of the do packages (doMC,etc). This works fine in most of the
situations, but there is a problem when I use the M5 algorithm.
Everything works well with only one core but computations seem to be stuck
with 2 or more registered cores.
I am using Rstudio with R 2.13.1 on a Redhat Linux 64-bit machine.
Here is an example:

library(doMC);library(randomForest);library(RWeka); library(caret)
library(mlbench)
data(BostonHousing)
registerDoMC()
options(cores=1)
withoutMC -  train(medv ~ ., data = BostonHousing, rf)#Works with
random forest
options(cores=2)
usingMC -  train(medv ~ ., data = BostonHousing, rf)#Works with random
forest
options(cores=1)
withoutMC -  train(medv ~ ., data = BostonHousing, M5)#Works with M5
options(cores=2)
usingMC -  train(medv ~ ., data = BostonHousing, M5)#Does not work

So I tried with another parallel backend (doSNOW), but got another error.

library(doSNOW)
cl - makeCluster(2, type = SOCK)
clusterEvalQ(cl,library(caret))
clusterEvalQ(cl,library(RWeka))

[[1]]
 [1] RWeka caret foreach   codetools iterators cluster
  reshape   plyr
 [9] lattice   snow  methods   stats graphics 
grDevices utils datasets
[17] base

[[2]]
 [1] RWeka caret foreach   codetools iterators cluster
  reshape   plyr
 [9] lattice   snow  methods   stats graphics 
grDevices utils datasets
[17] base

registerDoSNOW(cl)
usingSNOW -  train(medv ~ ., data = BostonHousing, M5)# Does not work

Error in { :
  task 1 failed - could not find function predictionFunction

Here, it does not find predictionFunction (part of the caret package I
believe),
while I loaded the package into the clusters with clusterEvalQ.

Any suggestions?

Here are my sessionInfo() and package versions:

sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C 
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C  LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

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

other attached packages:
 [1] doSNOW_1.0.5   snow_0.3-7 caret_5.01-001
cluster_1.14.0 reshape_0.8.4
 [6] plyr_1.6   lattice_0.19-30mlbench_2.1-0  RWeka_0.4-8 
  randomForest_4.6-2
[11] doMC_1.2.3 multicore_0.1-7foreach_1.3.2 
codetools_0.2-8iterators_1.0.5

loaded via a namespace (and not attached):
[1] compiler_2.13.1   grid_2.13.1   rJava_0.9-1  
RWekajars_3.7.4-1 tools_2.13.1

packageDescription(caret)

Package: caret
Version: 5.01-001
Date: 2011-09-01
Title: Classification and Regression Training
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and
   Allan Engelhardt
Description: Misc functions for training and plotting classification and
regression models
Maintainer: Max Kuhn max.k...@pfizer.com
Depends: R (= 2.10), lattice, reshape, stats, plyr, cluster, foreach
URL: http://caret.r-forge.r-project.org/
Suggests: gbm, pls, mlbench, rpart, ellipse, ipred, klaR, randomForest,
gpls, pamr, kernlab, mda,
   mgcv, nnet, class, MASS, mboost, earth (= 2.2-3), party (=
0.9-2), ada, affy,
   proxy, e1071, grid, elasticnet, SDDA, caTools, RWeka (=
0.4-1), superpc, penalized,
   sparseLDA (= 0.1-1), spls, sda, glmnet, relaxo, lars, vbmp,
nodeHarvest, rrcov, gam,
   stepPlr, GAMens (= 1.1.1), rocc, foba, partDSA, hda, fastICA,
neuralnet,
   quantregForest, rda, HDclassif, LogicReg, LogicForest, logicFS,
RANN, qrnn, Boruta,
   Hmisc, Cubist, bst, leaps
License: GPL-2
Packaged: 2011-09-02 14:09:50 UTC; kuhna03
Repository: CRAN
Date/Publication: 2011-09-02 18:25:30
Built: R 2.13.1; x86_64-redhat-linux-gnu; 2011-09-16 18:51:38 UTC; unix

Thank you very much,

Antoine Stevens
Earth and Life Institute
UCLouvain
Belgium

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[R] Reading data in lisp format

2011-09-21 Thread ESTEBAN ALFARO CORTES

Hi, 

 I am trying to read the credit.lisp file of the Japanese credit database in 
UCI repository, but it is in lisp format which I do not know how to read.  I  
have not found how to do that in the foreign library

http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening 
http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening  

Could anyone help me?

Best regards,

Esteban Alfaro

PS: This is my first time in r-help so I apologize for possible inconveniences.

 


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[R] R help on write.csv

2011-09-21 Thread Ashish Kumar

Hi,

 

I wanted to write the data created using R  on existing csv file. However
everytime I use write.csv, it overwrites the values already there in the
existing csv file. Any workaround on this. 

 

Thanks for your help

 

Ashish Kumar

 

Estee Advisors Pvt. Ltd.

Email: ashish.ku...@esteeadvisors.com

Cell: +91-9654072144

Direct: +91-124-4637-713

 


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Re: [R] Data

2011-09-21 Thread Paul Hiemstra

 On 09/20/2011 10:28 PM, barb wrote:
 Hey everybody,

 i am using the rugarch-package and its great! 
 I have a pretty easy problem, but i just dont get it, so thanks if you can
 help me. 

 Normally i use: 
 /
 data(DATANAME)
 spec = ugarchspec()
 fit = ugarchfit(data = x[,1], spec = spec)
 fit

 slotNames(fit)

 names(fit@fit)
 coef(fit)
 infocriteria(fit)
 likelihood(fit)
 nyblom(fit)
 signbias(fit)
 head(as.data.frame(fit))
 head(sigma(fit))
 head(residuals(fit))
 head(fitted(fit))
 gof(fit,c(20,30,40,50))
 uncmean(fit)
 uncvariance(fit)
 plot(fit,which=all)/
  
 I want to use my data now. 

 I figured out how to load excel sheets. 

 setwd(C:/Users/UserofComputer/Desktop)
 data - read.csv2(Dataname.csv,header=T)
 attach(data)

You do not need to attach 'data', this makes the columns of data
available as objects, which is generally not needed. Just refer to the
columns as data$column_name.

 x - CGE[200:1]
 dx - diff(log(x))

 How is my Dataname now safed?
 I cant use it as data(dataname) unfortunately. 

The information in Dataname.csv is now in the object data, see
summary(data) or str(data). Btw, data is also an R function. Redefining
data is not regarded as good programming practice. Furthermore, the use
of the data function (as I've used it) is primarily to load datasets
which have been packaged along side R. As you've already loaded the
dataset using read.csv2, the data(dataname) command is not needed.

It seems to me that, no insult intended, you do not know what you are
doing. I would recommend you either read some more online introductory
material [1], buy some R books, do some kind of R course or find someone
that can tutor you. The kind of assistance you need is hard to give via
a mailing list. Again, I do not mean to be harsh (we where all R noobs
at some stage).

good luck,
Paul

[1] see e.g. http://cran.r-project.org/manuals.html and
http://cran.r-project.org/other-docs.html


 Where is my mistake?

 Thank you

 --
 View this message in context: 
 http://r.789695.n4.nabble.com/Data-tp3828343p3828343.html
 Sent from the R help mailing list archive at Nabble.com.

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-- 
Paul Hiemstra, Ph.D.
Global Climate Division
Royal Netherlands Meteorological Institute (KNMI)
Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39
P.O. Box 201 | 3730 AE | De Bilt
tel: +31 30 2206 494

http://intamap.geo.uu.nl/~paul
http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770

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Re: [R] R help on write.csv

The append argument of write.csv()?

Michael

On Sep 21, 2011, at 8:01 AM, Ashish Kumar ashish.ku...@esteeadvisors.com 
wrote:

 Hi,
 
 
 
 I wanted to write the data created using R  on existing csv file. However
 everytime I use write.csv, it overwrites the values already there in the
 existing csv file. Any workaround on this. 
 
 
 
 Thanks for your help
 
 
 
 Ashish Kumar
 
 
 
 Estee Advisors Pvt. Ltd.
 
 Email: ashish.ku...@esteeadvisors.com
 
 Cell: +91-9654072144
 
 Direct: +91-124-4637-713
 
 
 
 
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 R-help@r-project.org mailing list
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] R help on write.csv

I don't think there is an append argument to write.csv() (well, actually 
there is one, but set to FALSE).

There is however one to write.table()
Ivan

Le 9/21/2011 14:54, R. Michael Weylandt michael.weyla...@gmail.com a 
écrit :

The append argument of write.csv()?

Michael

On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.ku...@esteeadvisors.com  
wrote:


Hi,



I wanted to write the data created using R  on existing csv file. However
everytime I use write.csv, it overwrites the values already there in the
existing csv file. Any workaround on this.



Thanks for your help



Ashish Kumar



Estee Advisors Pvt. Ltd.

Email: ashish.ku...@esteeadvisors.com

Cell: +91-9654072144

Direct: +91-124-4637-713




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--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php

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[R] Making ?source act as if it is run through the terminal

2011-09-21 Thread Tal Galili

Hello dear R help,

The motivation for my question is wanting to run HTMLStart {R2HTML package}
from source.

*Background:*

I was happy to discover the [ HTMLStart/HTMLStop, HTMLplot] functions in the
R2HTML package.

They allow my R code to run almost as is, but while writing most of the
output (including the figures, when using  HTMLplot) into an external HTML
file.
This method works rather well, but only when the script is running from the
terminal.
When I try using the code from ?source, the functions fails completely (with
both output and especially with figures)

I assume the reason is because of what is said in the help file:
Note that running code via source differs in a few respects from entering
it at the R command line. Since expressions are not executed at the top
level, auto-printing is not done. So you will need to include explicit print
calls for things you want to be printed

*Question:*
Hence my question is - can it be avoided?
Can the source be set to act just as if the code were to run from the
terminal?



Thanks,
Tal


Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
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Re: [R] R help on write.csv

2011-09-21 Thread Tyler Rinker


You haven't followed the rules of the posting guide.  No reproducible code.  No 
OS or R version.  I'm guessing you are a newer R user and didn't know this.  So 
please read that guide.  It'll help others to help you more quickly.
 
If you're new you may not know about using ?object.  So if you type 
?write.csv into the r console it will take you to a help page.  There you 
will see info about the object and in this case append is what you will most 
likely want to look at.
 
Tyler

 

 From: ashish.ku...@esteeadvisors.com
 To: r-help@r-project.org
 Date: Wed, 21 Sep 2011 17:31:01 +0530
 Subject: [R] R help on write.csv
 
 Hi,
 
 
 
 I wanted to write the data created using R on existing csv file. However
 everytime I use write.csv, it overwrites the values already there in the
 existing csv file. Any workaround on this. 
 
 
 
 Thanks for your help
 
 
 
 Ashish Kumar
 
 
 
 Estee Advisors Pvt. Ltd.
 
 Email: ashish.ku...@esteeadvisors.com
 
 Cell: +91-9654072144
 
 Direct: +91-124-4637-713
 
 
 
 
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Re: [R] Binary optimization problem in R

2011-09-21 Thread Hans W Borchers

Michael Haenlein haenlein at escpeurope.eu writes:

 Dear all,
 
 I would like to solve a problem similar to a multiple knapsack problem and
 am looking for a function in R that can help me.
 
 Specifically, my situation is as follows: I have a list of n items which I
 would like to allocate to m groups with fixed size. Each item has a certain
 profit value and this profit depends on the type of group the item is in.
 My problem is to allocate the items into groups so the overall profit is
 maximized while respecting the fixed size of each group.
 
 Take the following example with 20 items (n=5) and 5 groups (m=5):
 
 set.seed(1)
 profits - matrix(runif(100), nrow=20)
 size-c(2,3,4,5,6)
 
 The matrix profits describes the profit of each item when it is allocated
 to a certain group. For example, when item 1 is allocated to group 1 it
 generates a profit of 0.26550866. However, when item 1 is allocated to group
 2 it generates a profit of 0.93470523. The matrix size describes the size
 of each group. So group 1 can contain 2 items, group 2 3 items, group 4 4
 items, etc.
 
 I think this is probably something that could be done with constrOptim() but
 I'm not exactly sure how.

The task you describe is an integer optimization problem and can most likely
not be solved with a numeric optimization routine like constrOptim().

In the example above, the solution I get is a maximal profit of 16.31194
with these allocations:
group 1:   4, 18
  2:   1,  9, 15
  3:   3,  6, 11, 12
  4:   8, 10, 16, 17, 20
  5:   2,  5,  7, 13, 14, 19

(mis)using the mixed-integer package 'lpSolve' in the following way
(with 100 binary variables):

library(lpSolve)

obj - -c(profits)  # we will look for a minimum
dir - rep(==, 25)# discrete equality constraints
rhs - c(c(2,3,4,5,6), rep(1, 20))

# Assign 2, 3, 4, 5, 6 items to groups 1--5 resp.
mat - matrix(0, 25, 100); mat[1,  1: 20] - 1; mat[2, 21: 40] - 1
mat[3, 41: 60] - 1;   mat[4, 61: 80] - 1; mat[5, 81:100] - 1
# Assign each item to only one group
for (i in 1:20) {
mat[i+5, c(i, i+20, i+40, i+60, i+80)] - 1
}

sol - lp(min, obj, mat, dir, rhs, all.bin=TRUE)

# RESULT
-sol$objval # 16.31194
# ALLOCATIONS
which(sol$solution==1) - rep(seq(0, 80, 20), 2:6)
# 4 18  1  9 15  3  6 11 12  8 10 16 17 20  2  5  7 13 14 19

In case you have thousands of items and many groups, packages like 'lpSolve',
'Rglpk', or 'Rsymphony' will not be able to handle the task and you might be
forced to look for tools outside the R realm.

Hans Werner

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[R] heatmap.2 with colsep and sepwidth

2011-09-21 Thread Christian Ruckert

I am using attributes colsep and sepwidth from heatmap.2 function, 
however when using larger values for sepwidth the following columns are 
not moved to the right but the seperator is covering the column(s) with 
a white bar and the column labels and ColSideColors remain at their 
positions, is this intended? I expected the following columns to be 
shifted to the right by sepwidth. Is there a way to achieve this?


Here is a simple example

library(gplots)

col - c( rgb(0,100:0,0,maxColorValue=100), 
rgb(0:100,0,0,maxColorValue=100) )


heatmap.2(matrix(c(1,2,3,4,9,6,7,3), nrow=2), col=col, trace=none, 
density.info=density, key=FALSE, ColSideColors=rep(blue, 4), 
denscol=white, scale=row, dendrogram=none, colsep=c(2), sepwidth=1.8)



Regards,
Christian

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Re: [R] glmnet for Binary trait analysis

2011-09-21 Thread Bert Gunter

The man page tells you that y must be a factor. Is it?
-- Bert

On Tue, Sep 20, 2011 at 5:25 PM, Noah noah...@hotmail.com wrote:

 Hello,

 I got an error message saying

 Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs,  :
  NA/NaN/Inf in foreign function call (arg 5)

 when I try to analysis a binary trait using glmnet(R) by running the
 following code

 library(glmnet)
 Xori - read.table(c:\\SNP.txt, sep='\t');
 Yori - read.table(c:\\Trait.txt, sep=',');
 Y=as.matrix(Yori);
 X=t(as.matrix(Xori));
 fit1=glmnet(X, Y, family=binomial);

 in the above, X is a matrix with values 1, 0, and -1; Y is a one column
 matrix with values 1 and 0.

 I know how to analysis continuous traits using glmnet, but I have no idea
 about how to do it for binary dependent variables. I will appreciate it if
 you would give me any suggestion about this error or provide an example
 code
 for handling binary trait using glmnet.

 Looking forward for your kindly help.

 Thanks!

 Noah

 --
 View this message in context:
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 Sent from the R help mailing list archive at Nabble.com.

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-- 
Men by nature long to get on to the ultimate truths, and will often be
impatient with elementary studies or fight shy of them. If it were possible
to reach the ultimate truths without the elementary studies usually prefixed
to them, these would not be preparatory studies but superfluous diversions.

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics

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Re: [R] R help on write.csv

Touche -- perhaps we could make one though?

write.csv.append - function(..., append = TRUE)
{
Call - match.call(expand.dots = TRUE)
for (argname in c(col.names, sep, dec, qmethod)) if
(!is.null(Call[[argname]]))
warning(gettextf(attempt to set '%s' ignored, argname),
domain = NA)
rn - eval.parent(Call$row.names)
Call$col.names - if (is.logical(rn)  !rn)
TRUE
else NA
Call$sep - ,
Call$dec - .
Call$qmethod - double
Call[[1L]] - as.name(write.table)
eval.parent(Call)
}
write.csv.append(1:5,test.csv, append = FALSE)
write.csv.append(1:15, test.csv)

Output seems a little sloppy, but might work for the OP.

Michael Weylandt

On Wed, Sep 21, 2011 at 9:03 AM, Ivan Calandra ivan.calan...@uni-hamburg.de
 wrote:

 I don't think there is an append argument to write.csv() (well, actually
 there is one, but set to FALSE).
 There is however one to write.table()
 Ivan

 Le 9/21/2011 14:54, R. Michael Weylandt michael.weyla...@gmail.com a
 écrit :

  The append argument of write.csv()?

 Michael

 On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.kumar@**
 esteeadvisors.com ashish.ku...@esteeadvisors.com  wrote:

  Hi,



 I wanted to write the data created using R  on existing csv file. However
 everytime I use write.csv, it overwrites the values already there in the
 existing csv file. Any workaround on this.



 Thanks for your help



 Ashish Kumar



 Estee Advisors Pvt. Ltd.

 Email: ashish.ku...@esteeadvisors.com

 Cell: +91-9654072144

 Direct: +91-124-4637-713




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 --
 Ivan CALANDRA
 PhD Student
 University of Hamburg
 Biozentrum Grindel und Zoologisches Museum
 Dept. Mammalogy
 Martin-Luther-King-Platz 3
 D-20146 Hamburg, GERMANY
 +49(0)40 42838 6231
 ivan.calan...@uni-hamburg.de

 **
 http://www.for771.uni-bonn.de
 http://webapp5.rrz.uni-**hamburg.de/mammals/eng/1525_8_**1.phphttp://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php


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Re: [R] Poisson-Gamma computation (parameters and likelihood)

2011-09-21 Thread Jorge I Velez

Hi Sebatiano,

Take a look at

 require(MCMCpack)
 ?MCpoissongamma

HTH,
Jorge


On Wed, Sep 21, 2011 at 5:25 AM, Sebastiano Putoto  wrote:

 Good afternoon/morning readers. This is the first time I am trying to run
 some Bayesian computation in R, and am experiencing a few problems.

 I am working on a Poisson model for cancer rates which has a conjugate
 Gamma
 prior.

 1) The first question is precisely how I work out the parameters.

 #Suppose I assign values to theta with seq()
 theta-seq(0,1,len=500)

 #Then I try out the parameters that seem to fit with a certain prior idea
 on
 theta (see next)
 a=182
 b=3530
 gaprior-dgamma(theta,a,b)

 It should work by trial-and-error (according to Bayesian Computation with
 R) , but how can I check the parameters turned out well: should I just
 look
 at the plot, or evaluate it through the 1 - pgamma(x,a,b) function, having
 knowledge of the 5th percentile (data from US Cancer Statistics)?

 2) Then, the next problem I have regards the likelihood distribution.

 #Having the react table, I name the columns (with y=deaths, and
 x=exposures)
 react
x  y
 1   6 15
 2   5 16
 3   3 12
 4   4  6
 5  27 77
 6   7 17
 7   4 11
 8   5 10
 9  23 63
 10 11 29

 yr - react[,2]
 xr - react[,1]



 #I then compute the likelihood
 poislike=dpois(yr, theta*xr)

 #And this is what I come up with, which I really don't understand.
 poislike
 [1] 0 0 0 0 0 0 0 0 0 0

 The values shouldn't be all null, otherwise my posterior cannot be computed
 properly. Does anyone have any idea on where I could possibly have messed
 it
 up?

 Thank you very much for your attention.

 Regards,

 Sebastiano Putoto (University of Pavia, Italy)

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[R] Row percentage labels within mosaic graph

2011-09-21 Thread Luca Meyer

Hi, 

I have the following sample data 

x - c(1,2,1,1,2,3,1,2,3,2,3,1,2,2,1,3,2,3,1,3)
y - c(1,2,1,2,2,2,1,2,1,1,1,1,2,2,1,2,2,1,2,1)
w - c(1, 1, 1.5, 1, 1.2, 0.8, 0.9, 1.7,  1, 1.3, 1, 1, 0.7, 0.8, 1.4, 1.3, 1, 
1, 0.9, 0.7)
d1 - data.frame(x,y,w)

and I wish to build a x,y mosaic graphs that shows as labels both row 
percentages and number of cases. So far I have been using this script:

require(gmodels)
require(vcd)

d2 - xtabs(~ x + y, data=d1)
mosaic  (
d2,
gp = shading_max,
labeling_args = list(
gp_labels = gpar(fontsize = 10, fontface = 1),
rot_labels = c(0,90,90,0),
gp_varnames = gpar(fontsize = 0, fontface = 2)
),
main= title, main_gp = gpar(fontsize = 16, fontface = 2),
pop=FALSE
)
d3 - CrossTable(d1$x,d1$y)
etichette - ifelse(d2  5, 5, paste(round(d3$prop.row*100, 
digits=1),%\n(n=,d2,), sep=))
labeling_cells(text = etichette, clip = FALSE, gp_text=gpar(fontsize=10))(d2)

This works just fine but now I have to apply the weight w to the computation. I 
have modified the first part of the above script to

d2 -round(xtabs(w ~ x + y, data=d1), digits=0)
mosaic  (
d2,
gp = shading_max,
labeling_args = list(
gp_labels = gpar(fontsize = 10, fontface = 1),
rot_labels = c(0,90,90,0),
gp_varnames = gpar(fontsize = 0, fontface = 2)
),
main= title, main_gp = gpar(fontsize = 16, fontface = 2),
pop=FALSE
)

but I have some difficulty with the labeling part.  I can show number of 
observation in the labels using:

d3 - as.list(round(xtabs(w ~ x + y, data=d1)), digits=0) 
etichette - ifelse(d2  5, 5, paste((n=,d3,), sep=))
labeling_cells(text = etichette, clip = FALSE, gp_text=gpar(fontsize=10))(d2)

but I would need to show row proportions, do you know how I can do that?

Thanks,
Luca

Mr. Luca Meyer
www.lucameyer.com
R version 2.13.1 (2011-07-08)
Mac OS X 10.6.8







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Re: [R] adding labels to x,y points

2011-09-21 Thread Weidong Gu

A sample data would help. But you could modify as

text(x,y, label = row.names(colon[1:20,]))

HTH

Weidong Gu


On Tue, Sep 20, 2011 at 7:43 PM, baumeist mark.baumeist...@gmail.com wrote:
 Hi,
 I am new to R.

 I have a matrix that I have assigned to the object “colon”.

 colon-read.table(c:\\alon.txt,header=T,row.names=1)

 attach(colon)
 names(colon)

 The dimenstions are 2000   62.

 Each of the 62 columns (titled norm1, norm2, norm3, etc) has 2000
 different numbers (‘continuous’ values) within it.

 I have also assigned a name for each of the 2000 rows of the dataframe with
 a prefix (i.e. g1 …. g2000) using the code (not sure if I did this right):

 colon-paste(g,c(1:nrow(colon)),sep=)

 I have plotted the first 20 values from two of the columns(samples).

 x-c(norm1[1:20])

 y-c(norm2[1:20])

 plot(x,y,type='n',xlab='x norm1 sample',ylab='y norm2 sample',main='Norm1
 vs Norm2 - 20
 genes')

 points(x,y,pch=15,col='blue')

 Now I wish to assign labels to each point (above each point (i.e. pos=3) in
 the plot with “g1 to g20 corresponding to each row but I am having trouble
 with this step.

 I have tried:

 text(x,y, label = row.names(colon[1:20]))

 but nothing happens.

 Any suggestions?

 Thanks in advance
 MAB


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Re: [R] Reading data in lisp format

2011-09-21 Thread csrabak


Em 21/9/2011 07:39, ESTEBAN ALFARO CORTES escreveu:

Hi,

  I am trying to read the credit.lisp file of the Japanese credit database in 
UCI repository, but it is in lisp format which I do not know how to read.  I  have not 
found how to do that in the foreign library

http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screeninghttp://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening

Could anyone help me?



Esteban,

Lisp files may mean a lot of different things, so it is not enough for 
an authoritative answer without further qualifications.


They _may_ be files that can be read by XLisp-Stat or be a data format 
coming from another Lisp written program.


For the former you could have XLisp-Stat read the file and export in a 
more manageable format (plain text, csv and for some add ons [like 
VisTa] to Excel]), for the latter the only option would be to ask the 
developer of the program or for the structure of the file or for an 
export to another format R can read.


HTH

--
Cesar Rabak

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Re: [R] glmnet for Binary trait analysis

2011-09-21 Thread Bert Gunter

... another possibiity, probably more likely since you read your files in
from disk, is that there is a stray character of some sort (e.g. extra
comma, quotation mark, period) in your data that is causing what should be
numeric data to be read in as character. Check your data after you've read
them in.

-- Bert

On Wed, Sep 21, 2011 at 6:46 AM, Bert Gunter bgun...@gene.com wrote:

 The man page tells you that y must be a factor. Is it?
 -- Bert

 On Tue, Sep 20, 2011 at 5:25 PM, Noah noah...@hotmail.com wrote:

 Hello,

 I got an error message saying

 Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs,  :
  NA/NaN/Inf in foreign function call (arg 5)

 when I try to analysis a binary trait using glmnet(R) by running the
 following code

 library(glmnet)
 Xori - read.table(c:\\SNP.txt, sep='\t');
 Yori - read.table(c:\\Trait.txt, sep=',');
 Y=as.matrix(Yori);
 X=t(as.matrix(Xori));
 fit1=glmnet(X, Y, family=binomial);

 in the above, X is a matrix with values 1, 0, and -1; Y is a one column
 matrix with values 1 and 0.

 I know how to analysis continuous traits using glmnet, but I have no idea
 about how to do it for binary dependent variables. I will appreciate it if
 you would give me any suggestion about this error or provide an example
 code
 for handling binary trait using glmnet.

 Looking forward for your kindly help.

 Thanks!

 Noah

 --
 View this message in context:
 http://r.789695.n4.nabble.com/glmnet-for-Binary-trait-analysis-tp3828547p3828547.html
 Sent from the R help mailing list archive at Nabble.com.

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




 --
 Men by nature long to get on to the ultimate truths, and will often be
 impatient with elementary studies or fight shy of them. If it were possible
 to reach the ultimate truths without the elementary studies usually prefixed
 to them, these would not be preparatory studies but superfluous diversions.

 -- Maimonides (1135-1204)

 Bert Gunter
 Genentech Nonclinical Biostatistics






-- 
Men by nature long to get on to the ultimate truths, and will often be
impatient with elementary studies or fight shy of them. If it were possible
to reach the ultimate truths without the elementary studies usually prefixed
to them, these would not be preparatory studies but superfluous diversions.

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics

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Re: [R] Package dependency

2011-09-21 Thread Uwe Ligges




On 21.09.2011 06:20, Tyler Rinker wrote:


Greetings R community,

I am making my first package and have run into the need to use other packages.  
I  pass all the checks in the command prompt running Rcmd check package.name.  
In the Description file I have included:

Depends: R (= 2.13), plotrix
Repository: CRAN

Now I create the zip file for windows 7.  I delete my plotrix package from my 
library to create a setup where others might encounter when installing my package 
(perhaps they don't have the package dependency plotrix installed).  I now install 
the zip file in my R library and try to load it in R generating the following 
error:



if you have declared stuff as above and CRAN is among the current 
repositories, install.packages() will install the dependencies for you.


Uwe Ligges



library(genTools)

Loading required package: plotrix
Error: package ‘plotrix’ could not be loaded
In addition: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = 
lib.loc) :
   there is no package called ‘plotrix’

Now the question:  How do I get my package to automatically download 
dependencies from CRAN as other CRAN packages do when I install them to my 
library for the first time?

Tyler Rinker

R version 2.14 (beta)
Windows 7   
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Re: [R] problem with function Truncate in package distr

2011-09-21 Thread Uwe Ligges




On 21.09.2011 11:53, Duarte Viana wrote:

Hello all,

Can someone tell me why the following mixture of two log-normal
distributions does not get truncated? What puzzles me is that the
function works almost always, but for certain combinations (like the
one below), it does not.

# R code example
library(distr)
mix-UnivarMixingDistribution(Lnorm(3.2,0.5),Lnorm(5.4,0.6),mixCoeff=c(0.3,0.7))
mix.trunc-Truncate(mix,lower=0.001,upper=3000)
distr.sample-r(mix.trunc)(100)
range(distr.sample)

Why do I get values over 3000 (which was the defoned upper limit)?

Some help would be greatly appreciated.



Some question for the author of package distr, I believe.

Uwe Ligges




Duarte Viana

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[R] chippeakanno package: getAllPeakSequence problem

2011-09-21 Thread Nico902

Hi all,

I am using the package ChIPpeakAnno, and I have a problem with the function
getAllPeakSequence. This is related to object oriented programming I think,
I have the following message:

 peaksWithSequences - getAllPeakSequence(peakList, upstream = 100,
 downstream = 100, genome = Hsapiens)
Error in validObject(.Object) : 
  invalid class GRanges object: superclass Sequence not defined in the
environment of the object's class


Is the error coming from my configuration or from the code? I do not know
many things about OOP in R.

Thanks.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Reading data in lisp format

2011-09-21 Thread David Winsemius

If you think that R is loosely typed, then examining LiSP code will
change your mind, or at least give you a new data point further out on
the Loose-Tight axis. I think you will need to do the processing by
hand.

The organization of the data is fairly clear. There are logical
columns with values :neg and :pos, categorical columns with values in
(id value) pairs, numeric ones and then a group of computed columns
at the bottom. It also appears that after the first enumeration of ids
with logical values that subsequent logical variables are defined
possibly with pos: values only.

So I guess the counter-question is: How important is this particular
dataset to you??

And further question might be, are you sure that you don't want the
dataset that is right next to it: ftp://ftp.ics.uci.edu/pub/machine-learning-databases/credit-screening/crx.data

It is well-behaved comma-separated file.
--
David.

On Sep 21, 2011, at 6:39 AM, ESTEBAN ALFARO CORTES wrote:

Hi,

I am trying to read the credit.lisp file of the Japanese credit
database in UCI repository, but it is in lisp format which I do not
know how to read. I have not found how to do that in the foreign
library

http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening

Could anyone help me?

Best regards,

Esteban Alfaro

PS: This is my first time in r-help so I apologize for possible
inconveniences.

[[alternative HTML version deleted]]

David Winsemius, MD
West Hartford, CT

Re: [R] R help on write.csv

2011-09-21 Thread Jan van der Laan



Michael,

You example doesn't seem to work. Append isn't passed on to the  
write.table call. You will need to add a


 Call$append- append

to the function. And even then there will be a problem with the  
headers that are repeated when appending.



An easier solution is to use write.table directly (I am using  
Dutch/European csv format):


data - data.frame(a=1:10, b=1, c=letters[1:10])
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,  
col.names=TRUE)
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,  
col.names=FALSE, append=TRUE)



When first openening a file connection and passing that to write.csv  
or write.table data is also appended. The problem with write.csv is  
that writing the column names can not be suppressed which will result  
in repeated column names:


con - file(d:\\test2.csv, wt)
write.csv2(data, file=con, row.names=FALSE)
write.csv2(data, file=con, row.names=FALSE)
close(con)

So one will still have to use write.table to avoid this:

con - file(d:\\test2.csv, wt)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE, col.names=TRUE)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,  
col.names=FALSE, append=TRUE)

close(con)

Using a file connection is probably also more efficient when doing a  
large number of appends.


Jan






Quoting R. Michael Weylandt michael.weyla...@gmail.com:


Touche -- perhaps we could make one though?

write.csv.append - function(..., append = TRUE)
{
Call - match.call(expand.dots = TRUE)
for (argname in c(col.names, sep, dec, qmethod)) if
(!is.null(Call[[argname]]))
warning(gettextf(attempt to set '%s' ignored, argname),
domain = NA)
rn - eval.parent(Call$row.names)
Call$col.names - if (is.logical(rn)  !rn)
TRUE
else NA
Call$sep - ,
Call$dec - .
Call$qmethod - double
Call[[1L]] - as.name(write.table)
eval.parent(Call)
}
write.csv.append(1:5,test.csv, append = FALSE)
write.csv.append(1:15, test.csv)

Output seems a little sloppy, but might work for the OP.

Michael Weylandt

On Wed, Sep 21, 2011 at 9:03 AM, Ivan Calandra ivan.calan...@uni-hamburg.de

wrote:



I don't think there is an append argument to write.csv() (well, actually
there is one, but set to FALSE).
There is however one to write.table()
Ivan

Le 9/21/2011 14:54, R. Michael Weylandt michael.weyla...@gmail.com a
écrit :

 The append argument of write.csv()?


Michael

On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.kumar@**
esteeadvisors.com ashish.ku...@esteeadvisors.com  wrote:

 Hi,




I wanted to write the data created using R  on existing csv file. However
everytime I use write.csv, it overwrites the values already there in the
existing csv file. Any workaround on this.



Thanks for your help



Ashish Kumar



Estee Advisors Pvt. Ltd.

Email: ashish.ku...@esteeadvisors.com

Cell: +91-9654072144

Direct: +91-124-4637-713




   [[alternative HTML version deleted]]

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--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
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Re: [R] chippeakanno package: getAllPeakSequence problem

2011-09-21 Thread Uwe Ligges




On 21.09.2011 17:08, Nico902 wrote:

Hi all,

I am using the package ChIPpeakAnno, and I have a problem with the function
getAllPeakSequence. This is related to object oriented programming I think,
I have the following message:


peaksWithSequences- getAllPeakSequence(peakList, upstream = 100,
downstream = 100, genome = Hsapiens)

Error in validObject(.Object) :
   invalid class GRanges object: superclass Sequence not defined in the
environment of the object's class


We do not know, since we do not know what your objects peakList and 
Hsapiens are, hence we cannot reproduce anything here. The example 
works fine for me.


Moreover, please ask question related to BioConductor packages on the 
BioC mailing list.


Best,
Uwe Ligges











Is the error coming from my configuration or from the code? I do not know
many things about OOP in R.

Thanks.

--
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Re: [R] adding labels to x,y points

2011-09-21 Thread B77S

#This should work (again, without your data ??)

colon-read.table(c:\\alon.txt,header=T,row.names=1) 

row.names(colon) -paste(g,c(1:nrow(colon)),sep=)   
 
with(colon[1:20,], plot(norm1, norm2, type='n',xlab='x norm1 sample',ylab='y
norm2 sample',main='Norm1 vs Norm2 - 20 genes'))

with(colon, text(norm1, norm2, label = row.names(colon[1:20,])) 




baumeist wrote:
 
 Hi,
 I am new to R.
 
 I have a matrix that I have assigned to the object “colon”.
 
 colon-read.table(c:\\alon.txt,header=T,row.names=1)
 
 attach(colon)
 names(colon)
 
 The dimenstions are 2000   62.
 
 Each of the 62 columns (titled norm1, norm2, norm3, etc) has 2000
 different numbers (‘continuous’ values) within it.
 
 I have also assigned a name for each of the 2000 rows of the dataframe
 with a prefix (i.e. g1 …. g2000) using the code (not sure if I did this
 right):
 
 colon-paste(g,c(1:nrow(colon)),sep=)
 
 I have plotted the first 20 values from two of the columns(samples).
 
 x-c(norm1[1:20])
 
 y-c(norm2[1:20])
 
 plot(x,y,type='n',xlab='x norm1 sample',ylab='y norm2 sample',main='Norm1
 vs Norm2 - 20
 genes')
 
 points(x,y,pch=15,col='blue')
 
 Now I wish to assign labels to each point (above each point (i.e. pos=3)
 in the plot with “g1 to g20 corresponding to each row but I am having
 trouble with this step.
 
 I have tried:
 
 text(x,y, label = row.names(colon[1:20])) 
 
 but nothing happens. 
 
 Any suggestions?
 
 Thanks in advance
 MAB
 


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Re: [R] chippeakanno package: getAllPeakSequence problem

2011-09-21 Thread Martin Morgan


On 09/21/2011 08:08 AM, Nico902 wrote:

Hi all,

I am using the package ChIPpeakAnno, and I have a problem with the function
getAllPeakSequence. This is related to object oriented programming I think,
I have the following message:


peaksWithSequences- getAllPeakSequence(peakList, upstream = 100,
downstream = 100, genome = Hsapiens)

Error in validObject(.Object) :
   invalid class GRanges object: superclass Sequence not defined in the
environment of the object's class


Is the error coming from my configuration or from the code? I do not know
many things about OOP in R.


Hi Nico902

Please ask questions about this Bioconductor package on the Bioconductor 
mailing list.


http://bioconductor.org/help/mailing-list/

Likely your packages are not at a consistent version. Follow these 
instructions


http://bioconductor.org/install/#update-bioconductor-packages

to update your packages.

Martin



Thanks.

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--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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Re: [R] chippeakanno package: getAllPeakSequence problem

2011-09-21 Thread David Winsemius



On Sep 21, 2011, at 11:08 AM, Nico902 wrote:


Hi all,

I am using the package ChIPpeakAnno, and I have a problem with the  
function
getAllPeakSequence. This is related to object oriented programming I  
think,

I have the following message:


peaksWithSequences - getAllPeakSequence(peakList, upstream = 100,
downstream = 100, genome = Hsapiens)

Error in validObject(.Object) :
 invalid class GRanges object: superclass Sequence not defined  
in the

environment of the object's class


Is the error coming from my configuration or from the code? I do not  
know

many things about OOP in R.


I haven't ever seen that package mentioned on r-help befor, so it is  
probably a BioC package. Bioconductor which has its own mailing list.  
There are a small number of persons who are bicultural with ordinary-R  
and BioC, but they generally suggest to posters to use the BioC list.  
(I don't know if it has a Nabble interface. I'm guessing it does not.)


--

David Winsemius, MD
West Hartford, CT

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Re: [R] R help on write.csv

2011-09-21 Thread Jan van der Laan


Michael,

You example doesn't seem to work. Append isn't passed on to the  
write.table call. You

will need to add a

 Call$append- append

to the function. And even then there will be a problem with the  
headers that are repeated

when appending.


An easier solution is to use write.table directly (I am using  
Dutch/European csv format):


data - data.frame(a=1:10, b=1, c=letters[1:10])
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,  
col.names=TRUE)
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,  
col.names=FALSE,

append=TRUE)


When first openening a file connection and passing that to write.csv  
or write.table data
is also appended. The problem with write.csv is that writing the  
column names can not be

suppressed which will result in repeated column names:

con - file(d:test2.csv, wt)
write.csv2(data, file=con, row.names=FALSE)
write.csv2(data, file=con, row.names=FALSE)
close(con)

So one will still have to use write.table to avoid this:

con - file(d:test2.csv, wt)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE, col.names=TRUE)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,  
col.names=FALSE,

append=TRUE)
close(con)

Using a file connection is probably also more efficient when doing a  
large number of

appends.

Jan





Quoting R. Michael Weylandt michael.weyla...@gmail.com:


Touche -- perhaps we could make one though?

write.csv.append - function(..., append = TRUE)
{
Call - match.call(expand.dots = TRUE)
for (argname in c(col.names, sep, dec, qmethod)) if
(!is.null(Call[[argname]]))
warning(gettextf(attempt to set '%s' ignored, argname),
domain = NA)
rn - eval.parent(Call$row.names)
Call$col.names - if (is.logical(rn)  !rn)
TRUE
else NA
Call$sep - ,
Call$dec - .
Call$qmethod - double
Call[[1L]] - as.name(write.table)
eval.parent(Call)
}
write.csv.append(1:5,test.csv, append = FALSE)
write.csv.append(1:15, test.csv)

Output seems a little sloppy, but might work for the OP.

Michael Weylandt

On Wed, Sep 21, 2011 at 9:03 AM, Ivan Calandra ivan.calan...@uni-hamburg.de

wrote:



I don't think there is an append argument to write.csv() (well, actually
there is one, but set to FALSE).
There is however one to write.table()
Ivan

Le 9/21/2011 14:54, R. Michael Weylandt michael.weyla...@gmail.com a
écrit :

 The append argument of write.csv()?


Michael

On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.kumar@**
esteeadvisors.com ashish.ku...@esteeadvisors.com  wrote:

 Hi,




I wanted to write the data created using R  on existing csv file. However
everytime I use write.csv, it overwrites the values already there in the
existing csv file. Any workaround on this.



Thanks for your help



Ashish Kumar



Estee Advisors Pvt. Ltd.

Email: ashish.ku...@esteeadvisors.com

Cell: +91-9654072144

Direct: +91-124-4637-713




   [[alternative HTML version deleted]]

__**
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and provide commented, minimal, self-contained, reproducible code.


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and provide commented, minimal, self-contained, reproducible code.



--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
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Re: [R] R help on write.csv

2011-09-21 Thread Jan van der Laan


Michael,

You example doesn't seem to work. Append isn't passed on to the  
write.table call. You will need to add a


 Call$append- append

to the function. And even then there will be a problem with the  
headers that are repeated when appending.



An easier solution is to use write.table directly (I am using  
Dutch/European csv format):


data - data.frame(a=1:10, b=1, c=letters[1:10])
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,  
col.names=TRUE)
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,  
col.names=FALSE,

append=TRUE)


When first openening a file connection and passing that to write.csv  
or write.table data is also appended. The problem with write.csv is  
that writing the column names can not be suppressed which will result  
in repeated column names:


con - file(d:test2.csv, wt)
write.csv2(data, file=con, row.names=FALSE)
write.csv2(data, file=con, row.names=FALSE)
close(con)

So one will still have to use write.table to avoid this:

con - file(d:test2.csv, wt)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE, col.names=TRUE)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,  
col.names=FALSE,

append=TRUE)
close(con)

Using a file connection is probably also more efficient when doing a  
large number of appends.


Jan








Quoting R. Michael Weylandt michael.weyla...@gmail.com:


Touche -- perhaps we could make one though?

write.csv.append - function(..., append = TRUE)
{
Call - match.call(expand.dots = TRUE)
for (argname in c(col.names, sep, dec, qmethod)) if
(!is.null(Call[[argname]]))
warning(gettextf(attempt to set '%s' ignored, argname),
domain = NA)
rn - eval.parent(Call$row.names)
Call$col.names - if (is.logical(rn)  !rn)
TRUE
else NA
Call$sep - ,
Call$dec - .
Call$qmethod - double
Call[[1L]] - as.name(write.table)
eval.parent(Call)
}
write.csv.append(1:5,test.csv, append = FALSE)
write.csv.append(1:15, test.csv)

Output seems a little sloppy, but might work for the OP.

Michael Weylandt

On Wed, Sep 21, 2011 at 9:03 AM, Ivan Calandra ivan.calan...@uni-hamburg.de

wrote:



I don't think there is an append argument to write.csv() (well, actually
there is one, but set to FALSE).
There is however one to write.table()
Ivan

Le 9/21/2011 14:54, R. Michael Weylandt michael.weyla...@gmail.com a
écrit :

 The append argument of write.csv()?


Michael

On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.kumar@**
esteeadvisors.com ashish.ku...@esteeadvisors.com  wrote:

 Hi,




I wanted to write the data created using R  on existing csv file. However
everytime I use write.csv, it overwrites the values already there in the
existing csv file. Any workaround on this.



Thanks for your help



Ashish Kumar



Estee Advisors Pvt. Ltd.

Email: ashish.ku...@esteeadvisors.com

Cell: +91-9654072144

Direct: +91-124-4637-713




   [[alternative HTML version deleted]]

__**
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and provide commented, minimal, self-contained, reproducible code.


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--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de

**
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-**hamburg.de/mammals/eng/1525_8_**1.phphttp://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php


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[R] Power calculation for survival analysis

2011-09-21 Thread Duke

useR's,
I am trying to do a power calculation for a survival analysis using a
logrank test and I need some help properly doing this in R.  Here is the
information that I know:
- I have 2 groups, namely HG and LG
- Retrospective analysis with subjects gathered from archival data over 20
years. No new recruitment of subjects and no estimated time to target
accrual and accrual rate.
- Survival measured in both groups at 1 year, 3 years, 5 years.
- Assume 50% survival for LG and 30% survival for HG at 5 years.
- Assume a 6 month difference in overall survival to be statistically
significant.
- Total sample size is ~ N=500 with 15% of subjects comprising the LG group;
85% make up the HG group.

The main hypothesis is that HG group has shorter overall survival than LG
group.

Can someone please help me out with how to properly calculate the power for
such a situation using R? This is new to me.

Thanks,
D  

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[R] logistic regression: default computed probability

2011-09-21 Thread n

Hello all,

Suppose in a logistic regression model, the binary outcome is coded as
0 or 1.
In SAS, the default probability computed is for Y = 0 (smaller of the
two values) . However, in SPSS the probability computed is for Y = 1
(greater of the two values).

Which one does R compute, the probability for the smaller or the
greater value?

I went through the documentation in a hurry but couldn't find a clue.

Thanks

Nikhil

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Re: [R] logistic regression: default computed probability

On Sep 21, 2011, at 10:25 AM, n wrote:

 Hello all,
 
 Suppose in a logistic regression model, the binary outcome is coded as
 0 or 1.
 In SAS, the default probability computed is for Y = 0 (smaller of the
 two values) . However, in SPSS the probability computed is for Y = 1
 (greater of the two values).
 
 Which one does R compute, the probability for the smaller or the
 greater value?
 
 I went through the documentation in a hurry but couldn't find a clue.
 
 Thanks
 
 Nikhil


From ?glm in the Details section:

For binomial and quasibinomial families the response can also be specified as a 
factor (when the first level denotes failure and all others success) or as a 
two-column matrix with the columns giving the numbers of successes and failures.

So P(Y = 1) if using 0/1.

HTH,

Marc Schwartz

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Re: [R] help in interpreting paired t-test

2011-09-21 Thread Greg Snow

It looks like Bland-Altman procedures would be appropriate for this project 
(http://en.wikipedia.org/wiki/Bland-Altman_plot).  

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Pedro Mardones
Sent: Tuesday, September 20, 2011 11:47 AM
To: R-help@r-project.org
Subject: [R] help in interpreting paired t-test

Dear all;

A very basic question. I have the following data:

A - 1/1000*c(347,328,129,122,18,57,105,188,57,257,53,108,336,163,
62,112,334,249,45,244,211,175,174,26,375,346,153,32,
89,32,358,202,123,131,88,36,30,67,96,135,219,122,
89,117,86,169,179,54,48,40,54,568,664,277,91,290,
116,80,107,401,225,517,90,133,36,50,174,103,192,150,
225,29,80,199,55,258,97,109,137,90,236,109,204,160,
95,54,50,78,98,141,508,144,434,100,37,22,304,175,
72,71,111,60,212,73,50,92,70,148,28,63,46,85,
111,67,234,65,92,59,118,202,21,17,95,86,296,45,
139,32,21,70,185,172,151,129,42,14,13,75,303,119,
128,106,224,241,112,395,78,89,247,122,212,61,165,30,
65,261,415,159,316,182,141,184,124,223,39,141,103,149,
104,71,259,86,85,214,96,246,306,11,129)

B - 1/1000*c(351,313,130,119,17,50,105,181,58,255,51,98,335,162,
60,108,325,240,44,242,208,168,170,27,356,341,150,31,
85,29,363,185,124,131,85,35,27,63,92,147,217,117,
87,119,81,161,178,53,45,38,50,581,661,254,87,281,
110,76,100,401,220,507,94,123,36,47,154,99,184,146,
232,26,77,193,53,264,94,110,128,87,231,110,195,156,
95,51,50,75,93,134,519,139,435,96,37,21,293,169,
70,80,104,64,210,70,48,88,67,140,26,52,45,90,
106,63,219,62,91,56,113,187,18,14,95,86,284,39,
132,31,22,69,181,167,150,117,42,14,11,73,303,109,
129,106,227,249,111,409,71,88,256,120,200,60,159,27,
63,268,389,150,311,175,136,171,116,220,30,145,95,148,
102,70,251,88,83,199,94,245,305,9,129)

plot(A,B)
abline(0,1)

At a glance, the data look very similar. Data A and B are two
measurements of the same variable but using different devices (on a
same set of subjects). Thus, I thought that a paired t-test could be
appropriate to check if the diff between measurement devices = 0.

t.test(A-B)

One Sample t-test

data:  A - B
t = 7.6276, df = 178, p-value = 1.387e-12
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
 0.002451622 0.004162903
sample estimates:
  mean of x
0.003307263

The mean diff is 0.0033 but the p-value indicates a strong evidence to
reject H0.

I was expecting to find no differences so I'm wondering whether the
t-test is the appropriate test to use. I'll appreciate any comments or
suggestions.

BR,
PM

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Re: [R] help in interpreting paired t-test

2011-09-21 Thread Jeremy Miles

 cor(A, B)
[1] 0.9986861

The data are very, very highly correlated. The higher the correlation,
the greater the power of the t-test to detect the same difference
between the means.

Jeremy

On 20 September 2011 10:46, Pedro Mardones mardone...@gmail.com wrote:
 Dear all;

 A very basic question. I have the following data:

 

 A - 1/1000*c(347,328,129,122,18,57,105,188,57,257,53,108,336,163,
 62,112,334,249,45,244,211,175,174,26,375,346,153,32,
 89,32,358,202,123,131,88,36,30,67,96,135,219,122,
 89,117,86,169,179,54,48,40,54,568,664,277,91,290,
 116,80,107,401,225,517,90,133,36,50,174,103,192,150,
 225,29,80,199,55,258,97,109,137,90,236,109,204,160,
 95,54,50,78,98,141,508,144,434,100,37,22,304,175,
 72,71,111,60,212,73,50,92,70,148,28,63,46,85,
 111,67,234,65,92,59,118,202,21,17,95,86,296,45,
 139,32,21,70,185,172,151,129,42,14,13,75,303,119,
 128,106,224,241,112,395,78,89,247,122,212,61,165,30,
 65,261,415,159,316,182,141,184,124,223,39,141,103,149,
 104,71,259,86,85,214,96,246,306,11,129)

 B - 1/1000*c(351,313,130,119,17,50,105,181,58,255,51,98,335,162,
 60,108,325,240,44,242,208,168,170,27,356,341,150,31,
 85,29,363,185,124,131,85,35,27,63,92,147,217,117,
 87,119,81,161,178,53,45,38,50,581,661,254,87,281,
 110,76,100,401,220,507,94,123,36,47,154,99,184,146,
 232,26,77,193,53,264,94,110,128,87,231,110,195,156,
 95,51,50,75,93,134,519,139,435,96,37,21,293,169,
 70,80,104,64,210,70,48,88,67,140,26,52,45,90,
 106,63,219,62,91,56,113,187,18,14,95,86,284,39,
 132,31,22,69,181,167,150,117,42,14,11,73,303,109,
 129,106,227,249,111,409,71,88,256,120,200,60,159,27,
 63,268,389,150,311,175,136,171,116,220,30,145,95,148,
 102,70,251,88,83,199,94,245,305,9,129)

 

 plot(A,B)
 abline(0,1)

 At a glance, the data look very similar. Data A and B are two
 measurements of the same variable but using different devices (on a
 same set of subjects). Thus, I thought that a paired t-test could be
 appropriate to check if the diff between measurement devices = 0.

 t.test(A-B)

 

 One Sample t-test

 data:  A - B
 t = 7.6276, df = 178, p-value = 1.387e-12
 alternative hypothesis: true mean is not equal to 0
 95 percent confidence interval:
  0.002451622 0.004162903
 sample estimates:
  mean of x
 0.003307263

 
 The mean diff is 0.0033 but the p-value indicates a strong evidence to
 reject H0.

 I was expecting to find no differences so I'm wondering whether the
 t-test is the appropriate test to use. I'll appreciate any comments or
 suggestions.

 BR,
 PM

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Re: [R] Specifying Start/End Dates for X-axis Range in plot()/xyplot()

2011-09-21 Thread Rich Shepard


On Tue, 20 Sep 2011, David Winsemius wrote:

It seems likely even if you got past that error, you would encounter problems 
from the hashed up syntax in this portion of that plot call:


z[, $'Burns Mg']


David,

  Yes, that's not close to correct.

  If I specify
plot(z[, Burns Mg])  # returned by names(z)
I see the plot with the x-axis range from the earliest date for any data
(1980-01-01) to the latest date for any data (2011-06-09). What I'm
trying to learn is how to specify start and end dates for each of the z
names. I have these dates as a list returned by:
lapply(1:ncol(z), function(i) range(time(na.omit(z[, i]

  What I thought might wark was
	plot(z[, Burns Mg], start = as.Date(1994-01-20), end = 
as.Date(2009-11-11))  # wrapped in alpine; a single line in emacs


but this generates warnings and no plots.

  In the zoo-quickref vignette are examples of querying dates (bottom of
page 1) and selecting a range of dates of interest (page 5, using the
window() function), but I cannot extrapolat from these examples to to plot a
specified stream/param pair only within explicit start and end dates.

  Is there documentation I can read that will teach me the proper syntax?
Or, can you show me how to specify those dates when plotting z elements?

Rich

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Re: [R] tcltk freezes R

2011-09-21 Thread tm

was all prebuilt.

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Re: [R] help in interpreting paired t-test

Jeremy,

Correlation alone is irrelevant when comparing two separate sets of 
measurements on the same specimen. Correlation does not mean good agreement, 
but good agreement tends to infer high correlation.

T1 - rnorm(50, mean = 100)

 mean(T1)
[1] 99.80257

T2 - T1 * 1.5

 mean(T2)
[1] 149.7039

The two measures are off by a systematic 50%, but:

 cor(T1, T2)
[1] 1


The key here, as I noted in my reply yesterday and as Greg noted in his this 
morning regarding Bland-Altman, is whether or not the two measures agree within 
an acceptable margin of error and whether or not there is systematic bias in 
the measures, either overall or perhaps one measure tends to be low at one end 
of the range, while high at the other.

HTH,

Marc Schwartz


On Sep 21, 2011, at 11:20 AM, Jeremy Miles wrote:

 cor(A, B)
 [1] 0.9986861
 
 The data are very, very highly correlated. The higher the correlation,
 the greater the power of the t-test to detect the same difference
 between the means.
 
 Jeremy
 
 On 20 September 2011 10:46, Pedro Mardones mardone...@gmail.com wrote:
 Dear all;
 
 A very basic question. I have the following data:
 
 
 
 A - 1/1000*c(347,328,129,122,18,57,105,188,57,257,53,108,336,163,
 62,112,334,249,45,244,211,175,174,26,375,346,153,32,
 89,32,358,202,123,131,88,36,30,67,96,135,219,122,
 89,117,86,169,179,54,48,40,54,568,664,277,91,290,
 116,80,107,401,225,517,90,133,36,50,174,103,192,150,
 225,29,80,199,55,258,97,109,137,90,236,109,204,160,
 95,54,50,78,98,141,508,144,434,100,37,22,304,175,
 72,71,111,60,212,73,50,92,70,148,28,63,46,85,
 111,67,234,65,92,59,118,202,21,17,95,86,296,45,
 139,32,21,70,185,172,151,129,42,14,13,75,303,119,
 128,106,224,241,112,395,78,89,247,122,212,61,165,30,
 65,261,415,159,316,182,141,184,124,223,39,141,103,149,
 104,71,259,86,85,214,96,246,306,11,129)
 
 B - 1/1000*c(351,313,130,119,17,50,105,181,58,255,51,98,335,162,
 60,108,325,240,44,242,208,168,170,27,356,341,150,31,
 85,29,363,185,124,131,85,35,27,63,92,147,217,117,
 87,119,81,161,178,53,45,38,50,581,661,254,87,281,
 110,76,100,401,220,507,94,123,36,47,154,99,184,146,
 232,26,77,193,53,264,94,110,128,87,231,110,195,156,
 95,51,50,75,93,134,519,139,435,96,37,21,293,169,
 70,80,104,64,210,70,48,88,67,140,26,52,45,90,
 106,63,219,62,91,56,113,187,18,14,95,86,284,39,
 132,31,22,69,181,167,150,117,42,14,11,73,303,109,
 129,106,227,249,111,409,71,88,256,120,200,60,159,27,
 63,268,389,150,311,175,136,171,116,220,30,145,95,148,
 102,70,251,88,83,199,94,245,305,9,129)
 
 
 
 plot(A,B)
 abline(0,1)
 
 At a glance, the data look very similar. Data A and B are two
 measurements of the same variable but using different devices (on a
 same set of subjects). Thus, I thought that a paired t-test could be
 appropriate to check if the diff between measurement devices = 0.
 
 t.test(A-B)
 
 
 
 One Sample t-test
 
 data:  A - B
 t = 7.6276, df = 178, p-value = 1.387e-12
 alternative hypothesis: true mean is not equal to 0
 95 percent confidence interval:
  0.002451622 0.004162903
 sample estimates:
  mean of x
 0.003307263
 
 
 The mean diff is 0.0033 but the p-value indicates a strong evidence to
 reject H0.
 
 I was expecting to find no differences so I'm wondering whether the
 t-test is the appropriate test to use. I'll appreciate any comments or
 suggestions.
 
 BR,
 PM
 
 __
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Power calculation for survival analysis

On Sep 21, 2011, at 8:54 AM, Duke wrote:

 useR's,
 I am trying to do a power calculation for a survival analysis using a
 logrank test and I need some help properly doing this in R.  Here is the
 information that I know:
 - I have 2 groups, namely HG and LG
 - Retrospective analysis with subjects gathered from archival data over 20
 years. No new recruitment of subjects and no estimated time to target
 accrual and accrual rate.
 - Survival measured in both groups at 1 year, 3 years, 5 years.
 - Assume 50% survival for LG and 30% survival for HG at 5 years.
 - Assume a 6 month difference in overall survival to be statistically
 significant.
 - Total sample size is ~ N=500 with 15% of subjects comprising the LG group;
 85% make up the HG group.
 
 The main hypothesis is that HG group has shorter overall survival than LG
 group.
 
 Can someone please help me out with how to properly calculate the power for
 such a situation using R? This is new to me.
 
 Thanks,
 D  



Short answer, look at the cpower() function in Frank's Hmisc package on CRAN.

Longer answer:

Have you already performed the data collection and analysis? If so, then 
performing a post hoc power calculation is highly problematic. Do a Google 
search on post hoc power and you will find a myriad of resources/citations.

Given the sizable differences in the two samples and that this is a 
retrospective analysis, you are almost certainly going to have selection bias 
issues to deal with in comparing the two groups, since presumably they were not 
prospectively randomized to group, even with the ratio indicated. 

Is the HG group High Grade Lymphoma and the LG group Low Grade Lymphoma? That 
would help to explain some of the issues here, since you have two groups with 
differing diagnoses, differing baseline characteristics and known material 
differences in prognosis.

With a retrospective analysis over this time frame, loss to follow up (LTFU) is 
likely to be another issue, impacting your available data over time, especially 
if there is a bias in LTFU between the groups. LTFU is hard enough to manage in 
a prospective study.

Using your numbers, you also have the potential for temporal issues impacting 
your comparison. If you are looking out to 5 years and the data was collected 
over a 20 year time frame, that suggests a possible 15 year difference between 
your first patient Time 0 and your last patient Time 0. What changes in patient 
and/or treatment profiles occurred over time that might impact your findings? 
Were the two groups treated concurrently or is there a stagger of some time 
window? Are the patients a consecutive series in each group or is there other 
selection bias involved as to why one patient is in the study and another is 
not.

If you are not comfortable with these issues, you have a lot of resources at 
Duke (eg. DCRI) with some very experienced folks there.

HTH,

Marc Schwartz

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Re: [R] Power calculation for survival analysis

2011-09-21 Thread Duke

Thanks for your response, Marc.  HG and LG are high-grade/low-grade tumors. 
The data has not been collected yet, but will be soon.  It's all archived
data that will be pulled from computer records.  The IRB wants some mention
of power or sample size, but doing it for this scenario has been a bit of a
head scratcher for me.
If it's not really feasible to do a power analysis for this scenario, I can
work to explain why to the IRB.

D 

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Making ?source act as if it is run through the terminal

Maybe some of the source() options will work.

Suppose you have the following in an R file:

 junk.R 
1:5
x = 1:10
library(ggplot2)
data(VADeaths)
pl - ggplot(melt(VADeaths),aes(value, X1))+ geom_point() +
facet_wrap(~X2)+ylab()
pl

Then from the command line:

 source(junk.R)
## No output

 source(junk.R, print.eval = TRUE)
[1] 1 2 3 4 5

and a window displays a graph.

Not sure if this will work with the HTML stuff (don't know the first thing
about the package), but it seems like a start.

Hope this helps,

Michael Weylandt



On Wed, Sep 21, 2011 at 9:03 AM, Tal Galili tal.gal...@gmail.com wrote:

 Hello dear R help,

 The motivation for my question is wanting to run HTMLStart {R2HTML package}
 from source.

 *Background:*

 I was happy to discover the [ HTMLStart/HTMLStop, HTMLplot] functions in
 the
 R2HTML package.

 They allow my R code to run almost as is, but while writing most of the
 output (including the figures, when using  HTMLplot) into an external HTML
 file.
 This method works rather well, but only when the script is running from the
 terminal.
 When I try using the code from ?source, the functions fails completely
 (with
 both output and especially with figures)

 I assume the reason is because of what is said in the help file:
 Note that running code via source differs in a few respects from entering
 it at the R command line. Since expressions are not executed at the top
 level, auto-printing is not done. So you will need to include explicit
 print
 calls for things you want to be printed

 *Question:*
 Hence my question is - can it be avoided?
 Can the source be set to act just as if the code were to run from the
 terminal?



 Thanks,
 Tal


 Contact
 Details:---
 Contact me: tal.gal...@gmail.com |  972-52-7275845
 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
 www.r-statistics.com (English)

 --

[[alternative HTML version deleted]]

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Re: [R] glmnet for Binary trait analysis

2011-09-21 Thread Noah

Hi Bert,

You are correct. I checked the data and did find some empty values in the X
matrix. 

Thanks for your kindly help!

Noah

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Re: [R] help in interpreting paired t-test

2011-09-21 Thread Pedro Mardones

Thanks for all the replies and comments. I've followed Marc's
suggestion of using the Bland-Altman's approach which I found pretty
clarifying for comparing data collected on the same subjects.

BR,
PM

On Wed, Sep 21, 2011 at 1:39 PM, Marc Schwartz marc_schwa...@me.com wrote:
 Jeremy,

 Correlation alone is irrelevant when comparing two separate sets of 
 measurements on the same specimen. Correlation does not mean good agreement, 
 but good agreement tends to infer high correlation.

 T1 - rnorm(50, mean = 100)

 mean(T1)
 [1] 99.80257

 T2 - T1 * 1.5

 mean(T2)
 [1] 149.7039

 The two measures are off by a systematic 50%, but:

 cor(T1, T2)
 [1] 1


 The key here, as I noted in my reply yesterday and as Greg noted in his this 
 morning regarding Bland-Altman, is whether or not the two measures agree 
 within an acceptable margin of error and whether or not there is systematic 
 bias in the measures, either overall or perhaps one measure tends to be low 
 at one end of the range, while high at the other.

 HTH,

 Marc Schwartz


 On Sep 21, 2011, at 11:20 AM, Jeremy Miles wrote:

 cor(A, B)
 [1] 0.9986861

 The data are very, very highly correlated. The higher the correlation,
 the greater the power of the t-test to detect the same difference
 between the means.

 Jeremy

 On 20 September 2011 10:46, Pedro Mardones mardone...@gmail.com wrote:
 Dear all;

 A very basic question. I have the following data:

 

 A - 1/1000*c(347,328,129,122,18,57,105,188,57,257,53,108,336,163,
 62,112,334,249,45,244,211,175,174,26,375,346,153,32,
 89,32,358,202,123,131,88,36,30,67,96,135,219,122,
 89,117,86,169,179,54,48,40,54,568,664,277,91,290,
 116,80,107,401,225,517,90,133,36,50,174,103,192,150,
 225,29,80,199,55,258,97,109,137,90,236,109,204,160,
 95,54,50,78,98,141,508,144,434,100,37,22,304,175,
 72,71,111,60,212,73,50,92,70,148,28,63,46,85,
 111,67,234,65,92,59,118,202,21,17,95,86,296,45,
 139,32,21,70,185,172,151,129,42,14,13,75,303,119,
 128,106,224,241,112,395,78,89,247,122,212,61,165,30,
 65,261,415,159,316,182,141,184,124,223,39,141,103,149,
 104,71,259,86,85,214,96,246,306,11,129)

 B - 1/1000*c(351,313,130,119,17,50,105,181,58,255,51,98,335,162,
 60,108,325,240,44,242,208,168,170,27,356,341,150,31,
 85,29,363,185,124,131,85,35,27,63,92,147,217,117,
 87,119,81,161,178,53,45,38,50,581,661,254,87,281,
 110,76,100,401,220,507,94,123,36,47,154,99,184,146,
 232,26,77,193,53,264,94,110,128,87,231,110,195,156,
 95,51,50,75,93,134,519,139,435,96,37,21,293,169,
 70,80,104,64,210,70,48,88,67,140,26,52,45,90,
 106,63,219,62,91,56,113,187,18,14,95,86,284,39,
 132,31,22,69,181,167,150,117,42,14,11,73,303,109,
 129,106,227,249,111,409,71,88,256,120,200,60,159,27,
 63,268,389,150,311,175,136,171,116,220,30,145,95,148,
 102,70,251,88,83,199,94,245,305,9,129)

 

 plot(A,B)
 abline(0,1)

 At a glance, the data look very similar. Data A and B are two
 measurements of the same variable but using different devices (on a
 same set of subjects). Thus, I thought that a paired t-test could be
 appropriate to check if the diff between measurement devices = 0.

 t.test(A-B)

 

 One Sample t-test

 data:  A - B
 t = 7.6276, df = 178, p-value = 1.387e-12
 alternative hypothesis: true mean is not equal to 0
 95 percent confidence interval:
  0.002451622 0.004162903
 sample estimates:
  mean of x
 0.003307263

 
 The mean diff is 0.0033 but the p-value indicates a strong evidence to
 reject H0.

 I was expecting to find no differences so I'm wondering whether the
 t-test is the appropriate test to use. I'll appreciate any comments or
 suggestions.

 BR,
 PM

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Re: [R] help with installing tar.gz package

2011-09-21 Thread moldovean

Yay! Thanks! I installed it too!
Now the question would be how to use it

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[R] Weighted Average on More than One Variable in Data Frame

2011-09-21 Thread StellathePug

Dear R Users,
I have looked for a solution to the following problem and I have not been
able to find it on the archive, through Google or in the R documentation.

I have a data frame, say df, which has 4 variables, one of which I would
like to use as a grouping variable (g), another one that I would like to use
for my weights (w) The other two variables are variables (x1 and x2) for
which I would like to compute the weighted average by group.

df - data.frame(x1 = c(15, 12,  3, 10, 10, 14, 12), 
   x2 = c(10, 11, 16,  9,   7, 17, 18),
g = c(  1,   1,  1,  2,   2,   3,  3), 
w = c( 2,   3,  1,  5,   5,   2,  5)) 

wx1 - sapply(split(df, df$g), function(x){weighted.mean(x$x1, x$w)}) 
wx2 - sapply(split(df, df$g), function(x){weighted.mean(x$x2, x$w)})

The above code works, the result is:
 wx1
   123 
11.5 10.0 12.57143 
 wx2
   123 
11.5  8.0 17.71429

But is there not a more elegant way of acting on x1 and x2 simultaneously?
Something along the lines of

wdf - sapply(split(df, df$g), function(x){weighted.mean(df, x$w)})

which is wrong since df has two columns, while w only has one. I suppose,
one could write a loop but that strikes me as being highly inefficient.

Thank you very much for your help!
Rita

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Re: [R] package / function for monitoring processes?

2011-09-21 Thread jim holtman

Here is the function I use:

 my.stats - function (text = stats, reset = FALSE, oper = )
{
procTime - proc.time()[1:3]
if (reset) {
Level - 1
Stack[Level, ] - c(procTime[3], procTime[1] + procTime[2])
}
if (oper == push) {
if (Level  MaxLevel)
Level - Level + 1
Stack[Level, ] - c(procTime[3], procTime[1] + procTime[2])
}
.caller - sys.calls()
if (length(.caller) == 1)
.caller - Rgui
else .caller - as.character(.caller[[length(.caller) - 1]])[1]
cat(sprintf(%s (%d) - %s : %s %.1f %.1f %.1f : %.1fMB\n,
text, Level, .caller, format(Sys.time(), format = %H:%M:%S),
procTime[1] + procTime[2] - Stack[Level, 2], procTime[3] -
Stack[Level, 1], procTime[3], memory.size()))
if ((oper == pop)  (Level  1))
Level - Level - 1
else if (oper == reset)
Level - 1
invisible(flush.console())
}

Here is an example of its use:  inside the  is the total CPU and
elapsed time to that point.

 my.stats('start')
start (1) - Rgui : 14:29:27 30.7 20136.7 20136.7 : 107.8MB
 for (i in 1:1e6) i+1  # consume some CPU
 for (i in 1:10e6) i+1  # consume some CPU
 my.stats('end')  # used almost 8 secs of CPU time
end (1) - Rgui : 14:30:24 38.4 20193.0 20193.0 : 139.4MB




On Tue, Sep 20, 2011 at 9:16 PM, Benjamin Tyner bty...@gmail.com wrote:
 Hi

 I recall running across a function a while back which would return
 information about running processes (such as their cpu and memory usage),
 but I cannot seem to locate it. Wondering if someone would be kind enough to
 refresh my memory. I vaguely recall it was parsing the output of the 'ps'
 command.

 Thanks,
 Ben



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-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?

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Re: [R] R help on write.csv

Oh darn, I had that line and then when I copied it to gmail I thought I'd be
all slick and clean up my code: oh well...just not my day/thread...

It's possible to work around the repeated headers business (change to
something like Call$col.names - !append) but yeah, at this point I'm
thinking its perhaps better practice to direct the OP to the various
connection methods: sink() is nice, but he'll probably have to do something
to convert his object to a CSV like string before printing:

apply(OBJ, 1, paste, sep=,)

Michael Weylandt

On Wed, Sep 21, 2011 at 11:20 AM, Jan van der Laan e...@dds.nl wrote:

 Michael,

 You example doesn't seem to work. Append isn't passed on to the write.table
 call. You will need to add a

  Call$append- append

 to the function. And even then there will be a problem with the headers
 that are repeated when appending.


 An easier solution is to use write.table directly (I am using
 Dutch/European csv format):

 data - data.frame(a=1:10, b=1, c=letters[1:10])
 write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,
 col.names=TRUE)
 write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,
 col.names=FALSE,
 append=TRUE)


 When first openening a file connection and passing that to write.csv or
 write.table data is also appended. The problem with write.csv is that
 writing the column names can not be suppressed which will result in repeated
 column names:

 con - file(d:test2.csv, wt)
 write.csv2(data, file=con, row.names=FALSE)
 write.csv2(data, file=con, row.names=FALSE)
 close(con)

 So one will still have to use write.table to avoid this:

 con - file(d:test2.csv, wt)
 write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
 col.names=TRUE)
 write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
 col.names=FALSE,
 append=TRUE)
 close(con)

 Using a file connection is probably also more efficient when doing a large
 number of appends.

 Jan








 Quoting R. Michael Weylandt michael.weyla...@gmail.com:

  Touche -- perhaps we could make one though?

 write.csv.append - function(..., append = TRUE)
 {
Call - match.call(expand.dots = TRUE)
for (argname in c(col.names, sep, dec, qmethod)) if
 (!is.null(Call[[argname]]))
warning(gettextf(attempt to set '%s' ignored, argname),
domain = NA)
rn - eval.parent(Call$row.names)
Call$col.names - if (is.logical(rn)  !rn)
TRUE
else NA
Call$sep - ,
Call$dec - .
Call$qmethod - double
Call[[1L]] - as.name(write.table)
eval.parent(Call)
 }
 write.csv.append(1:5,test.**csv, append = FALSE)
 write.csv.append(1:15, test.csv)

 Output seems a little sloppy, but might work for the OP.

 Michael Weylandt

 On Wed, Sep 21, 2011 at 9:03 AM, Ivan Calandra 
 ivan.calan...@uni-hamburg.de

 wrote:


  I don't think there is an append argument to write.csv() (well, actually
 there is one, but set to FALSE).
 There is however one to write.table()
 Ivan

 Le 9/21/2011 14:54, R. Michael Weylandt michael.weyla...@gmail.com a
 écrit :

  The append argument of write.csv()?


 Michael

 On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.kumar@**
 esteeadvisors.com 
 ashish.kumar@esteeadvisors.**comashish.ku...@esteeadvisors.com
  wrote:

  Hi,




 I wanted to write the data created using R  on existing csv file.
 However
 everytime I use write.csv, it overwrites the values already there in
 the
 existing csv file. Any workaround on this.



 Thanks for your help



 Ashish Kumar



 Estee Advisors Pvt. Ltd.

 Email: ashish.ku...@esteeadvisors.com

 Cell: +91-9654072144

 Direct: +91-124-4637-713




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 http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html
 

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  --
 Ivan CALANDRA
 PhD Student
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 Biozentrum Grindel und Zoologisches Museum
 Dept. Mammalogy
 Martin-Luther-King-Platz 3
 D-20146 Hamburg, GERMANY
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[R] Quelplot

2011-09-21 Thread Hadley Wickham

Hi all,

Does anyone have an R implementation of the queplot (K. M. Goldberg
and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics,
34(3):pp. 307–320, 1992)?  I'm struggling with the estimation of the
asymmetry parameters.

Hadley

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

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Re: [R] Power calculation for survival analysis


On Sep 21, 2011, at 12:37 PM, Duke wrote:

 Thanks for your response, Marc.  HG and LG are high-grade/low-grade tumors. 
 The data has not been collected yet, but will be soon.  It's all archived
 data that will be pulled from computer records.  The IRB wants some mention
 of power or sample size, but doing it for this scenario has been a bit of a
 head scratcher for me.
 If it's not really feasible to do a power analysis for this scenario, I can
 work to explain why to the IRB.
 
 D 


Hi Derek,

My guess is that the IRB wants to have some CYA in terms of the justification 
for the study. In a design such as this, safety is not the typical concern, 
since the patients have already been treated and nothing that you are going to 
do will affect that. More than likely, there may be privacy (e.g. HIPAA) and 
ethical issues, pertaining to your accessing the medical records of the 
patients and having a reasonable level of assurance that you will be able to 
offer some scientific value at the end of the day as a consequence of that 
access.

I don't know the particulars of your IRB, so it may be of value to approach 
others at Duke who have experience in dealing with them in the setting of a 
retrospective chart review. You may be able to get a sense for what they are 
open to in terms of justification and where they may or may not be amenable to 
a discussion of the pros/cons of this particular approach.

It is not uncommon, in my experience, to simply indicate that n = 500 is a 
convenience sample, based upon some assessment of time/budget limitations and 
some attempt to assess the number of patients with some common set of 
characteristics that are likely to be available within a reasonable time frame. 
In that setting, power as a discrete quantity is not quoted and you don't have 
an explicit hypothesis to be tested. You get what you get and within the 
limitations of the study design, can offer some insight into the differences in 
the two groups. I have seen the same approach even with prospective, 
non-randomized designs.

All of that being said, you can use Frank's cpower() function in Hmisc, if they 
put a gun to your head. It would not be overly difficult to do that, you just 
need to be aware of your assumptions and how they can impact the resultant 
power calculation. Using the function itself is not overly complex.

HTH,

Marc

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Re: [R] Weighted Average on More than One Variable in Data Frame

2011-09-21 Thread Jean V Adams

Try this

sapply(split(df, df$g), function(x) apply(x[, 1:2], 2, weighted.mean, 
x$w))

Jean


StellathePug wrote on 09/21/2011 01:15:33 PM:
 
 Dear R Users,
 I have looked for a solution to the following problem and I have not 
been
 able to find it on the archive, through Google or in the R 
documentation.
 
 I have a data frame, say df, which has 4 variables, one of which I would
 like to use as a grouping variable (g), another one that I would like to 
use
 for my weights (w) The other two variables are variables (x1 and x2) for
 which I would like to compute the weighted average by group.
 
 df - data.frame(x1 = c(15, 12,  3, 10, 10, 14, 12), 
x2 = c(10, 11, 16,  9,   7, 17, 18),
 g = c(  1,   1,  1,  2,   2,   3,  3), 
 w = c( 2,   3,  1,  5,   5,   2,  5)) 
 
 wx1 - sapply(split(df, df$g), function(x){weighted.mean(x$x1, x$w)}) 
 wx2 - sapply(split(df, df$g), function(x){weighted.mean(x$x2, x$w)})
 
 The above code works, the result is:
  wx1
123 
 11.5 10.0 12.57143 
  wx2
123 
 11.5  8.0 17.71429
 
 But is there not a more elegant way of acting on x1 and x2 
simultaneously?
 Something along the lines of
 
 wdf - sapply(split(df, df$g), function(x){weighted.mean(df, x$w)})
 
 which is wrong since df has two columns, while w only has one. I 
suppose,
 one could write a loop but that strikes me as being highly inefficient.
 
 Thank you very much for your help!
 Rita
 

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[R] Limitations of audio processing in R

2011-09-21 Thread Ulisses.Camargo

Hello everybody

I am trying to process audio files in R and had some problems with files
size. I´m using R packages 'audio' and 'sound'. I´m trying a really simple
thing and it is working well with small sized .wav files. When I try to open
huge audio files I received this error message: cannot allocate vector of
size 2.7 Gb. My job is open in R a 3-hour .wav file, make six 5-minute
random audio subsamples, and than save these new files. I have to do the
same process +1500 times. My problems is not in build the function to do the
job, but in oppening the 3-hour files. Does anybody knows how to handle big
audio files in R? Another package that allows me to do this work? I believe
this is a really simple thing, but I really don´t know what to do to solve
that memory problem.

Thank you very much for your answers,
all the best! 

Ulisses

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Re: [R] Limitations of audio processing in R

If you are running Windows it may be as simple as using memory.limit() to
allow R more memory -- if you are on another OS, it may be possible to get
the needed memory by deleting various things in your workspace and running
gc()

Of course, if your computer's memory is 3GB, you are probably going to have
trouble with R's keeping all objects in memory and will have to get more
creative.

Michael

On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo
moliterno.cama...@gmail.com wrote:

Hello everybody

I am trying to process audio files in R and had some problems with files
size. I´m using R packages 'audio' and 'sound'. I´m trying a really simple
thing and it is working well with small sized .wav files. When I try to
open
huge audio files I received this error message: cannot allocate vector of
size 2.7 Gb. My job is open in R a 3-hour .wav file, make six 5-minute
random audio subsamples, and than save these new files. I have to do the
same process +1500 times. My problems is not in build the function to do
the
job, but in oppening the 3-hour files. Does anybody knows how to handle big
audio files in R? Another package that allows me to do this work? I believe
this is a really simple thing, but I really don´t know what to do to solve
that memory problem.

Thank you very much for your answers,
all the best!

Ulisses

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[R] Problem indexing a factor variable

2011-09-21 Thread Ahmed, Rizwan

Hi,

I have a dataframe gexp_1 with 115 rows of samples and 27000 columns of gene 
expression measurements with each column corresponding to one gene. I now have 
a smaller vector of genes tp for which I need to pull out the data form the 
data frame.

#  first gene from the list with 16 genes

x - tp[1,]
x
[1] geneA
16 Levels: geneA, geneB...

#unsuccessful
gexp_1$x
NULL

#or
gexp_1$x[1]
NULL

#but this works
gexp_1$geneA 

I am sure that this is a fundamental error on my part since I am new to R, I 
would appreciate any advice. I am trying to construct a for loop to analyze 
data for sets of genes at a time but stuck at this step.

Regards
Rizwan
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Re: [R] Problem indexing a factor variable

Your problem is a fairly common one and it has to do with how factors are
stored internally in R. They look like geneA,geneB, etc to you, but to R
(for many things) they are kept as integers 1,2,3.

It should suffice to set

x - as.character(tp[1,])

which forces x to be the string geneA and you can then put that into
gexp_1[,x]

More generally, you can probably do something like

gexp_1[,as.character(tp)]

to just get the columns of interest directly.

Hope this helps,

Michael Weylandt

On Wed, Sep 21, 2011 at 4:00 PM, Ahmed, Rizwan
rizwan.ah...@csc.mrc.ac.ukwrote:

 Hi,

 I have a dataframe gexp_1 with 115 rows of samples and 27000 columns of
 gene expression measurements with each column corresponding to one gene. I
 now have a smaller vector of genes tp for which I need to pull out the
 data form the data frame.

 #  first gene from the list with 16 genes

 x - tp[1,]
 x
 [1] geneA
 16 Levels: geneA, geneB...

 #unsuccessful
 gexp_1$x
 NULL

 #or
 gexp_1$x[1]
 NULL

 #but this works
 gexp_1$geneA

 I am sure that this is a fundamental error on my part since I am new to R,
 I would appreciate any advice. I am trying to construct a for loop to
 analyze data for sets of genes at a time but stuck at this step.

 Regards
 Rizwan
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Re: [R] Specifying Start/End Dates for X-axis Range in plot()/xyplot() [RESOLVED]

2011-09-21 Thread Rich Shepard


On Wed, 21 Sep 2011, Rich Shepard wrote:


 Is there documentation I can read that will teach me the proper syntax?
Or, can you show me how to specify those dates when plotting z elements?


  Got it: extract the window for the times of interest, then plot that
window.

Rich

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Re: [R] Limitations of audio processing in R

2011-09-21 Thread Ted Harding

Hi Ulisses!
Yes, get more creative -- or get more memory!

On the creative side, it may be worth thinking about
using an independent (non-R) audio file editor. I'm
writing from the standpoint of a Linux/Unixoid user
here -- I wouldn;t know how to set ebout this in WIndows.

You could use R to create a shell script which would run
the editor in such a way as to extract your 6 random samples,
and save them, where the script would be fed with the
randomly-chosen 5-minute intervals decided by R. This
could be done under the control of R, so you could set
it up for your 1500 or so sets of samples, which (with
the right editing program) could be done quite quickly.

On Linux (also available for Windows) a flexible audio
editor is 'sox' -- see:

  http://en.wikipedia.org/wiki/SoX

To take, say, a 5-minute sample starting at 1 hour,
10 min and 35sec into the audio file infile.wav,
and save this as outfile.wav, you can execute

  sox infile.wav outfile.wav trim 01:10:35 00:05:00 

and such a command could easily be generated by R and
fed to a shell script (or simply executed from R by
using the system() command). My test just now with
a 5-minute long sample from a .wav file was completed
in about 5 seconds, so it is quite efficient.

There is a huge number of options for 'sox', allowing
you to manipulate almost any aspect of the editing.

Hoping this helps,
Ted.


On 21-Sep-11 19:55:22, R. Michael Weylandt wrote:
 If you are running Windows it may be as simple as using
 memory.limit() to allow R more memory -- if you are on
 another OS, it may be possible to get the needed memory
 by deleting various things in your workspace and running
 gc()
 
 Of course, if your computer's memory is 3GB, you are
 probably going to have trouble with R's keeping all objects
 in memory and will have to get more creative.
 
 Michael
 
 On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo 
 moliterno.cama...@gmail.com wrote:
 
 Hello everybody

 I am trying to process audio files in R and had some problems
 with files size. I´m using R packages 'audio' and 'sound'.
 I´m trying a really simple thing and it is working well with
 small sized .wav files. When I try to open huge audio files
 I received this error message: cannot allocate vector of
 size 2.7 Gb. My job is open in R a 3-hour .wav file, make six
 5-minute random audio subsamples, and than save these new files.
 I have to do the same process +1500 times. My problems is not
 in build the function to do the job, but in oppening the 3-hour
 files. Does anybody knows how to handle big audio files in R?
 Another package that allows me to do this work? I believe
 this is a really simple thing, but I really don´t know what
 to do to solve that memory problem.

 Thank you very much for your answers,
 all the best!

 Ulisses


E-Mail: (Ted Harding) ted.hard...@wlandres.net
Fax-to-email: +44 (0)870 094 0861
Date: 21-Sep-11   Time: 22:05:55
-- XFMail --

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

Re: [R] Limitations of audio processing in R

2011-09-21 Thread Ken

Also with Linux you can add more swap memory(which I'm pretty sure R spills 
into if it hasn't reached it's  internal limits on 32 bit installations). 
Windows pagefile is kind of obnoxious.
   Ken Hutchison 

On Sep 21, 2554 BE, at 5:05 PM, (Ted Harding) ted.hard...@wlandres.net wrote:

 Hi Ulisses!
 Yes, get more creative -- or get more memory!
 
 On the creative side, it may be worth thinking about
 using an independent (non-R) audio file editor. I'm
 writing from the standpoint of a Linux/Unixoid user
 here -- I wouldn;t know how to set ebout this in WIndows.
 
 You could use R to create a shell script which would run
 the editor in such a way as to extract your 6 random samples,
 and save them, where the script would be fed with the
 randomly-chosen 5-minute intervals decided by R. This
 could be done under the control of R, so you could set
 it up for your 1500 or so sets of samples, which (with
 the right editing program) could be done quite quickly.
 
 On Linux (also available for Windows) a flexible audio
 editor is 'sox' -- see:
 
  http://en.wikipedia.org/wiki/SoX
 
 To take, say, a 5-minute sample starting at 1 hour,
 10 min and 35sec into the audio file infile.wav,
 and save this as outfile.wav, you can execute
 
  sox infile.wav outfile.wav trim 01:10:35 00:05:00 
 
 and such a command could easily be generated by R and
 fed to a shell script (or simply executed from R by
 using the system() command). My test just now with
 a 5-minute long sample from a .wav file was completed
 in about 5 seconds, so it is quite efficient.
 
 There is a huge number of options for 'sox', allowing
 you to manipulate almost any aspect of the editing.
 
 Hoping this helps,
 Ted.
 
 
 On 21-Sep-11 19:55:22, R. Michael Weylandt wrote:
 If you are running Windows it may be as simple as using
 memory.limit() to allow R more memory -- if you are on
 another OS, it may be possible to get the needed memory
 by deleting various things in your workspace and running
 gc()
 
 Of course, if your computer's memory is 3GB, you are
 probably going to have trouble with R's keeping all objects
 in memory and will have to get more creative.
 
 Michael
 
 On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo 
 moliterno.cama...@gmail.com wrote:
 
 Hello everybody
 
 I am trying to process audio files in R and had some problems
 with files size. I´m using R packages 'audio' and 'sound'.
 I´m trying a really simple thing and it is working well with
 small sized .wav files. When I try to open huge audio files
 I received this error message: cannot allocate vector of
 size 2.7 Gb. My job is open in R a 3-hour .wav file, make six
 5-minute random audio subsamples, and than save these new files.
 I have to do the same process +1500 times. My problems is not
 in build the function to do the job, but in oppening the 3-hour
 files. Does anybody knows how to handle big audio files in R?
 Another package that allows me to do this work? I believe
 this is a really simple thing, but I really don´t know what
 to do to solve that memory problem.
 
 Thank you very much for your answers,
 all the best!
 
 Ulisses
 
 
 E-Mail: (Ted Harding) ted.hard...@wlandres.net
 Fax-to-email: +44 (0)870 094 0861
 Date: 21-Sep-11   Time: 22:05:55
 -- XFMail --
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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

[R] raster plot is empty

Dear R-help,

I have a problem plotting maps using the raster package when I use R
on my workplace server, but not when I use my own desktop.  I suspect
the server version must be missing something and was wondering if
anyone would have any ideas.

The problem occurs after

library(raster)
f - system.file(external/test.grd, package=raster)
r - raster(f)
plot(f)

On my desktop computer this works perfectly.  If I run this on my
workplace server then the axes labels are identical, the legend
numbers are identical, but the plot is empty and the legend has no
colors in it.  This persists even if I specify a color explicitly

plot(f, col=red)

for example.

Any help would be appreciated.

Kind regards,
Alex

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

Re: [R] raster plot is empty

2011-09-21 Thread Sarah Goslee

Alex,

We definitely need the output of sessionInfo(), the version of raster,
and a reproducible example.


Without knowing the versions  OS, it's impossible to say. But my
first guess (and
it IS a guess) is that the server needs to be updated.

Sarah


On Wed, Sep 21, 2011 at 5:45 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear R-help,

 I have a problem plotting maps using the raster package when I use R
 on my workplace server, but not when I use my own desktop.  I suspect
 the server version must be missing something and was wondering if
 anyone would have any ideas.

 The problem occurs after

 library(raster)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)
 plot(f)

 On my desktop computer this works perfectly.  If I run this on my
 workplace server then the axes labels are identical, the legend
 numbers are identical, but the plot is empty and the legend has no
 colors in it.  This persists even if I specify a color explicitly

 plot(f, col=red)

 for example.

 Any help would be appreciated.

 Kind regards,
 Alex


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

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

Re: [R] Limitations of audio processing in R

2011-09-21 Thread Spencer Graves

A more general question:  What tools are available in R for reading 
parts of binary files?  'scan' allows you to 'skip' a certain number of 
records and read the next 'nlines'.  Unfortunately, scan only seems to 
work for text files not binary, and I cannot find a comparable function 
that would work for binary files.  I tried library(sos);  (rb - 
findFn('read binary')).  This produced 299 matches.  Something there 
might solve the problem, but I haven't taken the time to study it 
carefully.  I hope someone else will know.



  Spencer


On 9/21/2011 2:15 PM, Ken wrote:

Also with Linux you can add more swap memory(which I'm pretty sure R spills 
into if it hasn't reached it's  internal limits on 32 bit installations). 
Windows pagefile is kind of obnoxious.
Ken Hutchison

On Sep 21, 2554 BE, at 5:05 PM, (Ted Harding)ted.hard...@wlandres.net  wrote:


Hi Ulisses!
Yes, get more creative -- or get more memory!

On the creative side, it may be worth thinking about
using an independent (non-R) audio file editor. I'm
writing from the standpoint of a Linux/Unixoid user
here -- I wouldn;t know how to set ebout this in WIndows.

You could use R to create a shell script which would run
the editor in such a way as to extract your 6 random samples,
and save them, where the script would be fed with the
randomly-chosen 5-minute intervals decided by R. This
could be done under the control of R, so you could set
it up for your 1500 or so sets of samples, which (with
the right editing program) could be done quite quickly.

On Linux (also available for Windows) a flexible audio
editor is 'sox' -- see:

  http://en.wikipedia.org/wiki/SoX

To take, say, a 5-minute sample starting at 1 hour,
10 min and 35sec into the audio file infile.wav,
and save this as outfile.wav, you can execute

  sox infile.wav outfile.wav trim 01:10:35 00:05:00

and such a command could easily be generated by R and
fed to a shell script (or simply executed from R by
using the system() command). My test just now with
a 5-minute long sample from a .wav file was completed
in about 5 seconds, so it is quite efficient.

There is a huge number of options for 'sox', allowing
you to manipulate almost any aspect of the editing.

Hoping this helps,
Ted.


On 21-Sep-11 19:55:22, R. Michael Weylandt wrote:

If you are running Windows it may be as simple as using
memory.limit() to allow R more memory -- if you are on
another OS, it may be possible to get the needed memory
by deleting various things in your workspace and running
gc()

Of course, if your computer's memory is3GB, you are
probably going to have trouble with R's keeping all objects
in memory and will have to get more creative.

Michael

On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo
moliterno.cama...@gmail.com  wrote:


Hello everybody

I am trying to process audio files in R and had some problems
with files size. I´m using R packages 'audio' and 'sound'.
I´m trying a really simple thing and it is working well with
small sized .wav files. When I try to open huge audio files
I received this error message: cannot allocate vector of
size 2.7 Gb. My job is open in R a 3-hour .wav file, make six
5-minute random audio subsamples, and than save these new files.
I have to do the same process +1500 times. My problems is not
in build the function to do the job, but in oppening the 3-hour
files. Does anybody knows how to handle big audio files in R?
Another package that allows me to do this work? I believe
this is a really simple thing, but I really don´t know what
to do to solve that memory problem.

Thank you very much for your answers,
all the best!

Ulisses


E-Mail: (Ted Harding)ted.hard...@wlandres.net
Fax-to-email: +44 (0)870 094 0861
Date: 21-Sep-11   Time: 22:05:55
-- XFMail --

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

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



--
Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph:  408-655-4567
web:  www.structuremonitoring.com

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

Re: [R] Limitations of audio processing in R

2011-09-21 Thread Ted Harding

Once again, I would myself be inclined to farm this out
(in Linux) to the tools which come with the system. In this
case the command dd is useful (though one may need to be
careful about setting the options.

For instance,

  dd -bs=1 skip=54321 count=31415 if=infile of=outfile

would (having set block-size to bs=1 byte) copy count=31415
bytes (blocks) from the input file infile (if=infile),
starting at but position 54322 (skip=54321), and write
the result to outfile (of=outfile).

Ted.

On 21-Sep-11 22:08:02, Spencer Graves wrote:
 A more general question:  What tools are available in R for reading 
 parts of binary files?  'scan' allows you to 'skip' a certain number of
 records and read the next 'nlines'.  Unfortunately, scan only seems to 
 work for text files not binary, and I cannot find a comparable function
 that would work for binary files.  I tried library(sos);  (rb - 
 findFn('read binary')).  This produced 299 matches.  Something there 
 might solve the problem, but I haven't taken the time to study it 
 carefully.  I hope someone else will know.
 
 
Spencer
 
 
 On 9/21/2011 2:15 PM, Ken wrote:
 Also with Linux you can add more swap memory(which I'm pretty sure R
 spills into if it hasn't reached it's  internal limits on 32 bit
 installations). Windows pagefile is kind of obnoxious.
 Ken Hutchison

 On Sep 21, 2554 BE, at 5:05 PM, (Ted
 Harding)ted.hard...@wlandres.net  wrote:

 Hi Ulisses!
 Yes, get more creative -- or get more memory!

 On the creative side, it may be worth thinking about
 using an independent (non-R) audio file editor. I'm
 writing from the standpoint of a Linux/Unixoid user
 here -- I wouldn;t know how to set ebout this in WIndows.

 You could use R to create a shell script which would run
 the editor in such a way as to extract your 6 random samples,
 and save them, where the script would be fed with the
 randomly-chosen 5-minute intervals decided by R. This
 could be done under the control of R, so you could set
 it up for your 1500 or so sets of samples, which (with
 the right editing program) could be done quite quickly.

 On Linux (also available for Windows) a flexible audio
 editor is 'sox' -- see:

   http://en.wikipedia.org/wiki/SoX

 To take, say, a 5-minute sample starting at 1 hour,
 10 min and 35sec into the audio file infile.wav,
 and save this as outfile.wav, you can execute

   sox infile.wav outfile.wav trim 01:10:35 00:05:00

 and such a command could easily be generated by R and
 fed to a shell script (or simply executed from R by
 using the system() command). My test just now with
 a 5-minute long sample from a .wav file was completed
 in about 5 seconds, so it is quite efficient.

 There is a huge number of options for 'sox', allowing
 you to manipulate almost any aspect of the editing.

 Hoping this helps,
 Ted.


 On 21-Sep-11 19:55:22, R. Michael Weylandt wrote:
 If you are running Windows it may be as simple as using
 memory.limit() to allow R more memory -- if you are on
 another OS, it may be possible to get the needed memory
 by deleting various things in your workspace and running
 gc()

 Of course, if your computer's memory is3GB, you are
 probably going to have trouble with R's keeping all objects
 in memory and will have to get more creative.

 Michael

 On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo
 moliterno.cama...@gmail.com  wrote:

 Hello everybody

 I am trying to process audio files in R and had some problems
 with files size. IÂ´m using R packages 'audio' and 'sound'.
 IÂ´m trying a really simple thing and it is working well with
 small sized .wav files. When I try to open huge audio files
 I received this error message: cannot allocate vector of
 size 2.7 Gb. My job is open in R a 3-hour .wav file, make six
 5-minute random audio subsamples, and than save these new files.
 I have to do the same process +1500 times. My problems is not
 in build the function to do the job, but in oppening the 3-hour
 files. Does anybody knows how to handle big audio files in R?
 Another package that allows me to do this work? I believe
 this is a really simple thing, but I really donÂ´t know what
 to do to solve that memory problem.

 Thank you very much for your answers,
 all the best!

 Ulisses
 
 E-Mail: (Ted Harding)ted.hard...@wlandres.net
 Fax-to-email: +44 (0)870 094 0861
 Date: 21-Sep-11   Time: 22:05:55
 -- XFMail --

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

Re: [R] raster plot is empty

Dear Sarah,

I am not sure how to make a reproducible example.  The 3 lines of code
are exactly what I type in either system.  The code can be reproduced,
but the result is unlikely to be reproduced - for example on my
desktop this all works fine.  Is there something more I can do to make
this reproducible?

Is it helpful if I post the results of

sessionInfo()

?

Kind regards,
Alex

On 22 September 2011 09:55, Sarah Goslee sarah.gos...@gmail.com wrote:
 Alex,

 We definitely need the output of sessionInfo(), the version of raster,
 and a reproducible example.


 Without knowing the versions  OS, it's impossible to say. But my
 first guess (and
 it IS a guess) is that the server needs to be updated.

 Sarah


 On Wed, Sep 21, 2011 at 5:45 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear R-help,

 I have a problem plotting maps using the raster package when I use R
 on my workplace server, but not when I use my own desktop.  I suspect
 the server version must be missing something and was wondering if
 anyone would have any ideas.

 The problem occurs after

 library(raster)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)
 plot(f)

 On my desktop computer this works perfectly.  If I run this on my
 workplace server then the axes labels are identical, the legend
 numbers are identical, but the plot is empty and the legend has no
 colors in it.  This persists even if I specify a color explicitly

 plot(f, col=red)

 for example.

 Any help would be appreciated.

 Kind regards,
 Alex


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


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

Re: [R] Limitations of audio processing in R

2011-09-21 Thread Ulisses Camargo

Dear Ted,
Thank you very much about your answer, it really helped. Now I am working on
the function that will do all the job with sox help.
All the best,
Ulisses

2011/9/21 Ted Harding ted.hard...@wlandres.net

 Hi Ulisses!
 Yes, get more creative -- or get more memory!

 On the creative side, it may be worth thinking about
 using an independent (non-R) audio file editor. I'm
 writing from the standpoint of a Linux/Unixoid user
 here -- I wouldn;t know how to set ebout this in WIndows.

 You could use R to create a shell script which would run
 the editor in such a way as to extract your 6 random samples,
 and save them, where the script would be fed with the
 randomly-chosen 5-minute intervals decided by R. This
 could be done under the control of R, so you could set
 it up for your 1500 or so sets of samples, which (with
 the right editing program) could be done quite quickly.

 On Linux (also available for Windows) a flexible audio
 editor is 'sox' -- see:

  http://en.wikipedia.org/wiki/SoX

 To take, say, a 5-minute sample starting at 1 hour,
 10 min and 35sec into the audio file infile.wav,
 and save this as outfile.wav, you can execute

  sox infile.wav outfile.wav trim 01:10:35 00:05:00

 and such a command could easily be generated by R and
 fed to a shell script (or simply executed from R by
 using the system() command). My test just now with
 a 5-minute long sample from a .wav file was completed
 in about 5 seconds, so it is quite efficient.

 There is a huge number of options for 'sox', allowing
 you to manipulate almost any aspect of the editing.

 Hoping this helps,
 Ted.


 On 21-Sep-11 19:55:22, R. Michael Weylandt wrote:
  If you are running Windows it may be as simple as using
  memory.limit() to allow R more memory -- if you are on
  another OS, it may be possible to get the needed memory
  by deleting various things in your workspace and running
  gc()
 
  Of course, if your computer's memory is 3GB, you are
  probably going to have trouble with R's keeping all objects
  in memory and will have to get more creative.
 
  Michael
 
  On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo 
  moliterno.cama...@gmail.com wrote:
 
  Hello everybody
 
  I am trying to process audio files in R and had some problems
  with files size. Iæ´ using R packages 'audio' and 'sound'.
  Iæ´ trying a really simple thing and it is working well with
  small sized .wav files. When I try to open huge audio files
  I received this error message: cannot allocate vector of
  size 2.7 Gb. My job is open in R a 3-hour .wav file, make six
  5-minute random audio subsamples, and than save these new files.
  I have to do the same process +1500 times. My problems is not
  in build the function to do the job, but in oppening the 3-hour
  files. Does anybody knows how to handle big audio files in R?
  Another package that allows me to do this work? I believe
  this is a really simple thing, but I really donæ know what
  to do to solve that memory problem.
 
  Thank you very much for your answers,
  all the best!
 
  Ulisses

 
 E-Mail: (Ted Harding) ted.hard...@wlandres.net
 Fax-to-email: +44 (0)870 094 0861
 Date: 21-Sep-11   Time: 22:05:55
 -- XFMail --




-- 
Ulisses Moliterno de Camargo
Instituto Nacional de Pesquisas da AmazÃ´nia

[[alternative HTML version deleted]]

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

Re: [R] Weighted Average on More than One Variable in Data Frame

2011-09-21 Thread StellathePug

Thanks Jean, that worked perfectly!
Try this

sapply(split(df, df$g), function(x) apply(x[, 1:2], 2, weighted.mean, 
x$w))

Jean


StellathePug wrote on 09/21/2011 01:15:33 PM:
 
 I have a data frame, say df, which has 4 variables, one of which I would
 like to use as a grouping variable (g), another one that I would like to
 use
 for my weights (w) The other two variables are variables (x1 and x2) for
 which I would like to compute the weighted average by group.
 
 df - data.frame(x1 = c(15, 12,  3, 10, 10, 14, 12), 
x2 = c(10, 11, 16,  9,   7, 17, 18),
 g = c(  1,   1,  1,  2,   2,   3,  3), 
 w = c( 2,   3,  1,  5,   5,   2,  5)) 
 
 wx1 - sapply(split(df, df$g), function(x){weighted.mean(x$x1, x$w)}) 
 wx2 - sapply(split(df, df$g), function(x){weighted.mean(x$x2, x$w)})
 
 The above code works, the result is:
  wx1
123 
 11.5 10.0 12.57143 
  wx2
123 
 11.5  8.0 17.71429
 
 But is there not a more elegant way of acting on x1 and x2 
simultaneously?
 Something along the lines of
 
 wdf - sapply(split(df, df$g), function(x){weighted.mean(df, x$w)})
 
 which is wrong since df has two columns, while w only has one. I 
suppose, one could write a loop but that strikes me as being highly
inefficient.


--
View this message in context: 
http://r.789695.n4.nabble.com/Weighted-Average-on-More-than-One-Variable-in-Data-Frame-tp3830922p3831611.html
Sent from the R help mailing list archive at Nabble.com.

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

Re: [R] raster plot is empty

2011-09-21 Thread Sarah Goslee

Hi,

On Wed, Sep 21, 2011 at 6:31 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear Sarah,

 I am not sure how to make a reproducible example.  The 3 lines of code
 are exactly what I type in either system.  The code can be reproduced,
 but the result is unlikely to be reproduced - for example on my
 desktop this all works fine.  Is there something more I can do to make
 this reproducible?

Ah, I see. You were using data from the raster package, not a local file as it
seemed on first glance.

 Is it helpful if I post the results of

 sessionInfo()

 ?

Yes, that would be just what I'd asked for. Don't forget the version of raster.

Sarah

 Kind regards,
 Alex

 On 22 September 2011 09:55, Sarah Goslee sarah.gos...@gmail.com wrote:
 Alex,

 We definitely need the output of sessionInfo(), the version of raster,
 and a reproducible example.


 Without knowing the versions  OS, it's impossible to say. But my
 first guess (and
 it IS a guess) is that the server needs to be updated.

 Sarah


 On Wed, Sep 21, 2011 at 5:45 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear R-help,

 I have a problem plotting maps using the raster package when I use R
 on my workplace server, but not when I use my own desktop.  I suspect
 the server version must be missing something and was wondering if
 anyone would have any ideas.

 The problem occurs after

 library(raster)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)
 plot(f)

 On my desktop computer this works perfectly.  If I run this on my
 workplace server then the axes labels are identical, the legend
 numbers are identical, but the plot is empty and the legend has no
 colors in it.  This persists even if I specify a color explicitly

 plot(f, col=red)

 for example.

 Any help would be appreciated.

 Kind regards,
 Alex


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





-- 
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

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

Re: [R] raster plot is empty

2011-09-21 Thread Michael Sumner

Please ensure that it is really the exact same code, I'm sure you did
not mean to plot f, but r (for example).

Also, sessionInfo results are helpful always - see the posting guide
for ways to post better questions.

 library(raster)
Loading required package: sp
raster version 1.9-5 (28-July-2011)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)

Here is f - not r!  And the error here is to be expected since f
is just a character string.

 plot(f)
Error in plot.window(...) : need finite 'ylim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf

Cheers, Mike.


On Thu, Sep 22, 2011 at 8:31 AM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear Sarah,

 I am not sure how to make a reproducible example.  The 3 lines of code
 are exactly what I type in either system.  The code can be reproduced,
 but the result is unlikely to be reproduced - for example on my
 desktop this all works fine.  Is there something more I can do to make
 this reproducible?

 Is it helpful if I post the results of

 sessionInfo()

 ?

 Kind regards,
 Alex

 On 22 September 2011 09:55, Sarah Goslee sarah.gos...@gmail.com wrote:
 Alex,

 We definitely need the output of sessionInfo(), the version of raster,
 and a reproducible example.


 Without knowing the versions  OS, it's impossible to say. But my
 first guess (and
 it IS a guess) is that the server needs to be updated.

 Sarah


 On Wed, Sep 21, 2011 at 5:45 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear R-help,

 I have a problem plotting maps using the raster package when I use R
 on my workplace server, but not when I use my own desktop.  I suspect
 the server version must be missing something and was wondering if
 anyone would have any ideas.

 The problem occurs after

 library(raster)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)
 plot(f)

 On my desktop computer this works perfectly.  If I run this on my
 workplace server then the axes labels are identical, the legend
 numbers are identical, but the plot is empty and the legend has no
 colors in it.  This persists even if I specify a color explicitly

 plot(f, col=red)

 for example.

 Any help would be appreciated.

 Kind regards,
 Alex


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


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




-- 
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsum...@gmail.com

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

Re: [R] Limitations of audio processing in R

2011-09-21 Thread Michael Sumner

On Thu, Sep 22, 2011 at 8:08 AM, Spencer Graves
spencer.gra...@structuremonitoring.com wrote:
 A more general question:  What tools are available in R for reading parts of
 binary files?  'scan' allows you to 'skip' a certain number of records and
 read the next 'nlines'.  Unfortunately, scan only seems to work for text
 files not binary, and I cannot find a comparable function that would work
 for binary files.  I tried library(sos);  (rb - findFn('read binary')).
  This produced 299 matches.  Something there might solve the problem, but I
 haven't taken the time to study it carefully.  I hope someone else will
 know.


      Spencer


?readBin and ?seek

Also see Viewing Binary Files with the hexView Package in RNews
Volume 7/1, April 2007.

http://www.r-project.org/doc/Rnews/Rnews_2007-1.pdf

Cheers, Mike.



 On 9/21/2011 2:15 PM, Ken wrote:

 Also with Linux you can add more swap memory(which I'm pretty sure R
 spills into if it hasn't reached it's  internal limits on 32 bit
 installations). Windows pagefile is kind of obnoxious.
    Ken Hutchison

 On Sep 21, 2554 BE, at 5:05 PM, (Ted Harding)ted.hard...@wlandres.net
  wrote:

 Hi Ulisses!
 Yes, get more creative -- or get more memory!

 On the creative side, it may be worth thinking about
 using an independent (non-R) audio file editor. I'm
 writing from the standpoint of a Linux/Unixoid user
 here -- I wouldn;t know how to set ebout this in WIndows.

 You could use R to create a shell script which would run
 the editor in such a way as to extract your 6 random samples,
 and save them, where the script would be fed with the
 randomly-chosen 5-minute intervals decided by R. This
 could be done under the control of R, so you could set
 it up for your 1500 or so sets of samples, which (with
 the right editing program) could be done quite quickly.

 On Linux (also available for Windows) a flexible audio
 editor is 'sox' -- see:

  http://en.wikipedia.org/wiki/SoX

 To take, say, a 5-minute sample starting at 1 hour,
 10 min and 35sec into the audio file infile.wav,
 and save this as outfile.wav, you can execute

  sox infile.wav outfile.wav trim 01:10:35 00:05:00

 and such a command could easily be generated by R and
 fed to a shell script (or simply executed from R by
 using the system() command). My test just now with
 a 5-minute long sample from a .wav file was completed
 in about 5 seconds, so it is quite efficient.

 There is a huge number of options for 'sox', allowing
 you to manipulate almost any aspect of the editing.

 Hoping this helps,
 Ted.


 On 21-Sep-11 19:55:22, R. Michael Weylandt wrote:

 If you are running Windows it may be as simple as using
 memory.limit() to allow R more memory -- if you are on
 another OS, it may be possible to get the needed memory
 by deleting various things in your workspace and running
 gc()

 Of course, if your computer's memory is3GB, you are
 probably going to have trouble with R's keeping all objects
 in memory and will have to get more creative.

 Michael

 On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo
 moliterno.cama...@gmail.com  wrote:

 Hello everybody

 I am trying to process audio files in R and had some problems
 with files size. I´m using R packages 'audio' and 'sound'.
 I´m trying a really simple thing and it is working well with
 small sized .wav files. When I try to open huge audio files
 I received this error message: cannot allocate vector of
 size 2.7 Gb. My job is open in R a 3-hour .wav file, make six
 5-minute random audio subsamples, and than save these new files.
 I have to do the same process +1500 times. My problems is not
 in build the function to do the job, but in oppening the 3-hour
 files. Does anybody knows how to handle big audio files in R?
 Another package that allows me to do this work? I believe
 this is a really simple thing, but I really don´t know what
 to do to solve that memory problem.

 Thank you very much for your answers,
 all the best!

 Ulisses

 
 E-Mail: (Ted Harding)ted.hard...@wlandres.net
 Fax-to-email: +44 (0)870 094 0861
 Date: 21-Sep-11                                       Time: 22:05:55
 -- XFMail --

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

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


 --
 Spencer Graves, PE, PhD
 President and Chief Technology Officer
 Structure Inspection and Monitoring, Inc.
 751 Emerson Ct.
 San José, CA 95126
 ph:  408-655-4567
 web:

Re: [R] raster plot is empty

Yes, Mike you are correct.

In fact I did use

plot(r)

The code is exactly the same in both cases - the axis labels have the
same numbers, same with the legend - there is just no picture.

sessionInfo() for my desktop - where the code works

R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New Zealand.1252
[3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
[5] LC_TIME=English_New Zealand.1252

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

other attached packages:
[1] raster_1.9-13 sp_0.9-88

loaded via a namespace (and not attached):
[1] grid_2.13.1 lattice_0.19-30

sessionInfo() from the server

R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New Zealand.1252
[3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
[5] LC_TIME=English_New Zealand.1252

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

other attached packages:
[1] raster_1.9-13 sp_0.9-88

loaded via a namespace (and not attached):
[1] grid_2.13.1 lattice_0.19-30

And I can't see any difference!

Kind regards,
Alex

On 22 September 2011 11:17, Michael Sumner mdsum...@gmail.com wrote:
 Please ensure that it is really the exact same code, I'm sure you did
 not mean to plot f, but r (for example).

 Also, sessionInfo results are helpful always - see the posting guide
 for ways to post better questions.

 library(raster)
 Loading required package: sp
 raster version 1.9-5 (28-July-2011)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)

 Here is f - not r!  And the error here is to be expected since f
 is just a character string.

 plot(f)
 Error in plot.window(...) : need finite 'ylim' values
 In addition: Warning messages:
 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
 2: In min(x) : no non-missing arguments to min; returning Inf
 3: In max(x) : no non-missing arguments to max; returning -Inf

 Cheers, Mike.


 On Thu, Sep 22, 2011 at 8:31 AM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear Sarah,

 I am not sure how to make a reproducible example.  The 3 lines of code
 are exactly what I type in either system.  The code can be reproduced,
 but the result is unlikely to be reproduced - for example on my
 desktop this all works fine.  Is there something more I can do to make
 this reproducible?

 Is it helpful if I post the results of

 sessionInfo()

 ?

 Kind regards,
 Alex

 On 22 September 2011 09:55, Sarah Goslee sarah.gos...@gmail.com wrote:
 Alex,

 We definitely need the output of sessionInfo(), the version of raster,
 and a reproducible example.


 Without knowing the versions  OS, it's impossible to say. But my
 first guess (and
 it IS a guess) is that the server needs to be updated.

 Sarah


 On Wed, Sep 21, 2011 at 5:45 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear R-help,

 I have a problem plotting maps using the raster package when I use R
 on my workplace server, but not when I use my own desktop.  I suspect
 the server version must be missing something and was wondering if
 anyone would have any ideas.

 The problem occurs after

 library(raster)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)
 plot(f)

 On my desktop computer this works perfectly.  If I run this on my
 workplace server then the axes labels are identical, the legend
 numbers are identical, but the plot is empty and the legend has no
 colors in it.  This persists even if I specify a color explicitly

 plot(f, col=red)

 for example.

 Any help would be appreciated.

 Kind regards,
 Alex


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


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




 --
 Michael Sumner
 Institute for Marine and Antarctic Studies, University of Tasmania
 Hobart, Australia
 e-mail: mdsum...@gmail.com


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

Re: [R] raster plot is empty

2011-09-21 Thread Henrik Bengtsson

Adding $0.01 to this: Maybe comparing outputs of capabilities() gives
some clues.

/Henrik


On Wed, Sep 21, 2011 at 6:00 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Yes, Mike you are correct.

 In fact I did use

 plot(r)

 The code is exactly the same in both cases - the axis labels have the
 same numbers, same with the legend - there is just no picture.

 sessionInfo() for my desktop - where the code works

 R version 2.13.1 (2011-07-08)
 Platform: i386-pc-mingw32/i386 (32-bit)

 locale:
 [1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New Zealand.1252
 [3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
 [5] LC_TIME=English_New Zealand.1252

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

 other attached packages:
 [1] raster_1.9-13 sp_0.9-88

 loaded via a namespace (and not attached):
 [1] grid_2.13.1     lattice_0.19-30

 sessionInfo() from the server

 R version 2.13.1 (2011-07-08)
 Platform: i386-pc-mingw32/i386 (32-bit)

 locale:
 [1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New Zealand.1252
 [3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
 [5] LC_TIME=English_New Zealand.1252

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

 other attached packages:
 [1] raster_1.9-13 sp_0.9-88

 loaded via a namespace (and not attached):
 [1] grid_2.13.1     lattice_0.19-30

 And I can't see any difference!

 Kind regards,
 Alex

 On 22 September 2011 11:17, Michael Sumner mdsum...@gmail.com wrote:
 Please ensure that it is really the exact same code, I'm sure you did
 not mean to plot f, but r (for example).

 Also, sessionInfo results are helpful always - see the posting guide
 for ways to post better questions.

 library(raster)
 Loading required package: sp
 raster version 1.9-5 (28-July-2011)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)

 Here is f - not r!  And the error here is to be expected since f
 is just a character string.

 plot(f)
 Error in plot.window(...) : need finite 'ylim' values
 In addition: Warning messages:
 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
 2: In min(x) : no non-missing arguments to min; returning Inf
 3: In max(x) : no non-missing arguments to max; returning -Inf

 Cheers, Mike.


 On Thu, Sep 22, 2011 at 8:31 AM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear Sarah,

 I am not sure how to make a reproducible example.  The 3 lines of code
 are exactly what I type in either system.  The code can be reproduced,
 but the result is unlikely to be reproduced - for example on my
 desktop this all works fine.  Is there something more I can do to make
 this reproducible?

 Is it helpful if I post the results of

 sessionInfo()

 ?

 Kind regards,
 Alex

 On 22 September 2011 09:55, Sarah Goslee sarah.gos...@gmail.com wrote:
 Alex,

 We definitely need the output of sessionInfo(), the version of raster,
 and a reproducible example.


 Without knowing the versions  OS, it's impossible to say. But my
 first guess (and
 it IS a guess) is that the server needs to be updated.

 Sarah


 On Wed, Sep 21, 2011 at 5:45 PM, Alex Olssen alex.ols...@gmail.com wrote:
 Dear R-help,

 I have a problem plotting maps using the raster package when I use R
 on my workplace server, but not when I use my own desktop.  I suspect
 the server version must be missing something and was wondering if
 anyone would have any ideas.

 The problem occurs after

 library(raster)
 f - system.file(external/test.grd, package=raster)
 r - raster(f)
 plot(f)

 On my desktop computer this works perfectly.  If I run this on my
 workplace server then the axes labels are identical, the legend
 numbers are identical, but the plot is empty and the legend has no
 colors in it.  This persists even if I specify a color explicitly

 plot(f, col=red)

 for example.

 Any help would be appreciated.

 Kind regards,
 Alex


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


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




 --
 Michael Sumner
 Institute for Marine and Antarctic Studies, University of Tasmania
 Hobart, Australia
 e-mail: mdsum...@gmail.com


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


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

Re: [R] raster plot is empty