[R] Gene expression clustering using several dependent samples
Dear list. I am looking at a dataset comprised of Affy images from disease-affected tissue samples that I am trying to cluster. The problem is that we have 2+ biopsies per study subject, and I am not sure how to best account for their dependency. In contrast to cancer samples, these biopsies differ to a certain extent in their disease severity, i.e. they are not perfect replicates, but share certain similarities since they are from the same person. I first tried to just cluster all available biopsies using ConsensusClusterPlus. However, this produced clusters of biopsies according to their disease severity - often with different samples from the same patient assigned to different clusters - and that´s not what I want. I am trying to identify different classes between subjects, not biopsies. For the diff exp analyses, we dealt with this issue by adding the patient as a random effect to the model. Could I do something similar using model-based clustering, perhaps also adding a variable for disease severity? As an alternative, I have explored aggregating all available samples per subject into one expression profile, and cluster the pattients using these aggregates. I am, however, not convinced that this is right, since this approach creates 'artificial' data. Does anyone have an idea? Many thanks, Moritz [[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] Male and female signs as subscript in plot
Hello, I'd like to add labels to my plot that include a male or female symbol as subscript. I'm working in Windows Vista and R 3.0.0. I am able to add the male symbol to the plot as regular text (NOT as subscript), e.g. with: mtext(Male\u2642) This displays the word Male followed by the male symbol on the plot. But \u2642 does not work when I try to put it as a subscript. For example, mtext(expression(Male[\u2217])) successfully adds an asterisk as a subscript after the word Male. However, mtext(expression(Male[\u2642])) displays the word Male followed by a subscript of U+2642, i.e. the symbol is not displayed. How can I make the male symbol show as a subscript? Many thanks for any suggestions! Cheers, Emily [[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] Male and female signs as subscript in plot
On 01/07/2013 03:19, Emily Weiser wrote: Hello, I'd like to add labels to my plot that include a male or female symbol as subscript. I'm working in Windows Vista and R 3.0.0. I am able to add the male symbol to the plot as regular text (NOT as subscript), e.g. with: mtext(Male\u2642) This displays the word Male followed by the male symbol on the plot. But \u2642 does not work when I try to put it as a subscript. For example, mtext(expression(Male[\u2217])) successfully adds an asterisk as a subscript after the word Male. However, mtext(expression(Male[\u2642])) displays the word Male followed by a subscript of U+2642, i.e. the symbol is not displayed. How can I make the male symbol show as a subscript? You cannot use non-native text with plotmath. The issue is not that you used a subscript but that you passed an expression() call and hence invoked plotmath. And the help does say In non-UTF-8 locales there is normally no support for symbols not in the languages for which the current encoding was intended. Many thanks for any suggestions! Read all of ?plotmath. Cheers, Emily [[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. No HTML postings please. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Male and female signs as subscript in plot
On Jul 1, 2013, at 12:40 AM, Prof Brian Ripley wrote: On 01/07/2013 03:19, Emily Weiser wrote: Hello, I'd like to add labels to my plot that include a male or female symbol as subscript. I'm working in Windows Vista and R 3.0.0. I am able to add the male symbol to the plot as regular text (NOT as subscript), e.g. with: mtext(Male\u2642) This displays the word Male followed by the male symbol on the plot. But \u2642 does not work when I try to put it as a subscript. For example, mtext(expression(Male[\u2217])) successfully adds an asterisk as a subscript after the word Male. However, mtext(expression(Male[\u2642])) displays the word Male followed by a subscript of U+2642, i.e. the symbol is not displayed. How can I make the male symbol show as a subscript? You cannot use non-native text with plotmath. The issue is not that you used a subscript but that you passed an expression() call and hence invoked plotmath. And the help does say In non-UTF-8 locales there is normally no support for symbols not in the languages for which the current encoding was intended. After discovering in the documentation for ?points, ?plotmath, and ?Hershey that Hershey fonts which do support astrologic symbols cannot be used in plotmath expressions, my suggestion for a work-around is to use plotmath with a phantom() call ofappropriate length in the expression and then two calls to text with xpd=TRUE: text( locator(1), \\VE, vfont=c(sans serif,bold), xpd=TRUE) # Venus text( locator(1), \\MA, vfont=c(sans serif,bold), xpd=TRUE) # Mars I suppose this might work with approapriate modifications to the positioned parameters of that function. Many thanks for any suggestions! Read all of ?plotmath. Agree with Prof Ripley. If you are a bit slow as am I, it may take 3 or 4 readings. -- David Winsemius Alameda, CA, USA __ 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] Parallel processing random 'save' error
Platform: Windows 7
Package: parallel
Function: parLapply
I am running a lengthy program with 8 parallel processes running in main
memory.
The processes save data using the 'save' function, to distinct files so
that no conflicts writing to the same file are possible.
I have been getting errors like the one shown below on a random basis,
i.e., sometimes at one point in the execution, sometimes at another,
sometimes no error at all.
I should note that the directory referred to in the error message
( 'D:\_pgf\quantile_analysis2_f13\_save\dbz084_nump48\bins') contains, as I
write, 124 files saved to it by the program without any error; which
underscores the point that most of the time the saves occur with no problem.
Error in checkForRemoteErrors(val) :
one node produced an error: (converted from warning)
'D:\_pgf\quantile_analysis2_f13\_save\dbz084_nump48\bins' already exists
Enter a frame number, or 0 to exit
1: main_top(9)
2: main_top.r#26: eval(call_me)
3: eval(expr, envir, enclos)
4: quantile_analysis(2)
5: quantile_analysis.r#69: run_all(layr, prjp, np, rules_tb, pctiles_tb,
parx, logdir, logg)
6: run_all.r#73: parLapply(cl, ctrl_all$vn, qa1, prjp, dfr1, iu__bool,
parx, logdir, tstamp)
7: do.call(c, clusterApply(cl, x = splitList(X, length(cl)), fun = lapply,
fun, ...), quote = TRUE)
8: clusterApply(cl, x = splitList(X, length(cl)), fun = lapply, fun, ...)
9: staticClusterApply(cl, fun, length(x), argfun)
10: checkForRemoteErrors(val)
11: stop(one node produced an error: , firstmsg, domain = NA)
12: (function ()
{
error()
utils::recover()
})()
Following the latest error I checked the system's connections as follows:
Browse[1] showConnections()
description class mode text isopen can read can
write
3 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
4 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
5 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
6 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
7 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
8 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
9 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
10 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
Browse[1]
It seems that the parallel processes might be sharing the same
connection--or is it that they are utilizing connections that have the same
name but are actually distinct because they are running in parallel?
If the connections are the problem, how can I force each parallel process
to use a different connection?
If the connections are not the problem, then can someone suggest a
diagnostic I might apply to tease out what is going wrong? Or perhaps some
program setting that I may have neglected to consider?
Thanks in advance for your help.
[[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] Lexical scoping is not what I expect
On Jun 30, 2013, at 14:35 , Duncan Murdoch wrote: On 13-06-29 11:58 PM, Greg Snow wrote: If you want to write really confusing code it is possible to do: `1` - 2 `1` + 1 and things like that, but it is probably a good idea not to. This is actually pretty simple, as the White Knight could tell you. `1` is what the name of 2 is called. The name really is 2. It's called two, but that's only what it's called. It really is two. Duncan Murdoch Don't you mean 1 and one? As in as.name(1) `1` -pd On Fri, Jun 28, 2013 at 7:30 PM, Rolf Turner rolf.tur...@xtra.co.nz wrote: On 29/06/13 02:54, John Fox wrote: Dear Duncan and Steve, Since Steve's example raises it, I've never understood why it's legal to change the built-in global constants in R, including T and F. That just seems to me to set a trap for users. Why not treat these as reserved symbols, like TRUE, Inf, etc.? I rather enjoy being able to set pi - 3 :-) cheers, Rolf Turner __** 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. __ 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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Male and female signs as subscript in plot
On 01/07/2013 09:03, David Winsemius wrote: On Jul 1, 2013, at 12:40 AM, Prof Brian Ripley wrote: On 01/07/2013 03:19, Emily Weiser wrote: Hello, I'd like to add labels to my plot that include a male or female symbol as subscript. I'm working in Windows Vista and R 3.0.0. I am able to add the male symbol to the plot as regular text (NOT as subscript), e.g. with: mtext(Male\u2642) This displays the word Male followed by the male symbol on the plot. But \u2642 does not work when I try to put it as a subscript. For example, mtext(expression(Male[\u2217])) successfully adds an asterisk as a subscript after the word Male. However, mtext(expression(Male[\u2642])) displays the word Male followed by a subscript of U+2642, i.e. the symbol is not displayed. How can I make the male symbol show as a subscript? You cannot use non-native text with plotmath. The issue is not that you used a subscript but that you passed an expression() call and hence invoked plotmath. And the help does say In non-UTF-8 locales there is normally no support for symbols not in the languages for which the current encoding was intended. After discovering in the documentation for ?points, ?plotmath, and ?Hershey that Hershey fonts which do support astrologic symbols cannot be used in plotmath expressions, my suggestion for a work-around is to use plotmath with a phantom() call ofappropriate length in the expression and then two calls to text with xpd=TRUE: text( locator(1), \\VE, vfont=c(sans serif,bold), xpd=TRUE) # Venus text( locator(1), \\MA, vfont=c(sans serif,bold), xpd=TRUE) # Mars I suppose this might work with approapriate modifications to the positioned parameters of that function. Yes, you could use text() in the margin, in which case (at least on windows()) you can use \u notation and don't need Hershey fonts. I considered mentioning that, but the positioning is going to be really tricky to do programatically. Many thanks for any suggestions! Read all of ?plotmath. Agree with Prof Ripley. If you are a bit slow as am I, it may take 3 or 4 readings. -- David Winsemius Alameda, CA, USA -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Distance Measurement between probability distributions
Dear R -Users, I wanted to know about some existing functions (despite of euclidiean) to compute the distance between multiple histograms. I have found some examples like kullbakc -Leibler DIvergenz but the syntax for this is not available? Does anybody have an idea? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Distance-Measurement-between-probability-distributions-tp4670646.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Empty pdf
Dear all, I am comparing R CMD BATCH script.R with running the following code snippet within R: pdf(Rplots.pdf) source(script.R) dev.off() q(save=no) Among other things, one difference is that the former produces no Rplots.pdf while the latter produces an empty Rplots.pdf, if script.R does not contain plotting commands (R version 3.0.1, i486-pc-linux-gnu (32-bit)). What is the difference between the two with respect to pdf plotting? Best regards Adrian -- Dr. Adrian Trapletti Steinstrasse 9b CH-8610 Uster Switzerland Phone : +41 (0) 44 9945630 Mobile : +41 (0) 79 1037131 Email : adr...@trapletti.org WWW : www.trapletti.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] Empty pdf
On Jul 1, 2013, at 14:35 , Adrian Trapletti wrote: Dear all, I am comparing R CMD BATCH script.R with running the following code snippet within R: pdf(Rplots.pdf) source(script.R) dev.off() q(save=no) Among other things, one difference is that the former produces no Rplots.pdf while the latter produces an empty Rplots.pdf, if script.R does not contain plotting commands (R version 3.0.1, i486-pc-linux-gnu (32-bit)). What is the difference between the two with respect to pdf plotting? Same as on the command line: If you type quartz() (or whatever is the default device for you), you get an empty window if no plotting follows. If you type plot(0:9), the quartz() device is opened for you and plotted into. You could try options(device=pdf) source(script.R) q(save=no) -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Empty pdf
Thank you Adrian On 07/01/2013 03:04 PM, peter dalgaard wrote: On Jul 1, 2013, at 14:35 , Adrian Trapletti wrote: Dear all, I am comparing R CMD BATCH script.R with running the following code snippet within R: pdf(Rplots.pdf) source(script.R) dev.off() q(save=no) Among other things, one difference is that the former produces no Rplots.pdf while the latter produces an empty Rplots.pdf, if script.R does not contain plotting commands (R version 3.0.1, i486-pc-linux-gnu (32-bit)). What is the difference between the two with respect to pdf plotting? Same as on the command line: If you type quartz() (or whatever is the default device for you), you get an empty window if no plotting follows. If you type plot(0:9), the quartz() device is opened for you and plotted into. You could try options(device=pdf) source(script.R) q(save=no) -- Dr. Adrian Trapletti Steinstrasse 9b CH-8610 Uster Switzerland Phone : +41 (0) 44 9945630 Mobile : +41 (0) 79 1037131 Email : adr...@trapletti.org WWW : www.trapletti.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] Gene expression clustering using several dependent samples
Hello Moritz, You may want to take a look at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3052263/ . DeSantis et al. (2009) identified different genomic profiles using a Bayesian Latent Class methodology. Best, James On Sun, Jun 30, 2013 at 2:47 PM, Moritz Kebschull mor...@kebschull.mewrote: Dear list. I am looking at a dataset comprised of Affy images from disease-affected tissue samples that I am trying to cluster. The problem is that we have 2+ biopsies per study subject, and I am not sure how to best account for their dependency. In contrast to cancer samples, these biopsies differ to a certain extent in their disease severity, i.e. they are not perfect replicates, but share certain similarities since they are from the same person. I first tried to just cluster all available biopsies using ConsensusClusterPlus. However, this produced clusters of biopsies according to their disease severity - often with different samples from the same patient assigned to different clusters - and that´s not what I want. I am trying to identify different classes between subjects, not biopsies. For the diff exp analyses, we dealt with this issue by adding the patient as a random effect to the model. Could I do something similar using model-based clustering, perhaps also adding a variable for disease severity? As an alternative, I have explored aggregating all available samples per subject into one expression profile, and cluster the pattients using these aggregates. I am, however, not convinced that this is right, since this approach creates 'artificial' data. Does anyone have an idea? Many thanks, Moritz [[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. -- *James C. Whanger* * * [[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] Add constraints to rbinom
You don't need a constraint (rbinom won't give xn), but you need to make sure
you are using the n you want to use: try
x - cbind(x,rbinom(300,n[i],p[i]))# mind the [i] after the n
at the respective line. Furthermore, you need to remove one transformation of x
to make sure you divide by the right n, try
rate - t(x/n)
I think that should do the trick. I didn't check the remainder of the code,
though.
HTH, Michael
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Anamika Chaudhuri
Sent: Freitag, 28. Juni 2013 04:06
To: r-help@r-project.org
Subject: [R] Add constraints to rbinom
Hi:
I am trying to generate Beta-Binomial random variables and then calculate
Binomial exact confidence intervals to the rate..I was wondering if I needed
to add a constraint such that x=n to it, how do I go about it. The reason is
I
am getting data where xn which is giving a rate1. Heres my code:
set.seed(111)
k-63
x-NULL
p-rbeta(k,3,3)# so that the mean nausea rate is alpha/(alpha+beta)
min-10
max-60
n-as.integer(runif(k,min,max))
for(i in 1:k)
x-cbind(x,rbinom(300,n,p[i]))
x-t(x)
rate-t(t(x)/n)
se_rate-sqrt(rate*(1-rate)/n)
# Exact Confidence Interval
l_cl_exact-qbeta(.025,x,n-x+1)
u_cl_exact-qbeta(.975,x+1,n-x)
for (i in 1:63){
for (j in 1:300)
{
if (x[i,j]==0)
{
l_cl_exact[i,j]-0
u_cl_exact[i,j]-u_cl_exact[i,j]
}
else if (x[i,j]==n[i])
{
l_cl_exact[i,j]-l_cl_exact[i,j]
u_cl_exact[i,j]-1
}
else
l_cl_exact[i,j]-l_cl_exact[i,j]
u_cl_exact[i,j]-u_cl_exact[i,j]
#print(c(i,j))
}
}
Really appreciate any help.
Thanks
Anamika
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Parallel processing random 'save' error
Error in checkForRemoteErrors(val) :
one node produced an error: (converted from warning)
'D:\_pgf\quantile_analysis2_f13\_save\dbz084_nump48\bins' already exists
That warning looks like it comes from dir.create(). Do you have
code that looks like:
if (!file.exists(tempDir)) {
dir.create(tempDir)
}
If so that could be the problem. The directory may not exist when file.exists()
is called but by the time dir.create is called another process may have created
it. Try replacing such code with
suppressWarnings(dir.create(tempDir))
if (!isTRUE(file.info(tempDir)$isdir)) {
stop(Cannot create tempDir=, tempDir)
}
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf
Of Rguy
Sent: Monday, July 01, 2013 1:07 AM
To: r-help@r-project.org
Subject: [R] Parallel processing random 'save' error
Platform: Windows 7
Package: parallel
Function: parLapply
I am running a lengthy program with 8 parallel processes running in main
memory.
The processes save data using the 'save' function, to distinct files so
that no conflicts writing to the same file are possible.
I have been getting errors like the one shown below on a random basis,
i.e., sometimes at one point in the execution, sometimes at another,
sometimes no error at all.
I should note that the directory referred to in the error message
( 'D:\_pgf\quantile_analysis2_f13\_save\dbz084_nump48\bins') contains, as I
write, 124 files saved to it by the program without any error; which
underscores the point that most of the time the saves occur with no problem.
Error in checkForRemoteErrors(val) :
one node produced an error: (converted from warning)
'D:\_pgf\quantile_analysis2_f13\_save\dbz084_nump48\bins' already exists
Enter a frame number, or 0 to exit
1: main_top(9)
2: main_top.r#26: eval(call_me)
3: eval(expr, envir, enclos)
4: quantile_analysis(2)
5: quantile_analysis.r#69: run_all(layr, prjp, np, rules_tb, pctiles_tb,
parx, logdir, logg)
6: run_all.r#73: parLapply(cl, ctrl_all$vn, qa1, prjp, dfr1, iu__bool,
parx, logdir, tstamp)
7: do.call(c, clusterApply(cl, x = splitList(X, length(cl)), fun = lapply,
fun, ...), quote = TRUE)
8: clusterApply(cl, x = splitList(X, length(cl)), fun = lapply, fun, ...)
9: staticClusterApply(cl, fun, length(x), argfun)
10: checkForRemoteErrors(val)
11: stop(one node produced an error: , firstmsg, domain = NA)
12: (function ()
{
error()
utils::recover()
})()
Following the latest error I checked the system's connections as follows:
Browse[1] showConnections()
description class mode text isopen can read can
write
3 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
4 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
5 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
6 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
7 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
8 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
9 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
10 -LAPTOP_32G_01:11741 sockconn a+b binary opened yes
yes
Browse[1]
It seems that the parallel processes might be sharing the same
connection--or is it that they are utilizing connections that have the same
name but are actually distinct because they are running in parallel?
If the connections are the problem, how can I force each parallel process
to use a different connection?
If the connections are not the problem, then can someone suggest a
diagnostic I might apply to tease out what is going wrong? Or perhaps some
program setting that I may have neglected to consider?
Thanks in advance for your help.
[[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.
[R] Missing data problem and ROC curves
Hello all,
Trying to get this piece of code to work on my data set. It is from
http://www.itc.nl/personal/rossiter.
logit.roc - function(model, steps=100)
{
field.name - attr(attr(terms(formula(model)), factors),
dimnames)[[1]][1]
eval(parse(text=paste(tmp - , ifelse(class(model$data) ==
data.frame,
model$data$, ), field.name, sep=)))
r - data.frame(pts = seq(0, 1-(1/steps), by=1/steps), sens =
0, spec=0);
for (i in 0:steps)
{
thresh - i/steps;
r$sens[i] - sum((fitted(model) = thresh)
tmp)/sum(tmp);
r$spec[i] - sum((fitted(model) thresh)
!tmp)/sum(!tmp)
}
return(r)}
where model is the output of a glm.
The problem is the sum((fitted(model) = thresh) tmp) bit. The lengths
of fitted(model) and tmp are not equal because some of the cases were
deleted from the model due to missing data! fitted(model) is a set of named
numbers while tmp is a set of integers.
My question is:
- How do I determine which cases were deleted from the model and then delete
the associated cases from tmp?
I hope this makes sense and would really appreciate any help that people may
have.
Thanks,
Tim
--
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http://r.789695.n4.nabble.com/Missing-data-problem-and-ROC-curves-tp4670661.html
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and provide commented, minimal, self-contained, reproducible code.
[R] Dunnett's T3 test (DTK package) problem
Hello, I would like to ask a question about using DTK.test() to do the T3 test. The data file is downloadable here: http://ubuntuone.com/0zBl8QgUg1lAG6iK1CUicD My question is: in the result of T3 test, is it possible for the following three statements to hold without conflict? 1. m_a and m_b to be significantly different 2. m_a and m_c are not significantly different. 3. (m_c - m_a) = (m_c- m_b) where m_i is the mean value of group i. I know that for Tukey test, the above three statements can't hold without conflict. The code to run the test is: BEGIN library(DTK) df - read.csv(./tmpData.csv) DTK_result - DTK.test(df$measurement, df$model, .05) print(DTK_result) END Part of the result is displayed below. It says model05 and model01 are significantly different, while model04 and model01 are not. BEGIN DiffLower CI Upper CI model02-model01 0.068468884 -0.04765040 0.1845882 model03-model01 0.143238920 -0.05589008 0.3423679 model04-model01 0.149002642 0.02900301 0.2690023 model05-model01 0.151504289 -0.04775209 0.3507607 model06-model01 0.193093625 0.07023934 0.3159479 ... END The mean value of the groups are shown below. It shows (m_5 - m_1) (m_4 - m_1), where m_i is the mean value of model i. BEGIN library(plyr) ddply(df, ~model, summarise, mean=mean(measurement)) model mean 1 model01 0.5352273 2 model02 0.6036962 3 model03 0.6784662 4 model04 0.6842300 5 model05 0.6867316 6 model06 0.7283210 7 model07 0.7489938 8 model08 0.7941213 9 model09 0.7944798 10 model10 1.1399370 11 model11 1.2582504 12 model12 1.2928783 13 model13 1.5789970 END -- View this message in context: http://r.789695.n4.nabble.com/Dunnett-s-T3-test-DTK-package-problem-tp4670649.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Lee carter model
Hi everybody, I'm running codes for for a Lee carter modeling. I compute the demogdata function in the package demography. Age is a class of factor Base-demogdata(data=x,pop=y,ages=AGE,years=YEAR,type=mortality,label=City,name=Hommes,lambda=1) Now, I try to run codes for lee carter model, and i always get the following message: Error in Summary.factor(c(1L, 2L, 24L, 35L, 46L, 57L, 68L, 79L, 90L, 101L, : max not meaningful for factors Please can you help to understand what means this message. Many Thanks Achille [[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] functions and matrices
Dear R-user,
May I seek your help, please. I have two matrices, u and v, elements of
which are some functions
of x. I just want to multiply them and express the determinant of the
resulting matrix as a function of
x and of course, this is for some reason. Actually the original problem has
more matrices to multiply and I'm just wondering whether I can simplify it
anyway through the R codes. It may even be non-sense, but just want to hear
from you. The below is the code.
-
f1-function(x) {x}
f2-function(x) {x^2}
f3-function(x) {x^3}
f4-function(x) {x^4}
f5-function(x) {x^2+7}
f6-function(x) {x^3+14*x}
f7-function(x) {x^2+2*x}
f8-function(x) {x^4+10*x}
u-matrix(c(f1,f2,f3,f4), nrow=2, ncol=2, byrow=TRUE)
v-matrix(c(f5,f6,f7,f8), nrow=2, ncol=2, byrow=TRUE)
det(u %*% v) # Is that possible?
Any suggestion will be more than great!
Regards,
Jamil.
[[alternative HTML version deleted]]
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[R] writing to the screen and extra 0
I am using the write function like so (R 3.0.1 on linux):
wrt -
function()
{
write(system(ls *),file=)
}
When the files are listed to the screen with wrt(), there is a 0
character prepended to the output on the screen. Worse, when I remove
the 'file=' argument to write, a file named data is created in my
default directory, with a zero in it.
All I am trying to do is output the ls of files in my directory,
without any extra characters or type-attribute information. Thanks for
your help!
Thomas Grzybowski
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing to the screen and extra 0
Hello,
Try instead
list.files(pattern = *)
Hope this helps,
Rui Barradas
Em 01-07-2013 19:23, Thomas Grzybowski escreveu:
I am using the write function like so (R 3.0.1 on linux):
wrt -
function()
{
write(system(ls *),file=)
}
When the files are listed to the screen with wrt(), there is a 0
character prepended to the output on the screen. Worse, when I remove
the 'file=' argument to write, a file named data is created in my
default directory, with a zero in it.
All I am trying to do is output the ls of files in my directory,
without any extra characters or type-attribute information. Thanks for
your help!
Thomas Grzybowski
__
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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] Missing data problem and ROC curves
On Jul 1, 2013, at 10:57 AM, tfj24 wrote:
Hello all,
Trying to get this piece of code to work on my data set. It is from
http://www.itc.nl/personal/rossiter.
logit.roc - function(model, steps=100)
{
field.name - attr(attr(terms(formula(model)), factors),
dimnames)[[1]][1]
eval(parse(text=paste(tmp - , ifelse(class(model$data) ==
data.frame,
model$data$, ), field.name, sep=)))
r - data.frame(pts = seq(0, 1-(1/steps), by=1/steps), sens =
0, spec=0);
for (i in 0:steps)
{
thresh - i/steps;
r$sens[i] - sum((fitted(model) = thresh)
tmp)/sum(tmp);
r$spec[i] - sum((fitted(model) thresh)
!tmp)/sum(!tmp)
}
return(r)}
where model is the output of a glm.
The problem is the sum((fitted(model) = thresh) tmp) bit. The lengths
of fitted(model) and tmp are not equal because some of the cases were
deleted from the model due to missing data! fitted(model) is a set of named
numbers while tmp is a set of integers.
My question is:
- How do I determine which cases were deleted from the model and then delete
the associated cases from tmp?
?glm
model$na.action
--
David.
I hope this makes sense and would really appreciate any help that people may
have.
Thanks,
Tim
--
View this message in context:
http://r.789695.n4.nabble.com/Missing-data-problem-and-ROC-curves-tp4670661.html
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
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Re: [R] writing to the screen and extra 0
Hi.
list.files(pattern = *)
gives me output with the R list indices at the left of each line on the
screen. I want only file names.
Thanks!
Tom Grzybowski
On 07/01/2013 02:55 PM, Rui Barradas wrote:
Hello,
Try instead
list.files(pattern = *)
Hope this helps,
Rui Barradas
Em 01-07-2013 19:23, Thomas Grzybowski escreveu:
I am using the write function like so (R 3.0.1 on linux):
wrt -
function()
{
write(system(ls *),file=)
}
When the files are listed to the screen with wrt(), there is a 0
character prepended to the output on the screen. Worse, when I remove
the 'file=' argument to write, a file named data is created in my
default directory, with a zero in it.
All I am trying to do is output the ls of files in my directory,
without any extra characters or type-attribute information. Thanks for
your help!
Thomas Grzybowski
__
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] writing to the screen and extra 0
Hi Thomas,
If you put the list.files statement inside the write function you won't
have the indices.
Try:
write(list.files(pattern=*), file=my_files.txt)
Cheers,
Charles
On Mon, Jul 1, 2013 at 2:03 PM, Thomas Grzybowski
thomasgrzybow...@gmail.com wrote:
Hi.
list.files(pattern = *)
gives me output with the R list indices at the left of each line on the
screen. I want only file names.
Thanks!
Tom Grzybowski
On 07/01/2013 02:55 PM, Rui Barradas wrote:
Hello,
Try instead
list.files(pattern = *)
Hope this helps,
Rui Barradas
Em 01-07-2013 19:23, Thomas Grzybowski escreveu:
I am using the write function like so (R 3.0.1 on linux):
wrt -
function()
{
write(system(ls *),file=)
}
When the files are listed to the screen with wrt(), there is a 0
character prepended to the output on the screen. Worse, when I remove
the 'file=' argument to write, a file named data is created in my
default directory, with a zero in it.
All I am trying to do is output the ls of files in my directory,
without any extra characters or type-attribute information. Thanks for
your help!
Thomas Grzybowski
__**
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.
__**
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PLEASE do read the posting guide http://www.R-project.org/**
posting-guide.html http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Charles Determan
Integrated Biosciences PhD Candidate
University of Minnesota
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing to the screen and extra 0
On 01-07-2013, at 21:03, Thomas Grzybowski thomasgrzybow...@gmail.com wrote:
Hi.
list.files(pattern = *)
gives me output with the R list indices at the left of each line on the
screen. I want only file names.
cat(list.files(pattern = *),sep=\n)
Berend
Thanks!
Tom Grzybowski
On 07/01/2013 02:55 PM, Rui Barradas wrote:
Hello,
Try instead
list.files(pattern = *)
Hope this helps,
Rui Barradas
Em 01-07-2013 19:23, Thomas Grzybowski escreveu:
I am using the write function like so (R 3.0.1 on linux):
wrt -
function()
{
write(system(ls *),file=)
}
When the files are listed to the screen with wrt(), there is a 0
character prepended to the output on the screen. Worse, when I remove
the 'file=' argument to write, a file named data is created in my
default directory, with a zero in it.
All I am trying to do is output the ls of files in my directory,
without any extra characters or type-attribute information. Thanks for
your help!
Thomas Grzybowski
__
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
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and provide commented, minimal, self-contained, reproducible code.
[R] Bhattacharyya in R
Dear R-user, I am trying to apply bhattacharyya-distance function to my data. Did anybody use it before ? My code is the following #Bhattacharya Distance measure #a and b are vectors a - (1,2,3,4,2,2,2,2,2,2,2,1,4,5,6,-1,-1,-1,-1,-1,-3,-3,-3) b - (1.1,1.1,1.2,1.2,1.2,1.2,1.2,2.1,2.1,2.2,2.2,2,0,0,0,0,2,2,2,2,2,3.1,3.1) dist - bhattacharyya.matrix(a,b,missclasification = TRUE) plot(dist) Could somebody give me a guide on the syntax ? Thanks Dizem -- View this message in context: http://r.789695.n4.nabble.com/Bhattacharyya-in-R-tp4670671.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bhattacharyya in R
There is a built-in guide to syntax called the help system. If you have read it you should be able to be mitre specific with your questions. I had never heard of this function. Your example code is not reproducible, nor does it indicate what result you got from running it. I used RSiteSearch(bhattacharya) and there appears to be a function bhattacharyya.matrix in the fpc package. The syntax indicated in the help for that function mentions wanting input matrices, not vectors. It also mentions another function bhattacharyya.dist which does accept vectors, but it does not accept the misclassification.bound argument. You should read the help file and ask more specific questions and provide reproducible examples per the Posting Guide recommendations. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Dzu dizem.ue...@alumni.fh-aachen.de wrote: Dear R-user, I am trying to apply bhattacharyya-distance function to my data. Did anybody use it before ? My code is the following #Bhattacharya Distance measure #a and b are vectors a - (1,2,3,4,2,2,2,2,2,2,2,1,4,5,6,-1,-1,-1,-1,-1,-3,-3,-3) b - (1.1,1.1,1.2,1.2,1.2,1.2,1.2,2.1,2.1,2.2,2.2,2,0,0,0,0,2,2,2,2,2,3.1,3.1) dist - bhattacharyya.matrix(a,b, misclassification.bound = TRUE) plot(dist) Could somebody give me a guide on the syntax ? Thanks Dizem -- View this message in context: http://r.789695.n4.nabble.com/Bhattacharyya-in-R-tp4670671.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lee carter model
The Posting Guide warns you to not post in HTML format (it messes up R code examples). It also warns you to supply reproducible examples (we should be able to paste your code into a fresh R session and see essentially what you see). The warning message means you have given the function a factor where it expected a numeric value (max does not work on factors). I suggest that you learn how to use the str() function on your data so you know that you have imported it successfully before you give it to analysis functions. You may need to review the Introduction to R and R Data Import/Export PDF files that come with R if you don't know what a factor is or how to import numeric data. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. ntamjo achille ntamjo2...@yahoo.fr wrote: Hi everybody, I'm running codes for for a Lee carter modeling. I compute the demogdata function in the package demography.� Age is a class of factor Base-demogdata(data=x,pop=y,ages=AGE,years=YEAR,type=mortality,label=City,name=Hommes,lambda=1) � Now, I try to run codes for lee carter model, and i always get the following message: Error in Summary.factor(c(1L, 2L, 24L, 35L, 46L, 57L, 68L, 79L, 90L, 101L, �:� � max not meaningful for factors Please can you help to understand what means this message.� Many Thanks Achille [[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] subset of factors in a regression
suppose state is a variable in a dataframe containing abbreviations of the US states, as a factor. What I'd like to do is to include dummy variables for a few of the states, (say, CA and MA) among the independent variables in my regression formula. (This would be the equivalent of, creating, eg, ca-state==CA) and then including that). I know I can create all the necessary dummy variables by using the outer function on the factor and then renaming them appropriately; but is there a solution that's more direct, ie that doesn't involve a lot of new variables? Thanks! Philip A. Viton City Planning, Ohio State University 275 West Woodruff Avenue, Columbus OH 43210 vito...@osu.edu __ 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] Optimum of lm
Hi All, I am trying to do some D o E. I would like to find the optima (maxima) of a 2 dimensional lm with quadratic terms. I'm sure there is a really simple solution but i can't find it. Also would there be any way to find some sort of confidence limits on these optima? Any help most appreciated! Cheers, Ben -- View this message in context: http://r.789695.n4.nabble.com/Optimum-of-lm-tp4670674.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Trying to predict from a time series with Additive Outliers: Error in as.matrix(newxreg) %*% coefs[-(1L:narma)] : non-conformable arguments
Hi, I am trying to work through an example in Cryer Chan's book with regards to an ARIMA model with Interventions and Outliers The model fit is: m=arimax(log(airmiles),order=c(0,1,1),seasonal=list(order=c(0,1,1),period=12),xtransf=data.frame(I911=1*(seq(airmiles)==69), I911a=1*(seq(airmiles)==69)),transfer=list(c(0,0),c(1,0)),xreg=data.frame(I12=1*(seq(airmiles)==12),I25=1*(seq(airmiles)==25),I84=1*(seq(airmiles)==84)),io=c(81),method='ML') I now want to predict from this model. I understand that since we use xreg in the model fit, I have to specify newxreg in the predict statement. Since xreg only contains information about additive outliers, the vectors provided in newxreg should all be zeros. I thus try the following nxr=data.frame(I12=seq(0,0,length=5),I25=seq(0,0,length=5),I84=seq(0,0,length=5)) predict(m,na.ahead=5,newxreg=nxr) But I get the following error: Error in as.matrix(newxreg) %*% coefs[-(1L:narma)] : non-conformable arguments Any thoughts? Thanks. __ 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] functions and matrices
Basically R does things *numerically* and what you want to do really
amounts to symbolic manipulation. Of course R could be cajoled into
doing it --- see fortune(Yoda) --- but probably only with a great deal of
effort and code-writing.
OTOH you could quite easily write a function that would calculate
det(u%*%v)(x) for any given numerical value of x:
foo - function(a,b,x){
a1 - apply(a,c(1,2),function(m,x){m[[1]](x)},x=x)
b1 - apply(b,c(1,2),function(m,x){m[[1]](x)},x=x)
det(a1%*%b1)
}
Then doing
foo(u,v,2)
gives 0. (In fact foo(u,v,anything) gives 0 for your collection of
functions;
the matrix u(x) is singular for any x --- the second row is x^2 times the
first row.)
Perhaps this is good enough for your purposes? If not, you should probably
be looking at a symbolic manipulation package. The R package Ryacas has
some capabilities in this regard, but I have no experience with it and
cannot
advise.
cheers,
Rolf Turner
On 02/07/13 05:37, Naser Jamil wrote:
Dear R-user,
May I seek your help, please. I have two matrices, u and v, elements of
which are some functions
of x. I just want to multiply them and express the determinant of the
resulting matrix as a function of
x and of course, this is for some reason. Actually the original problem has
more matrices to multiply and I'm just wondering whether I can simplify it
anyway through the R codes. It may even be non-sense, but just want to hear
from you. The below is the code.
-
f1-function(x) {x}
f2-function(x) {x^2}
f3-function(x) {x^3}
f4-function(x) {x^4}
f5-function(x) {x^2+7}
f6-function(x) {x^3+14*x}
f7-function(x) {x^2+2*x}
f8-function(x) {x^4+10*x}
u-matrix(c(f1,f2,f3,f4), nrow=2, ncol=2, byrow=TRUE)
v-matrix(c(f5,f6,f7,f8), nrow=2, ncol=2, byrow=TRUE)
det(u %*% v) # Is that possible?
Any suggestion will be more than great!
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Re: [R] functions and matrices
On Jul 1, 2013, at 3:32 PM, Rolf Turner wrote:
Basically R does things *numerically* and what you want to do really
amounts to symbolic manipulation. Of course R could be cajoled into
doing it --- see fortune(Yoda) --- but probably only with a great deal of
effort and code-writing.
OTOH you could quite easily write a function that would calculate
det(u%*%v)(x) for any given numerical value of x:
foo - function(a,b,x){
a1 - apply(a,c(1,2),function(m,x){m[[1]](x)},x=x)
b1 - apply(b,c(1,2),function(m,x){m[[1]](x)},x=x)
det(a1%*%b1)
}
Then doing
foo(u,v,2)
I would have thought that (u %*% v) would be:
u[1,1]( v[1,1](x) ) + u[1,2]( v[2,1](x) ) u[1,1]( v[1,2](x) ) + u[1,2](
v[2,2](x) )
u[2,1]( v[1,1](x) ) + u[2,2]( v[2,1](x) ) u[2,1]( v[2,1](x) ) + u[2,2](
v[2,2](x) )
(Crossing my fingers that I got the row and column conventions correct for
matrix multiplication.)
gives 0. (In fact foo(u,v,anything) gives 0 for your collection of functions;
the matrix u(x) is singular for any x --- the second row is x^2 times the
first row.)
Perhaps this is good enough for your purposes? If not, you should probably
be looking at a symbolic manipulation package. The R package Ryacas has
some capabilities in this regard, but I have no experience with it and cannot
advise.
cheers,
Rolf Turner
On 02/07/13 05:37, Naser Jamil wrote:
Dear R-user,
May I seek your help, please. I have two matrices, u and v, elements of
which are some functions
of x. I just want to multiply them and express the determinant of the
resulting matrix as a function of
x and of course, this is for some reason. Actually the original problem has
more matrices to multiply and I'm just wondering whether I can simplify it
anyway through the R codes. It may even be non-sense, but just want to hear
from you. The below is the code.
-
f1-function(x) {x}
f2-function(x) {x^2}
f3-function(x) {x^3}
f4-function(x) {x^4}
f5-function(x) {x^2+7}
f6-function(x) {x^3+14*x}
f7-function(x) {x^2+2*x}
f8-function(x) {x^4+10*x}
u-matrix(c(f1,f2,f3,f4), nrow=2, ncol=2, byrow=TRUE)
v-matrix(c(f5,f6,f7,f8), nrow=2, ncol=2, byrow=TRUE)
det(u %*% v) # Is that possible?
Any suggestion will be more than great!
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[R] similarity and dissimilarity index
Hallo every one I have this table and tried to find similarity and dissimilarity index in r by vegan package but I couldn't. I really don't know why I couldn't as I spend a lot of time working on it, so would you be so kind to calculate or give me some advise about my problem? Ismael, Khasro Abdulrahman Bremen University Mary-Astell-Straße 25 Wohnung 149 28539 Bremen Germany __ 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] similarity and dissimilarity index
On 02/07/13 11:46, Khasro Abdulrahman Ismael wrote: Hallo every one I have this table and tried to find similarity and dissimilarity index in r by vegan package but I couldn't. I really don't know why I couldn't as I spend a lot of time working on it, so would you be so kind to calculate or give me some advise about my problem? Another nominee for the Obtuse Question of the Month award. cheers, Rolf Turner P.S. I.e. read the expletive deleted posting guide. R. T. __ 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] Fwd: functions and matrices
With permission I offer this exchange. Rolf and I have different notions of
what u %*% v should mean, but the arbiter is obviously the original poster:
Begin forwarded message:
From: David Winsemius dwinsem...@comcast.net
Subject: Re: [R] functions and matrices
Date: July 1, 2013 6:21:09 PM PDT
To: Rolf Turner rolf.tur...@xtra.co.nz
On Jul 1, 2013, at 5:09 PM, Rolf Turner wrote:
On 02/07/13 11:37, David Winsemius wrote:
On Jul 1, 2013, at 3:32 PM, Rolf Turner wrote:
Basically R does things *numerically* and what you want to do really
amounts to symbolic manipulation. Of course R could be cajoled into
doing it --- see fortune(Yoda) --- but probably only with a great deal of
effort and code-writing.
OTOH you could quite easily write a function that would calculate
det(u%*%v)(x) for any given numerical value of x:
foo - function(a,b,x){
a1 - apply(a,c(1,2),function(m,x){m[[1]](x)},x=x)
b1 - apply(b,c(1,2),function(m,x){m[[1]](x)},x=x)
det(a1%*%b1)
}
Then doing
foo(u,v,2)
I would have thought that (u %*% v) would be:
u[1,1]( v[1,1](x) ) + u[1,2]( v[2,1](x) ) u[1,1]( v[1,2](x) ) +
u[1,2]( v[2,2](x) )
u[2,1]( v[1,1](x) ) + u[2,2]( v[2,1](x) ) u[2,1]( v[2,1](x) ) +
u[2,2]( v[2,2](x) )
(Crossing my fingers that I got the row and column conventions correct for
matrix multiplication.)
SNIP
Not quite sure what you're getting at here. It looks to me that you are
calculating the *composition* of the functions rather than their *product*.
Exactly. That is how I understood successive application of functions
embedded in matrices . The symbol used in my differential topology course lo
those 40 years ago was an open circle, but I assumed the OP wanted something
along those lines to perform a composite mapping:
compose - function(u, v, x) matrix( c(
u[1,1][[1]]( v[1,1][[1]](x) ) + u[1,2][[1]]( v[2,1][[1]](x) ) ,
u[1,1][[1]]( v[1,2][[1]](x) ) + u[1,2][[1]]( v[2,2][[1]](x) ),
u[2,1][[1]]( v[1,1][[1]](x) ) + u[2,2][[1]]( v[2,1][[1]](x) ),
u[2,1][[1]]( v[2,1][[1]](x) ) + u[2,2][[1]]( v[2,2][[1]](x) ) ),
2,2,byrow=TRUE)
compose(u,v,2)
[,1][,2]
[1,] 751332
[2,] 5427 1680128
(Noting that I may have reversed the roles of u and v.)
I.e. you are taking the (i,j)th entry of u%*%v (evaluated at x) to be the
sum over k of
u[i,k](v[k,j](x))
This is not what I understood the OP to want. I assumed he wanted the
product of the function values rather than the composition of the functions,
i.e. that he wanted the (i,j)th entry to be the sum over k of
u[i,k](x) * v[k,j](x)
which is what my function provides. This seems to me to be the most
reasonable interpretation, but I could be wrong.
BTW --- you cannot actually do u[i,k](x). E.g.
u[1,2](2)
gives Error: attempt to apply non-function. One needs to do u[1,2][[1]](2)
(which gives 4, as it should).
Yes. I was playing fast and loose with notation. I didn't think the code
would really run as offered.I was a bit surprise that this worked, but I
suppose you bear credit (and blame?) for pushing my program closer to
completion.
v[1,1][[1]]( u[1,1][[1]]( 2 ))
[1] 11
Any problem with me copying this to the list?
cheers,
Rolf
Best;
David Winsemius
Alameda, CA, USA
David Winsemius
Alameda, CA, USA
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Re: [R] KalmanForecast (stats)
Gabriella, There is no function KalmanForecast in package stats, so I am not quite sure about what you are talking about. That said, it may help a review paper that I wrote a couple of years ago about the different packages available in R for state space modeling (Petris Petrone, State space models in R, Journal of Statistical Software 41, 2011). Another good review paper is Tusell, Kalman filtering in R, JSS 39, 2011. Hope this helps you to get started. Best, Giovanni From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] on behalf of Csima Gabriella [csim...@met.hu] Sent: Friday, June 28, 2013 6:27 AM To: r-help@r-project.org Subject: [R] KalmanForecast (stats) Dear List members, I would like to use the Kalman-filter program for forecasting - namely for postprocessing numerical model results of 2m temperature. I have looked through the help of the Kalman-filtering programs, mainly the KalmanForecast and I have read about the newer packages like KFAS as well. I always uderstand and use new R programs that first I try out the example(s), it makes me a base for my new program. My problem is that there is no any example (with data that I can run immediately), and I do not understand, or cannot imagine how - e.g. the mod - have to be as the input of the program. Could you send me a simple example of KalmanForecast (with input data) that I can run and can see how it works exactly? Cheers, Gabriella [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] KalmanForecast (stats)
Oops... Correction: The function KalmanForecast does exist in package stats. The references that I gave in my other reply are still valid, though. It is my impression that Kalman filtering facilities in stats are not meant to be used directly by the end user of R, but their main purpose is to serve as workhorses for other model fitting and forecasting functions (e.g., StructTS). Best, Giovanni From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] on behalf of Csima Gabriella [csim...@met.hu] Sent: Friday, June 28, 2013 6:27 AM To: r-help@r-project.org Subject: [R] KalmanForecast (stats) Dear List members, I would like to use the Kalman-filter program for forecasting - namely for postprocessing numerical model results of 2m temperature. I have looked through the help of the Kalman-filtering programs, mainly the KalmanForecast and I have read about the newer packages like KFAS as well. I always uderstand and use new R programs that first I try out the example(s), it makes me a base for my new program. My problem is that there is no any example (with data that I can run immediately), and I do not understand, or cannot imagine how - e.g. the mod - have to be as the input of the program. Could you send me a simple example of KalmanForecast (with input data) that I can run and can see how it works exactly? Cheers, Gabriella [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] KalmanForecast (stats)
On 1 July 2013 19:24, Giovanni Petris gpet...@uark.edu wrote: Could you send me a simple example of KalmanForecast (with input data) that I can run and can see how it works exactly? There's an explanation of the Kalman Filter available at http://www.swarthmore.edu/NatSci/echeeve1/Ref/Kalman/ScalarKalman.html -- I've summarised it below: The kalman filter is used to reduce the noise in an indirectly measured signal, s, approximated by the formula -- x[t] = a*x[t-1] + b*u[t], to which a random amount of white noise is added, making the equation x[t] = a*x[t-1]+b*u[t] + w[t]. The white noise varies with time, hence it's a series. Each measure of x[t] brings you closer to the actual signal. I hope this helps... -- H -- Sent from my mobile device Envoyé de mon portable __ 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] KalmanForecast (stats)
Below... On Mon, Jul 1, 2013 at 7:24 PM, Giovanni Petris gpet...@uark.edu wrote: Oops... Correction: The function KalmanForecast does exist in package stats. The references that I gave in my other reply are still valid, though. It is my impression that Kalman filtering facilities in stats are not meant to be used directly by the end user of R, ... and on what, pray tell, do you base **that** strange pronouncement?? -- Bert but their main purpose is to serve as workhorses for other model fitting and forecasting functions (e.g., StructTS). Best, Giovanni From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] on behalf of Csima Gabriella [csim...@met.hu] Sent: Friday, June 28, 2013 6:27 AM To: r-help@r-project.org Subject: [R] KalmanForecast (stats) Dear List members, I would like to use the Kalman-filter program for forecasting - namely for postprocessing numerical model results of 2m temperature. I have looked through the help of the Kalman-filtering programs, mainly the KalmanForecast and I have read about the newer packages like KFAS as well. I always uderstand and use new R programs that first I try out the example(s), it makes me a base for my new program. My problem is that there is no any example (with data that I can run immediately), and I do not understand, or cannot imagine how - e.g. the mod - have to be as the input of the program. Could you send me a simple example of KalmanForecast (with input data) that I can run and can see how it works exactly? Cheers, Gabriella [[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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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] subset of factors in a regression
Philip A. Viton viton.1 at osu.edu writes: suppose state is a variable in a dataframe containing abbreviations of the US states, as a factor. What I'd like to do is to include dummy variables for a few of the states, (say, CA and MA) among the independent variables in my regression formula. (This would be the equivalent of, creating, eg, ca-state==CA) and then including that). I know I can create all the necessary dummy variables by using the outer function on the factor and then renaming them appropriately; but is there a solution that's more direct, ie that doesn't involve a lot of new variables? Thanks! You could use model.matrix(~state-1) and select the columns you want, e.g. state - state.abb; m - model.matrix(~state-1) m[,colnames(m) %in% c(stateCA,stateMA)] -- but this will actually create a bunch of vectors you want before throwing them away. more compactly: m - sapply(cstates,==,state) storage.mode(m) - numeric ## or m[] - as.numeric(m) __ 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] Automating the running of MVLN model in R using R2WinBUGS
Hi:
To test the situation below I am creating 2 datasets
.#Set working directory
setwd(C://Tina/USB_Backup_042213/Testing/CSV)
matrix=NULL
csvs - paste(MVN, 1:2, .csv, sep=)
for(i in 1:length(csvs)){
matrix[[i]] - read.csv(file=csvs[i], header=T)
print(matrix[[i]])
}
So now I have read in 2 simulated datasets which look like
Y1 Y2
1 11 6
2 8 5
3 25 13
4 1 13
5 8 22
Y1 Y2
1 9 1
2 7 9
3 25 13
4 1 18
5 9 12
My next step is to run a multivariate logit normal model on these datasets
and automate this process for 300 such simulated datasets. Heres the model
statement:
model
{
for (j in 1 : Nf)
{
p1[j, 1:2 ] ~ dmnorm(gamma[1:2 ], T[1:2 ,1:2 ])
for (i in 1:2)
{
logit(p[j,i])-p1[j,i]
Y[j,i] ~ dbin(p[j,i],n)
}}
I am trying to use the following code to run it in R2WinBUGS
bugs.output - list()
for(i in 1:2){ # for 2 simulated datasets for
now
*Y -(matrix[i])* * *
bugs.output[[i]] - bugs(
data=list(Y=Y, Nf=5), # change for no of sites
inits=NULL,
model.file=M-LN_model_trial.txt,
parameters.to.save = c(p,rho,sigma2),
n.chains=1, n.iter=12000, n.burnin=5000,
bugs.directory=C://Tina/USB_Backup_042213/winbugs14/WinBUGS14,
working.directory=NULL)}
Any suggestion would be helpful.
Thanks!
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