Re: [R] A slight trap in read.table/read.csv.
On Tue, 09-Mar-2010 at 08:14AM +0100, Petr PIKAL wrote:
| I would respectfully oppose it. It may be quite convenient for making code
| for functions and other programming stuff but all using R more or less in
| interactive way this change could be quite a burden especially when there
| are many functions which use TRUE/FALSE for setting its parameters.
|
| In those (and many others) instances I almost exclusively use T/F
| shortcut.
|
| read.delim(file, header = TRUE, sep = \t, quote=\, dec=., fill =
| TRUE, comment.char=, ...)
| lm(formula, data, subset, weights, na.action,method = qr, model = TRUE,
| x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE, contrasts = NULL,
| offset, ...)
If you use ESS, you have the benefit of completions. Depending on
what else could begin with T or F, you can press the TAB key after
typing the first letter or two. Admittedly, three keystrokes isn't
much shorter than TRUE -- but they are all with the left hand. You
always get at least a 40% discount with FALSE. :-) -- except in the
'unlikely event' that you have objects named FALLOW or something
else a lot like FALSE.
|
| If this had to be changed I would vote for some change which allow users
| some other shortcut for setting interactively parameters in functions.
|
| Regards
| Petr
|
|
|
|
| The only immediate solution to this accretion of overly clever
| behavior would be for someone to write new functions (say,
| Read.csv) that didn't do all those conversions behind the
| scenes. I'm not about to do that. Are you?
|
|
| NFL!!!
|
|cheers,
|
| Rolf
|
| ##
| Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
|
| __
| R-help@r-project.org mailing list
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| PLEASE do read the posting guide
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| and provide commented, minimal, self-contained, reproducible code.
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| and provide commented, minimal, self-contained, reproducible code.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) . Eleanor Roosevelt
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Re: [R] setClass or setValidity?
Hi Martin, Thanks. Your remark about setValidity makes sense. One question about try() though. Isn't that a (crude) implementation of duck typing? Give a method some type of data, 'try' if it works with that type of data, and if not, do something else? I think I agree with you that if-then is less of a let's see what happens kind of statement. Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ --- On Mon, 3/8/10, Martin Morgan mtmor...@fhcrc.org wrote: From: Martin Morgan mtmor...@fhcrc.org Subject: Re: [R] setClass or setValidity? To: Albert-Jan Roskam fo...@yahoo.com Cc: r-help@r-project.org Date: Monday, March 8, 2010, 10:56 PM On 03/08/2010 07:18 AM, Albert-Jan Roskam wrote: Sorry: there was an error in the last sentence: And, inside those validity checks, is most of the checking done with 'if' 'else' computations, or is it also common to use try()? For me it's a matter of taste, and usual to use if... (because you know explicitly what you're trying to validate, whereas try() implies a kind of 'something might go wrong...'). I find myself using setValidity() to separate out class definition from implementation. Best, Martin Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ --- On Mon, 3/8/10, Albert-Jan Roskam fo...@yahoo.com wrote: From: Albert-Jan Roskam fo...@yahoo.com Subject: [R] setClass or setValidity? To: r-help@r-project.org Date: Monday, March 8, 2010, 4:14 PM Hi, I'm reading up on S4 classes *). There seem to be at least two ways of input validation: setClass() (using the 'validity' argument) and setValidity(). Is it a matter of taste which function is used? Or should more complex validation code better be put in a setValiditity call? *) A (Not So) Short Introduction to S4 Object Oriented Programming in R V0.5.1 Christophe Genolini August 20, 2008 And, inside those validity checks, is most of the checking done with 'if' 'else' computations, or is it also common to use except()? Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ [[alternative HTML version deleted]] -Inline Attachment Follows- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 [[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] how can I look at .Internal(model.matrix(t, data))?
I imagine it's in https://svn.r-project.org/R/trunk/src/main/model.c -Peter Ehlers On 2010-03-05 12:43, Werner W. wrote: Hi, I would like to see how model.matrix expands factor column to a set of dummy columns. I think that is done int .Internal(model.matrix(t, data)) which is called from model.matrix.default. But I have not idea how I can look at this function. How can I get to such internal functions? Thanks so much! Werner einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.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. -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how can I look at .Internal(model.matrix(t, data))?
Also see Uwe's article in R news : Accessing the source : http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf On 03/09/2010 09:22 AM, Peter Ehlers wrote: I imagine it's in https://svn.r-project.org/R/trunk/src/main/model.c -Peter Ehlers On 2010-03-05 12:43, Werner W. wrote: Hi, I would like to see how model.matrix expands factor column to a set of dummy columns. I think that is done int .Internal(model.matrix(t, data)) which is called from model.matrix.default. But I have not idea how I can look at this function. How can I get to such internal functions? Thanks so much! Werner -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/OIXN : raster images and RImageJ |- http://tr.im/OcQe : Rcpp 0.7.7 `- http://tr.im/O1wO : highlight 0.1-5 __ 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] Package for Sieve Bootstrap Methods
Hello R-users. Is there a package which handles sieve bootstrap methods in various time series applications? Method of Sieve Bootstrap by Bühlmann, P. (1995, Technical Report; published 1997 in the Journal of the Bernoulli Society): http://ftp.stat.berkeley.edu/tech-reports/431.pdf Thank you in advance. Sincerely, Andreas. __ Do You Yahoo!? Sie sind Spam leid? http://mail.yahoo.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] A slight trap in read.table/read.csv.
On Tue, Mar 9, 2010 at 8:11 AM, Patrick Connolly p_conno...@slingshot.co.nz wrote: If you use ESS, you have the benefit of completions. Depending on what else could begin with T or F, you can press the TAB key after typing the first letter or two. Admittedly, three keystrokes isn't much shorter than TRUE -- but they are all with the left hand. You always get at least a 40% discount with FALSE. :-) -- except in the 'unlikely event' that you have objects named FALLOW or something else a lot like FALSE. FALSETTO? Anyone analysing choral music in R? I'd somehow got the impression that T and F were going to be removed as values, but there's no mention of it in ?FALSE. The package check utilities warn you if you use them. Just looking at the source for the underlying cause of the read.csv behaviour, which is type.convert in R which is do_typecvt in C, and it admits: /* This is a horrible hack There's a couple of instances of: if (strcmp(s, F) == 0 || strcmp(s, FALSE) which are what do it. And are obviously not language-dependent - do French people have 'VRAI' and 'FAUX' in their CSV files? Do they call them DSV files: http://translate.google.com/#en|fr|comma-separated%20file Got to keep the Academie Francaise happy... Barry -- blog: http://geospaced.blogspot.com/ web: http://www.maths.lancs.ac.uk/~rowlings web: http://www.rowlingson.com/ twitter: http://twitter.com/geospacedman pics: http://www.flickr.com/photos/spacedman __ 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! I turned my data into junk!
I posted my data for a midterm into notepad and it turned into symbols. The other bit I posted turned out just fine, but for some reason this one messed up. I need this stuff for a class. Anyone know how to get my data back. Please help soon! -- View this message in context: http://n4.nabble.com/Help-I-turned-my-data-into-junk-tp1585481p1585481.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] A slight trap in read.table/read.csv.
To answer your questions, French people don't have 'Vrai' and 'Faux'. Since most of people have no idea what csv means, there's no use for using dsv! The Académie Française would not be happy indeed. But to keep on the subject, I personally never had troubles using T or F. I sometimes use T/F, sometimes TRUE/FALSE, depending on my mood! Looks like I should think about using TRUE/FALSE all the time, but since I've never had problems, I don't feel bad with it! Ivan Le 3/9/2010 10:00, Barry Rowlingson a écrit : On Tue, Mar 9, 2010 at 8:11 AM, Patrick Connolly p_conno...@slingshot.co.nz wrote: If you use ESS, you have the benefit of completions. Depending on what else could begin with T or F, you can press the TAB key after typing the first letter or two. Admittedly, three keystrokes isn't much shorter than TRUE -- but they are all with the left hand. You always get at least a 40% discount with FALSE. :-) -- except in the 'unlikely event' that you have objects named FALLOW or something else a lot like FALSE. FALSETTO? Anyone analysing choral music in R? I'd somehow got the impression that T and F were going to be removed as values, but there's no mention of it in ?FALSE. The package check utilities warn you if you use them. Just looking at the source for the underlying cause of the read.csv behaviour, which is type.convert in R which is do_typecvt in C, and it admits: /* This is a horrible hack There's a couple of instances of: if (strcmp(s, F) == 0 || strcmp(s, FALSE) which are what do it. And are obviously not language-dependent - do French people have 'VRAI' and 'FAUX' in their CSV files? Do they call them DSV files: http://translate.google.com/#en|fr|comma-separated%20file Got to keep the Academie Francaise happy... Barry -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere 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/mitarbeiter.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] arbitrary scaling
On 03/09/2010 01:37 AM, Petr PIKAL wrote: Hi all I know I probably reinvented wheel but it was maybe simpler then search in docs or ask help before I did my part. I made a simple function which can scale a vector between chosen values. Do anybody know simpler/better approach? ... x- c(5,30,50) myscale(x) [1] 0.500 0.778 1.000 Hi Petr, Try this: library(plotrix) rescale(x,c(0.5,1)) Jim __ 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] Removing Zeros from matrix
Hi Everybody, I have a matrix of about 45 columns. Some of the rows contain zeros. Using data1-data[complete.cases(data),], I can remove the NA rows. But I am unable to tackle that of zeros. Can anybody give me an idea of how to remove rows containing zeros in a matrix. Thanks so much Best Ogbos [[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] Removing Zeros from matrix
one approach is the following: mat - matrix(rnorm(100*45), 100, 45) mat[sample(100*45, 50)] - 0 index - rowMeans(mat == 0) == 0 mat[index, ] I hope it helps. Best, Dimitris On 3/9/2010 11:05 AM, ogbos okike wrote: Hi Everybody, I have a matrix of about 45 columns. Some of the rows contain zeros. Using data1-data[complete.cases(data),], I can remove the NA rows. But I am unable to tackle that of zeros. Can anybody give me an idea of how to remove rows containing zeros in a matrix. Thanks so much Best Ogbos [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] confused by classes and methods.
Hi Rob,
I just started reading about classes (and also learning R), so I apologize if
the following code is confusing you more. I simplified the code somewhat in
order to better understand what's going on. I was wondering: are you
deliberately reimplementing the builtin update() function?
setClass(Class=StatisticInfo,
representation( oldData = data.frame,
newData = data.frame
)
)
# declare the update method, even though it exists already.
setGeneric (
name=update,
def=function(object){standardGeneric(update)}
)
setMethod(f=update, signature (StatisticInfo),
definition = function(object){
min = min(obj...@newdata, obj...@olddata, na.rm=T)
avg = mean(mean(cbind(obj...@newdata, obj...@olddata)))
max = max(obj...@newdata, obj...@olddata, na.rm=T)
return(list(min, avg, max))
}
)
old - data.frame(runif(10, 1, 10))
new - data.frame(runif(10, 1, 9))
instance - new(Class=StatisticInfo, oldData=old, newData=new)
update(instance)
Does this make sense to you?
Cheers!!
Albert-Jan
~~
In the face of ambiguity, refuse the temptation to guess.
~~
--- On Tue, 3/9/10, Rob Forler rfor...@uchicago.edu wrote:
From: Rob Forler rfor...@uchicago.edu
Subject: [R] confused by classes and methods.
To: r-help@r-project.org
Date: Tuesday, March 9, 2010, 12:09 AM
Hello, I have a simple class that looks like:
setClass(statisticInfo,
representation( max = numeric,
min = numeric,
beg = numeric,
current = numeric,
avg = numeric,
obs = vector
)
)
and the following function
updateStatistic - function(statistic, newData){
statis...@obs = c(statis...@obs, newData)
statis...@max = max(newData, statis...@max, na.rm=T)
statis...@min = min(newData, statis...@min, na.rm=T)
statis...@avg = mean(statis...@obs)
statis...@current = newData
if(length(statis...@obs)==1 || is.na(statis...@beg)){
statis...@beg = newData
}
return(statistic)
}
Firstly,
I know you can use methods which seems to add some value. I looked at
http://developer.r-project.org/methodDefinition.html but I try
setMethod(update, signature(statistic=statisticInfo, newData=numeric),
function(statistic, newData){
statis...@obs = c(statis...@obs, newData)
statis...@max = max(newData, statis...@max, na.rm=T)
statis...@min = min(newData, statis...@min, na.rm=T)
statis...@avg = mean(statis...@obs)
statis...@current = newData
if(length(statis...@obs)==1 || is.na(statis...@beg)){
statis...@beg = newData
}
return(statistic)
}
)
Creating a new generic function for update in .GlobalEnv
Error in match.call(fmatch, fcall) :
unused argument(s) (statistic = statisticInfo, newData = numeric)
1: source(tca.init.R, chdir = T)
2: eval.with.vis(ei, envir)
3: eval.with.vis(expr, envir, enclos)
4: source(../../studies/tca.tradeClassifyFuncs.R)
5: eval.with.vis(ei, envir)
6: eval.with.vis(expr, envir, enclos)
7: setMethod(update, signature(statistic = statisticInfo, newData =
numeric), function(statistic, newData) {
8: isSealedMethod(f, signature, fdef, where = where)
9: getMethod(f, signature, optional = TRUE, where = where, fdef = fGen)
10: matchSignature(signature, f
I don't understand this any help would be appreciated.
Secondly, can anyone give any examples of where methods are used that makes
sense besides just checking the class inputs?
Thirdly, I've looked into passing by reference in R, and some options come
up, but in general they seem to be fairly complicated.
I would like update to work more like my update function to work without
having to return a a new object.
Something like
statList = list(new(statisticInfo))
updateStatistic(statList[[1]],3)
statList[[1]]
#this would then have the updated one and not the old one.
Anyways,
The main reason I'm asking these questions is because I can't really find a
good online resource for this. Any help would be greatly appreciated.
Thanks,
Rob
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[R] Source code for the t-distribution
I have tried looking for the source code for the pt() function in https://svn.r-project.org/R/trunk/src/library/stats/ and am unable to find it there. Can someone please tell me where to find it? Thanks, Ravi Kulkarni -- View this message in context: http://n4.nabble.com/Source-code-for-the-t-distribution-tp1585875p1585875.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] Removing Zeros from matrix
Dimitris Rizopoulos wrote: one approach is the following: mat - matrix(rnorm(100*45), 100, 45) mat[sample(100*45, 50)] - 0 index - rowMeans(mat == 0) == 0 mat[index, ] Dimitris, You use quite a complicated syntax to get the index. I think the following syntax using apply is more easy to understand: # Note, MARGIN equal to 1 means loop over rows # If any member of a row is zero index = apply(mat == 0, MARGIN = 1, any) # If all members of a row are zero index = apply(mat == 0, MARGIN = 1, all) cheers and hope it helps, Paul I hope it helps. Best, Dimitris On 3/9/2010 11:05 AM, ogbos okike wrote: Hi Everybody, I have a matrix of about 45 columns. Some of the rows contain zeros. Using data1-data[complete.cases(data),], I can remove the NA rows. But I am unable to tackle that of zeros. Can anybody give me an idea of how to remove rows containing zeros in a matrix. Thanks so much Best Ogbos [[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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] using near-zero probabilities in optimization
Hi there I am using mle2 for a multinomial likelihood optimization problem. My function works fine when I'm using simulated data, however my cell probabilities of the true data for the multinomial likelihood are sometimes very small (in some cases 0.00...) and the estimated point estimates fit the true vlaues quite poorly. Is there a way how to handle near zero probabilities in maximum likelihood optimization? Thanks a lot for the help best wishes Benedikt __ 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] IMPORTANT - To remove the null elements from a vector
I have a vector that have null elements. How to remove these elements? For example: x=[10 0 30 40 0 0] I want the vector y=[10 30 40] Thanks [[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] IMPORTANT - Add a plot to another plot
I have a graphic that I design with the command plot, and I want to add another graphic. If I use another time the command plot with parameter add=TRUE It's wrong. Why? How I can resolve this problem? Thanks [[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] IMPORTANT - Add a plot to another plot
try: plot(0) # first plot par(new=TRUE) plot(1) # second plot # need to make sure ranges agrees and whether to plot axes or not. Or you probably really want to use 'lines'/'points' On Tue, Mar 9, 2010 at 7:52 AM, barbara.r...@uniroma1.it wrote: I have a graphic that I design with the command plot, and I want to add another graphic. If I use another time the command plot with parameter add=TRUE It's wrong. Why? How I can resolve this problem? Thanks [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] find out commands in package
Dears, I am trying to implement some R package which is still under construction and has not yet been submitted to CRAN (RSSA, http://anton.korobeynikov.info/software). Documentation is yet very poor (or i just did not find it), so I am wondering whether there is any way to retrieve a list of commands available in this package from within R? And to find out whether the package is successfully installed. After downloading the zip and installing it within R I only got the error message that it was created with an earlier R version and help would not work Thanks for your help! Jannis __ D usragenden Schutz gegen Massenmails. http://mail.yahoo.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] Problem with mean
Hi all, I got one intresting problem with caliculating mean that is while i am taking mean of values *0.6, -0.8, 4, -3.8* using *val-c(0.6, -0.8, 4, -3.8)* *mean(val)* it given result as *2.775558e-17* but the actual result is *0* can any one suggest how can I get correct mean result in this case can any one suggest how I can farward thanks in regards kiran [[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] error in a function
Hallo!
I have the following function:
cLL_beta - function(beta){
sumterm=0
a=1
b=0
S=I_n-lambda*w
R=I_n-rho*w
det_R=det(S)
det_S=det(R)
for (i in 1:t){
b=i*n
y_ausgew=y_tilde[a:b]#y_ausgew ist numeric
y_aus=matrix(y_ausgew)#Typen anpassen
X_ausgew=X[a:b,]#X_ausgew ist eine Matrix
x_tilde=X_ausgew-1/t*x_t #x_tilde ist auch eine Matrix
X_aus=matrix(X_ausgew)
V1=R%*%(S%*%y_aus-x_tilde%*%beta)
V11=t(V1)
V2=V11%*%J_n
V_tilde=V2%*%V1
sumterm=sumterm+V_tilde
a=b+1
}
-((n*t)/2)*log(2*pi*sigm_sq)+t*(log(det_S)+log(det_R))-1/(2*sigm_sq)*sumterm
}
where beta is a matrix (2x1), X is a matrix (n*tx1) and y is numeric with
length nt.
My error message is: X_ausgew%*%beta - non-conformable arguments
Can anybody help me?
THANKS
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Re: [R] Odp: how to convert character variables into numeric variables directly
Thanks! Xumin Petr PIKAL petr.pi...@precheza.cz 03/09/2010 01:57 AM To Xumin Zeng xumin.z...@abbott.com cc r-help r-help@r-project.org Subject Odp: [R] how to convert character variables into numeric variables directly Hi r-help-boun...@r-project.org napsal dne 08.03.2010 18:55:10: Here is the example. age=18:29 height=c(76.1,77,78.1,78.2,78.8,79.7,79.9,81.1,81.2,81.8,82.8,83.5) type=c(A, B, C, D,A, B, C, D,A, B, C, D) typec=c(0,4,2,9,0,7,2,3,0,1,2,3) typen=c(0,1,2,3,0,1,2,3,0,1,2,3) data1=data.frame(age=age,height=height, type=type, typec=typec, typen=typen) With data1=data.frame(age=age,height=height, type=type, typec=typec, typen=typen, stringsAsFactors=F) your conversion shall work Regards Petr data1[,3]=as.numeric(data1[,3]) data1[,4]=as.numeric(data1[,4]) data1[,5]=as.numeric(data1[,5]) print(data1) and I got the output as: age height type typec typen 1 18 76.11 1 0 2 19 77.02 5 1 3 20 78.13 3 2 4 21 78.24 7 3 5 22 78.81 1 0 6 23 79.72 6 1 7 24 79.93 3 2 8 25 81.14 4 3 9 26 81.21 1 0 10 27 81.82 2 1 11 28 82.83 3 2 12 29 83.54 4 3 The typec is not what I expected. How can I get the direct conversion from character to numeric and get the following output? age height type typec typen 1 18 76.11 0 0 2 19 77.02 4 1 3 20 78.13 2 2 4 21 78.24 9 3 5 22 78.81 0 0 6 23 79.72 7 1 7 24 79.93 2 2 8 25 81.14 3 3 9 26 81.21 0 0 10 27 81.82 1 1 11 28 82.83 2 2 12 29 83.54 3 3 Thanks. Xumin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] IMPORTANT - To remove the null elements from a vector
x - x[x != 0] If for null elements you intend the value of zero. Ciao! mario On 09-Mar-10 13:48, barbara.r...@uniroma1.it wrote: I have a vector that have null elements. How to remove these elements? For example: x=[10 0 30 40 0 0] I want the vector y=[10 30 40] Thanks [[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. -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ 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] IMPORTANT - To remove the null elements from a vector
barbara.r...@uniroma1.it wrote: I have a vector that have null elements. How to remove these elements? For example: x=[10 0 30 40 0 0] I want the vector y=[10 30 40] Thanks [[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. and, to add to the options already posted: subset(x, x != 0) cheers, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] Removing Zeros from matrix
Dimitris Rizopoulos wrote: On 3/9/2010 1:36 PM, Paul Hiemstra wrote: Dimitris Rizopoulos wrote: one approach is the following: mat - matrix(rnorm(100*45), 100, 45) mat[sample(100*45, 50)] - 0 index - rowMeans(mat == 0) == 0 mat[index, ] Dimitris, You use quite a complicated syntax to get the index. I think the following syntax using apply is more easy to understand: well, this way is much more efficient to compute, especially if you have many rows. Compare the following to see the difference: mat - matrix(rnorm(2*1e06), 1e06, 2) mat[sample(2*1e06, 50)] - 0 system.time(index1 - !apply(mat == 0, MARGIN = 1, any)) system.time(index2 - rowMeans(mat == 0) == 0 ) all.equal(index1, index2) Point taken, I totally agree that for large matrices you should use your approach. Didn't know that it made such a difference, great to learn something new :). But I still like the other syntax more ;). cheers, Paul Best, Dimitris # Note, MARGIN equal to 1 means loop over rows # If any member of a row is zero index = apply(mat == 0, MARGIN = 1, any) # If all members of a row are zero index = apply(mat == 0, MARGIN = 1, all) cheers and hope it helps, Paul I hope it helps. Best, Dimitris On 3/9/2010 11:05 AM, ogbos okike wrote: Hi Everybody, I have a matrix of about 45 columns. Some of the rows contain zeros. Using data1-data[complete.cases(data),], I can remove the NA rows. But I am unable to tackle that of zeros. Can anybody give me an idea of how to remove rows containing zeros in a matrix. Thanks so much Best Ogbos [[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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] using sprintf to pass a variable to a RMySQL query
Hi all,
Thanks for help with the paste and sprintf syntax.
So I've decided to use paste and or sprintf. 'gsubfn' looks like a
great package but unfortunately I've had problems installing it, as I
don't think it likes the version of tcltk that is installed. I'm
working on a few unix clusters with many computers and there seems to be
problems with different versions of R and different versions of the
packages on different computers.
So, the other problem is that I want to rename the data.frames and names
of the output jpeg files resulting from the queries. I've tried a few
different approaches but none seem to work, using sprintf and paste
turns the data frame into just a string of the name.
I have a complicated loop here as I'd like to do some summary output
after every 4 queries (ie. after MG1, MG 19, MG 37, MG 54) then I want
to start again and do for MG2, MG20 etc..
Here's my code below, there are probably error in the loop structure
that I can work out, but I need help with renaming the data frames based
on the parameters i and j
thanks
i-1
j-1
for (i=72 and j=4){{
sqlcmd_ScaffLen- paste(SELECT scaffold.length
FROM scaffold, scaffold2contig, contig2read
WHERE scaffold.scaffold_id=scaffold2contig.scaffold_id AND
scaffold2contig.contig_id=contig2read.contig_id AND
contig2read.read_id LIKE '%MG, i ,%', sep='')
sqlcmd_contigs-paste(SELECT length FROM contig WHERE external_id LIKE
'%MG,i,%',sep='' )
sqlcmd_singletons-paste(SELECT COUNT(*) FROM contig WHERE
read_count=1 AND external_id LIKE '%MG,i,%',sep='')
MGi_ScaffoldLen-dbGetQuery(con,sqlcmd_ScaffLen)
MGi_ContigsLen-dbGetQuery(con,sqlcmd_contigs)
MGi_SingletonsCount-dbGetQuery(con,sqlcmd_singletons)
MGi_ScaffoldLen_Summ-as.data.frame(c(summary(MGi_ScaffoldLen$length),MGi_SingletonsCount))
MGi_ContigsLen_Summ-summary(MGi_ContigsLen$length)
write.table(MGi_ScaffoldLen_Summ,file=ScaffoldLen_SummStats.txt,append=TRUE,sep='\t')
write.table(MGi_ContigsLen_Summ,file=ContigsLen_SummStats.txt,append=TRUE,sep='\t')
i-i+18
j-j+1
}
### Summary Plots For each Treatment ##
jpeg(file=sprintf(Boxplots_%d.jpeg,i)
boxplot(MGi_ScaffoldLen$length,MG(i+18*j)_ScaffoldLen$length,MG(i+_ScaffoldLen$length,MG59_ScaffoldLen$length,Main=400spec_10virus)
dev.off()
jpeg(file=sprintf(Scaffold_histograms_%d.jpeg,i)
hist(MGi_ScaffoldLen$length)
hist(MG(i+j*18)_ScaffoldLen$length)
hist(MG(i+j*18_ScaffoldLen$length)
hist(MG(i+j*18_ScaffoldLen$length)
dev.off()
jpeg(file=sprintf(Contig_histograms_%d.jpeg,i)
hist(MGi_ContigsLen$length)
hist(MG(i+j*18)_ContigsLen$length)
hist(MG(i+j*18_ContigsLen$length)
hist(MG(i+j*18_ContigsLen$length)
dev.off()
j-1
i-2
}
On 03/08/10 21:02, Don MacQueen wrote:
I always use paste()
i - 1
sqlcmd_ScaffLen - paste(SELECT scaffold.length
FROM scaffold, scaffold2contig, contig2read
WHERE scaffold.scaffold_id=scaffold2contig.scaffold_id AND
scaffold2contig.contig_id=contig2read.contig_id AND
contig2read.read_id LIKE '%MG, i ,%', sep='')
That should create bits like
LIKE '%MG1%'
LIKE '%MG2%'
and so on.
You just have to get the nesting of the single and double quotes
correct - the SQL requires single quotes, so use double quotes for the
fixed character strings insidte paste(). That, and use sep='' to get
rid of unwanted space characters.
Using paste is also effective for constructs like
IN (3,4,5)
or
IN ('a','b','c')
though it can be necessary to nest one paste within another
-Don
At 2:06 PM +0100 3/8/10, alison waller wrote:
Hello,
I am using RmySQL and would like to iterate through a few queries.
I would like to use sprintf but I think I'm having problems mixing and
matching the sprintf syntax and the SQL regex.
I have checked my sqlcmd and it works when I wan to match %MG1% but how
do I iterate for i 1-72? Escape characters,?
thanks in advance
i-1
sqlcmd_ScaffLen-sprintf('SELECT scaffold.length
FROM scaffold,scaffold2contig,contig2read
WHERE scaffold.scaffold_id=scaffold2contig.scaffold_id AND
scaffold2contig.contig_id=contig2read.contig_id AND
contig2read.read_id LIKE
'%MG%s%' ,i)
= Here is my vague error message
Error: unexpected input in:
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Re: [R] Help! I turned my data into junk!
On 03/09/2010 01:49 PM, Brienne wrote: I posted my data for a midterm into notepad and it turned into symbols. The other bit I posted turned out just fine, but for some reason this one messed up. I need this stuff for a class. Anyone know how to get my data back. Please help soon! Hi Brienne, As far as I am aware, you can't post something into Notepad. You can open a file, and it almost always has to be a text file, otherwise you will see a mess of symbols. My guess is that you were supplied with a data file for an assignment, and when you opened it in Notepad, it was a mess. As Ravi noted, you can often work out what application to use by looking at the extension (the part of the filename after the last period). So .xls or .xlsx is for Excel, .doc or .docx is for Word, and .mdb is for Access. I'm pretty sure that you will find that one of these applications is the one you want. Jim __ 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] create picture (k -the nearest neighbours)
Hi I want to create a nice picture about my result of k -the nearest neighbours algorithm. Here is my easy code: # library(klaR) library(ipred) library(mlbench) data(PimaIndiansDiabetes2) dane=na.omit(PimaIndiansDiabetes2)[,c(2,5,9)] dane[,2]=log(dane[,2]) dane[,1:2]=scale(dane[,1:2]) zbior.uczacy=sample(1:nrow(dane),nrow(dane)/2,F) KNN=ipredknn(diabetes~glucose+insulin,data=dane,subset=zbior.uczacy,k=3) KNN=ipredknn(diabetes~glucose+insulin,data=dane,subset=zbior.uczacy,k=3) b= ifelse((a==1),'red','blue' ) a=as.numeric(KNN$learn$y) plot(KNN$learn$X[,1], KNN$learn$X[,2],pch=a,col = ifelse((a==1),'red','blue' )) # and my problem is (it's difficult for me to explain it in english): What I should do if I want to get in my picture area (in different colors) which will be show my clasters. Like in picture (dark blue and bright blue). http://n4.nabble.com/file/n1585911/dec.jpg -- View this message in context: http://n4.nabble.com/create-picture-k-the-nearest-neighbours-tp1585911p1585911.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] Problem with mean
See FAQ 7.31 venkata kirankumar wrote: Hi all, I got one intresting problem with caliculating mean that is while i am taking mean of values *0.6, -0.8, 4, -3.8* using *val-c(0.6, -0.8, 4, -3.8)* *mean(val)* it given result as *2.775558e-17* but the actual result is *0* can any one suggest how can I get correct mean result in this case can any one suggest how I can farward thanks in regards kiran [[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] Deltas or changes
You can try this: Reduce(/, as.data.frame(embed(x, 2))) On Tue, Mar 9, 2010 at 10:37 AM, ManInMoon xmoon2...@googlemail.com wrote: How can I generate a vector of differences between each elemtn of an vector? i.e. a[i]=x[i]/x[i-1] -- View this message in context: http://n4.nabble.com/Deltas-or-changes-tp1585960p1585960.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Problem with mean
round(mean(val), digits=16) -Ista On Tue, Mar 9, 2010 at 10:23 AM, venkata kirankumar kiran4u2...@gmail.com wrote: Hi all, I got one intresting problem with caliculating mean that is while i am taking mean of values *0.6, -0.8, 4, -3.8* using *val-c(0.6, -0.8, 4, -3.8)* *mean(val)* it given result as *2.775558e-17* but the actual result is *0* can any one suggest how can I get correct mean result in this case can any one suggest how I can farward thanks in regards kiran [[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. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.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.
[R] Help with ANOVA in R
Hi I am attempting Anova analysis to compare results from four groups (Samp1-4) which are lists of intensities from the experiment. I am doing this by first creating a structured list of the data and then conducting the ANOVA (Script provided below). Im an R beginner so am not sure if I am using this correctly. Two major questions I have are: 1) Is using the code (zzz.aov - aov(Intensity ~ Group + Error(Sample), data = zzzanova)) the correct method to calculate the variances between the four groups (samp 1-4). I am unsure of the inclusion of the error portion. 2) I beleive this method (aov) assumes equal variances. How can I adjust this to do an ANOVA with unequal variances #SCRIPT STARTS #Creates a structured list suitable for ANOVA analysis # Intensity Group (1,2,3,4) Sample(1:62) zzzanova - structure(list(Intensity = c(t(Samp1), t(Samp2), t(Samp3), t(Samp4)), Group = structure(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2, 3,3,3,3,3,3,3,3,3,3,3,3,3,3, 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4), .Label = c(Group1, Group2, Group3, Group4), class = factor), Sample = structure(c( 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62) )) , .Names = c(Intensity, Group, Sample), row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62),class = data.frame) #Conducts the ANOVA for that PCI zzz.aov - aov(Intensity ~ Group + Error(Sample), data = zzzanova) #SCRIPT ENDS THANKS IN ADVANCE __ 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] find out commands in package
If the package is installed: ls(findPackageEnv(package:RSSA)) On Tue, Mar 9, 2010 at 7:54 AM, Jannis bt_jan...@yahoo.de wrote: Dears, I am trying to implement some R package which is still under construction and has not yet been submitted to CRAN (RSSA, http://anton.korobeynikov.info/software). Documentation is yet very poor (or i just did not find it), so I am wondering whether there is any way to retrieve a list of commands available in this package from within R? And to find out whether the package is successfully installed. After downloading the zip and installing it within R I only got the error message that it was created with an earlier R version and help would not work Thanks for your help! Jannis __ D usragenden Schutz gegen Massenmails. http://mail.yahoo.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Removing Zeros from matrix:Problem fixed
Hey, Thanks for your great inputs. While index = apply(mat == 0, MARGIN = 1, any) gives you an idea of the rows containing zero(s), index-data[!apply(data==0,MARGIN=1,any),] does the actual job of removing the rows with zeros. Kind regards Ogbos On 9 March 2010 15:12, Paul Hiemstra p.hiems...@geo.uu.nl wrote: Dimitris Rizopoulos wrote: On 3/9/2010 1:36 PM, Paul Hiemstra wrote: Dimitris Rizopoulos wrote: one approach is the following: mat - matrix(rnorm(100*45), 100, 45) mat[sample(100*45, 50)] - 0 index - rowMeans(mat == 0) == 0 mat[index, ] Dimitris, You use quite a complicated syntax to get the index. I think the following syntax using apply is more easy to understand: well, this way is much more efficient to compute, especially if you have many rows. Compare the following to see the difference: mat - matrix(rnorm(2*1e06), 1e06, 2) mat[sample(2*1e06, 50)] - 0 system.time(index1 - !apply(mat == 0, MARGIN = 1, any)) system.time(index2 - rowMeans(mat == 0) == 0 ) all.equal(index1, index2) Point taken, I totally agree that for large matrices you should use your approach. Didn't know that it made such a difference, great to learn something new :). But I still like the other syntax more ;). cheers, Paul Best, Dimitris # Note, MARGIN equal to 1 means loop over rows # If any member of a row is zero index = apply(mat == 0, MARGIN = 1, any) # If all members of a row are zero index = apply(mat == 0, MARGIN = 1, all) cheers and hope it helps, Paul I hope it helps. Best, Dimitris On 3/9/2010 11:05 AM, ogbos okike wrote: Hi Everybody, I have a matrix of about 45 columns. Some of the rows contain zeros. Using data1-data[complete.cases(data),], I can remove the NA rows. But I am unable to tackle that of zeros. Can anybody give me an idea of how to remove rows containing zeros in a matrix. Thanks so much Best Ogbos [[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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul http://intamap.geo.uu.nl/%7Epaul [[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] MASS package not on CRAN ?
On 09.03.2010 15:39, Ista Zahn wrote: MASS is a recommended package, so is probably already installed on your machine. Try And if installation fails, it is either your internet connection that does not download the file in its original form or you have a broken installation of R (which would also be indicated if MASS is not already installed given you installed a released version of R). Best, Uwe Ligges library(MASS) -Ista On Tue, Mar 9, 2010 at 9:32 AM, Markus Loechermarkus.loec...@gmail.com wrote: The MASS package is listed on the CRAN web site ( http://cran.r-project.org/web/packages/MASS/index.html) but I am unable to install it via install.packages(). The error is that the package is unavailable. When I manually download the source tar ball and try to install it on a Linux machine, installation fails because it is not a valid package. Do I need to search different repositories ? Thanks, Markus [[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] rcom package
Hi, I would like to make a program that reads excel files, and writes the cells of which contents is not a formula to another file. I don't think this is possible with RODBC, but it may be possible with rcom. I read the documentation of the rcom package, but I was hoping somebody knows a good web resource for more eleborate info. I tried Googling, but alas (did you know rcom also is a kind of egg incubator? ;-). In particular, I would like to have a list of the possible values for the 'property' argument. Thanks in advance! Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ [[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] ggplot2 rose diagram
Dear R gurus - consider this plot: library(ggplot2) dat - sample(1:8,100,replace=TRUE) smp - ggplot(data.frame(dat), aes(x=factor(dat),fill=factor(dat))) + geom_bar(width=1) smp + coord_polar() Q1. How do I change the font size and weight of bar labels (1,2,3...)? I've been wallowing in the 'Themes' structure and I just can't figure out the correct place to change the definitions. Along these same lines, what does 'strip' mean when referring to strip text? Q2. How can I move the legend defining bar height into the plot, so that it overlays the lines they refer to? Consider the same figure using Circstats: library(CircStats) dat.rad - (dat*((2*pi)/8)) -(2*pi)/16 rose.diag(dat.rad, bins = 8) #note the origin is to the right rather than on top Q3. The key difference is that CircStats uses an area-based calculation for the size of each slice, which makes for a different presentation than ggplot2. Any suggestions on how to use this calculation method in the ggplot framework? Thanks in advance for your help. Tim Howard New York Natural Heritage Program __ 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] error with adaboost: replacement has 186 rows, data has 62
Hi, all, When running AB.fit=adaboost(ylearn, xlearn, xtest, presel=0) I got the following error: Error in `[[-.data.frame`(`*tmp*`, preds, value = c(4L, 6L, 6L, 6L, 3L, : replacement has 186 rows, data has 62 The data structure is attached below: [1] ylearn [1] 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 [40] 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 [1] xlearn rs2289472 rs1551398 rs7927894 X18 CT AA CT X19 TT AA CC X33 TT AG TT X35 TT AA CT X36 CC AA CT X41 CT AA CT X46 TT AA CT X65 CT AG CT X77 CC AA CT X25 TT AG TT X26 CT GG CC X53 CT GG CC X55 CT AG CC X57 CT AG TT X71 CT AA CT X4 TT AA CT X7 CT AG CT X21 TT AA CT X22 TT AA TT X31 CT AG CT X32 CT AG TT X37 CT AA CT X50 TT AA CT X66 CC AA CC X28 CT AG CC X29 CT AG CT X30 CT GG CT X56 CT AG CC X62 CT GG CC X63 TT GG CT X1 CT AG CT X3 TT AG TT X8 CC GG CC X9 TT AA CT X38 CT GG TT X40 TT AG CT X43 CT AG CC X45 TT AA CC X47 TT AA TT X11 TT AA TT X13 CT GG CT X15 CT AG TT X16 TT AA CT X27 CT AG CC X58 TT AG CC X70 CT AA CC X2 CC AA CT X6 CT AA CT X10 CC AA CC X14 TT AA TT X39 TT GG CT X44 CT AG CT X49 TT AG TT X51 TT AA CT X67 CT AA CC X12 CT AG CT X54 CT AG CC X61 CT AA CC X68 CT AG CC X69 CT AG TT X73 TT AA CC X74 TT GG CT [1] xtest rs2289472 rs1551398 rs7927894 5 TT AA TT 20 CT AG CC 23 CT AG CT 24 CC GG TT 34 CC AA TT 42 CT AA CT 48 CC AG CC 59 CT AA CC 75 CT AG CT 17 CT AG CT 52 CT AA TT 60 CT AG CT 64 TT AA CT 72 TT AG CT 76 TT AA CT do you know what's the protential problem? Thanks in advance. Xumin [[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] MASS package not on CRAN ?
In fact, I must have a broken installation of R then (though I have not noticed any other problems so far). The library MASS is neither pre-installed nor can I explicitly install it (though the internet connection is up and functional). Thanks for all the help ! Markus 2010/3/9 Uwe Ligges lig...@statistik.tu-dortmund.de On 09.03.2010 15:39, Ista Zahn wrote: MASS is a recommended package, so is probably already installed on your machine. Try And if installation fails, it is either your internet connection that does not download the file in its original form or you have a broken installation of R (which would also be indicated if MASS is not already installed given you installed a released version of R). Best, Uwe Ligges library(MASS) -Ista On Tue, Mar 9, 2010 at 9:32 AM, Markus Loechermarkus.loec...@gmail.com wrote: The MASS package is listed on the CRAN web site ( http://cran.r-project.org/web/packages/MASS/index.html) but I am unable to install it via install.packages(). The error is that the package is unavailable. When I manually download the source tar ball and try to install it on a Linux machine, installation fails because it is not a valid package. Do I need to search different repositories ? Thanks, Markus [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source code for the t-distribution
Here it is. https://svn.r-project.org/R/trunk/src/nmath/pt.c --sundar On Tue, Mar 9, 2010 at 4:24 AM, Ravi Kulkarni ravi.k...@gmail.com wrote: I have tried looking for the source code for the pt() function in https://svn.r-project.org/R/trunk/src/library/stats/ and am unable to find it there. Can someone please tell me where to find it? Thanks, Ravi Kulkarni -- View this message in context: http://n4.nabble.com/Source-code-for-the-t-distribution-tp1585875p1585875.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] error with adaboost: replacement has 186 rows, data has 62
When running AB.fit=adaboost(ylearn, xlearn, xtest, presel=0) I got the following error: Error in `[[-.data.frame`(`*tmp*`, preds, value = c(4L, 6L, 6L, 6L, 3L, : replacement has 186 rows, data has 62 The data structure is attached below: [1] ylearn [1] 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 [40] 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 [1] xlearn rs2289472 rs1551398 rs7927894 X18 CT AA CT X19 TT AA CC X33 TT AG TT X35 TT AA CT X36 CC AA CT X41 CT AA CT X46 TT AA CT X65 CT AG CT X77 CC AA CT X25 TT AG TT X26 CT GG CC X53 CT GG CC X55 CT AG CC X57 CT AG TT X71 CT AA CT X4 TT AA CT X7 CT AG CT X21 TT AA CT X22 TT AA TT X31 CT AG CT X32 CT AG TT X37 CT AA CT X50 TT AA CT X66 CC AA CC X28 CT AG CC X29 CT AG CT X30 CT GG CT X56 CT AG CC X62 CT GG CC X63 TT GG CT X1 CT AG CT X3 TT AG TT X8 CC GG CC X9 TT AA CT X38 CT GG TT X40 TT AG CT X43 CT AG CC X45 TT AA CC X47 TT AA TT X11 TT AA TT X13 CT GG CT X15 CT AG TT X16 TT AA CT X27 CT AG CC X58 TT AG CC X70 CT AA CC X2 CC AA CT X6 CT AA CT X10 CC AA CC X14 TT AA TT X39 TT GG CT X44 CT AG CT X49 TT AG TT X51 TT AA CT X67 CT AA CC X12 CT AG CT X54 CT AG CC X61 CT AA CC X68 CT AG CC X69 CT AG TT X73 TT AA CC X74 TT GG CT [1] xtest rs2289472 rs1551398 rs7927894 5 TT AA TT 20 CT AG CC 23 CT AG CT 24 CC GG TT 34 CC AA TT 42 CT AA CT 48 CC AG CC 59 CT AA CC 75 CT AG CT 17 CT AG CT 52 CT AA TT 60 CT AG CT 64 TT AA CT 72 TT AG CT 76 TT AA CT do you know what's the protential problem? Thanks in advance. Xumin [[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] rcom package
If you just want to read tabular data from Excel then there are many options in R: http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windows On Tue, Mar 9, 2010 at 10:35 AM, Albert-Jan Roskam fo...@yahoo.com wrote: Hi, I would like to make a program that reads excel files, and writes the cells of which contents is not a formula to another file. I don't think this is possible with RODBC, but it may be possible with rcom. I read the documentation of the rcom package, but I was hoping somebody knows a good web resource for more eleborate info. I tried Googling, but alas (did you know rcom also is a kind of egg incubator? ;-). In particular, I would like to have a list of the possible values for the 'property' argument. Thanks in advance! Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ [[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] Help! I turned my data into junk!
Am 09.03.2010 03:49, schrieb Brienne: I posted my data for a midterm into notepad and it turned into symbols. The other bit I posted turned out just fine, but for some reason this one messed up. I need this stuff for a class. Anyone know how to get my data back. Please help soon! Hello! You copied it from where? With Ctrl-C / Ctrl-V, you are on windows, I assume? Just a wild guess: You have a problem with encodings: What happens if you copy it back from where ever you fetched the data? But not to give hope place, I think you (better your data) are/is lost... But without knowing the source, nothing more can be said... Albin -- - | Albin Blaschka, Mag. rer.nat - Salzburg, Austria | http://www.albinblaschka.info http://www.thinkanimal.info | It's hard to live in the mountains, hard, but not hopeless! __ 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] wavethresh: length must be power of two
Hello. I am using the 4.2 version of the wavethresh package available from here: http://www.stats.bris.ac.uk/~wavethresh/ trying to follow the book of Nason (http://www.springer.com/978-0-387-75960-9). I am interested in the analysis of several years time series of daily data with wavelets methods. But the functions of this package only accept data whose lengths are power of two, even for non-decimated DWT. For example: data=rnorm(365) wdS - wd(data, type=station) Error en wd(data, type = station) : Data length is not power of two A possible solution is to analyse a window with a length power of two. For this example: data2=data[1:(2^trunc(log(365,2)))] wdS2 - wd(data2, type=station) or pad with zeros: data3=data length(data3)-2^ceiling(log(length(data),2)) data3[is.na(data3)]-0 wdS3-wd(data3,type='station') Is there any other solution? By the way, does anybody knows why the wavethresh package at CRAN is not being updated? Thank you very much! Oscar Perpiñán Lamigueiro Department of Electrical Engineering Universidad Politécnica de Madrid __ 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] is there an inverse method for table()?
Hi, In R, I know the method table(), which builds a contingency table of the counts y at each level for the factor x. But I would like to know what is the inverse method of table(), if it exists, to obtain the vector z, from the two vectors x and y? x - (86, 90, 94, 98, 102, 106, 110, 114, 118, 122, 126, 130, 134, 138, 142, 146, 150, 154, 158, 162, 166, 170, 174) y - c(2, 5, 10, 17, 26, 60, 94, 128, 137, 128, 77, 68, 65, 60, 51, 26, 17, 9, 5, 2, 3, 7, 3) z [1] 86 86 90 90 90 90 90 94 94 94 94 94 94 94 94 94 94 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 102 102 102 102 102 [40] 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102... [976] ...170 170 170 170 170 170 170 174 174 174 If such a method does not exist, what code should I type to obtain the complete series quickly? Thank you for your help. I use version 2.10-1 2009-08-24 for Mac OS. Vincent Laperrière. [[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] counting the number of ones in a vector
Thank you Gavin and Bert 2010/3/4 Gavin Simpson gavin.simp...@ucl.ac.uk On Thu, 2010-03-04 at 00:03 +0100, Randall Wrong wrote: Thanks to all of you ! (Benjamin Nutter, Henrique Dallazuanna, Tobias Verbeke, Jorge Ivan Velez, David Reinke and Gavin Simpson) x - c(1, 1, 1, NA, NA, 2, 1, NA) table(x)[1] 1 4 Why do I get two numbers ? It is a printing a named vector. The 1 is the group of factor level, the 4 is the count, try: unname(table(x)[1]) and str(table(x)[1]) etc to see what is going on. HTH G Thanks, Randall 2010/2/26 Nutter, Benjamin nutt...@ccf.org But if x has any missing values: x - c(1, 1, 1, NA, NA, 2, 1, NA) sum( x == 1) [1] NA sum(x==1, na.rm=TRUE) [1] 4 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Henrique Dallazuanna Sent: Friday, February 26, 2010 9:47 AM To: Randall Wrong Cc: r-help@r-project.org Subject: Re: [R] counting the number of ones in a vector Try: sum(x == 1) On Fri, Feb 26, 2010 at 11:40 AM, Randall Wrong randall.wr...@gmail.com wrote: Dear R users, I want to count the number of ones in a vector x. That's what I did : length( x[x==1] ) Is that a good solution ? Thank you very much, Randall [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.ukhttp://gavin.simpsonatnospamucl.ac.uk/ Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% [[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] is there an inverse method for table()?
z - rep(x, each = y) Hope this helps, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: vincent laperriere vincent_laperri...@yahoo.fr Date: Tuesday, March 9, 2010 10:59 am Subject: [R] is there an inverse method for table()? To: r-help@r-project.org Hi, In R, I know the method table(), which builds a contingency table of the counts y at each level for the factor x. But I would like to know what is the inverse method of table(), if it exists, to obtain the vector z, from the two vectors x and y? x - (86, 90, 94, 98, 102, 106, 110, 114, 118, 122, 126, 130, 134, 138, 142, 146, 150, 154, 158, 162, 166, 170, 174) y - c(2, 5, 10, 17, 26, 60, 94, 128, 137, 128, 77, 68, 65, 60, 51, 26, 17, 9, 5, 2, 3, 7, 3) z [1] 86 86 90 90 90 90 90 94 94 94 94 94 94 94 94 94 94 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 102 102 102 102 102 [40] 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102... [976] ...170 170 170 170 170 170 170 174 174 174 If such a method does not exist, what code should I type to obtain the complete series quickly? Thank you for your help. I use version 2.10-1 2009-08-24 for Mac OS. Vincent Laperrière. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list PLEASE do read the posting guide 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] Computation of AIC for gls models
Dear Colleagues, We are using the phylog.gls.fit() function from the R package PHYLOGR (Diaz-Uriarte R, Garland T: PHYLOGR: Functions for phylogenetically based statistical analyses. 2007. Available at [http://cran.r-project.org/web/packages/PHYLOGR/index.html]) to correct for lack of independence between data points. (In our particular case, the lack of independence is due to common ancestry, hence the choice of PHYLOGR package.) The output provides P values for the variables included in the model, but according to Diaz-Uriarte and Garland (2007) the total F is unreliable. Because there are a number of variables that we could potentially include in the analysis, we would want to use AIC values for model selection. We can obtain these values directly with the function AIC(), or from the log-likelihood obtained with the logLik() function. (The two methods give the same results.) We have two questions concerning this procedure: 1. Does anybody know whether the output we obtain from the AIC() and logLik() functions is reliable? Does the algorithm used for calculating the model likelihood and AIC take into account the non-independence of data points? Or are the log-likelihood and AIC calculated using some standard R algorithm that is not valid for phylog.gls models or gls? 2. Is the logLik extracted from phylog.gls suitable for a type-III log-likelhood ratio test? Thanks so much, Miguel Rodriguez-Girones Estación Experimental de Zonas Aridas, CSIC [[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] is there an inverse method for table()?
Sorry, I mean to say: z - rep(x, y) Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: Ravi Varadhan rvarad...@jhmi.edu Date: Tuesday, March 9, 2010 11:02 am Subject: Re: [R] is there an inverse method for table()? To: vincent laperriere vincent_laperri...@yahoo.fr Cc: r-help@r-project.org z - rep(x, each = y) Hope this helps, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: vincent laperriere vincent_laperri...@yahoo.fr Date: Tuesday, March 9, 2010 10:59 am Subject: [R] is there an inverse method for table()? To: r-help@r-project.org Hi, In R, I know the method table(), which builds a contingency table of the counts y at each level for the factor x. But I would like to know what is the inverse method of table(), if it exists, to obtain the vector z, from the two vectors x and y? x - (86, 90, 94, 98, 102, 106, 110, 114, 118, 122, 126, 130, 134, 138, 142, 146, 150, 154, 158, 162, 166, 170, 174) y - c(2, 5, 10, 17, 26, 60, 94, 128, 137, 128, 77, 68, 65, 60, 51, 26, 17, 9, 5, 2, 3, 7, 3) z [1] 86 86 90 90 90 90 90 94 94 94 94 94 94 94 94 94 94 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 102 102 102 102 102 [40] 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102... [976] ...170 170 170 170 170 170 170 174 174 174 If such a method does not exist, what code should I type to obtain the complete series quickly? Thank you for your help. I use version 2.10-1 2009-08-24 for Mac OS. Vincent Laperrière. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list PLEASE do read the posting guideand 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] is there an inverse method for table()?
On Tue, Mar 9, 2010 at 3:58 PM, vincent laperriere vincent_laperri...@yahoo.fr wrote: Hi, In R, I know the method table(), which builds a contingency table of the counts y at each level for the factor x. But I would like to know what is the inverse method of table(), if it exists, to obtain the vector z, from the two vectors x and y? x - (86, 90, 94, 98, 102, 106, 110, 114, 118, 122, 126, 130, 134, 138, 142, 146, 150, 154, 158, 162, 166, 170, 174) y - c(2, 5, 10, 17, 26, 60, 94, 128, 137, 128, 77, 68, 65, 60, 51, 26, 17, 9, 5, 2, 3, 7, 3) z [1] 86 86 90 90 90 90 90 94 94 94 94 94 94 94 94 94 94 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 102 102 102 102 102 [40] 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102... [976] ...170 170 170 170 170 170 170 174 174 174 If such a method does not exist, what code should I type to obtain the complete series quickly? rep(x,y)? repeats each element in x the number of times in y. Looks about right. 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] IMPORTANT - To remove the null elements from a vector
Hi Barbara, Try x[ x != 0 ] HTH, Jorge On Tue, Mar 9, 2010 at 7:48 AM, wrote: I have a vector that have null elements. How to remove these elements? For example: x=[10 0 30 40 0 0] I want the vector y=[10 30 40] Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using sprintf to pass a variable to a RMySQL query
On Tue, Mar 9, 2010 at 7:10 AM, alison waller alison.wal...@embl.de wrote: Hi all, Thanks for help with the paste and sprintf syntax. So I've decided to use paste and or sprintf. 'gsubfn' looks like a great package but unfortunately I've had problems installing it, as I don't think it likes the version of tcltk that is installed. I'm working on a few unix clusters with many computers and there seems to be problems with different versions of R and different versions of the packages on different computers. The fn$ functionality that I mentioned does not use the tcltk package so the version of tcltk should not matter. The only part of the package that uses tcltk is strapply, which is not used here, and even in that case there is R code to it as well if you use strapply(..., engine = R) or use ostrapply. Also the older 0.3-9 version of the gsubfn package did not use tcltk at all. __ 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] Deltas or changes
How can I generate a vector of differences between each elemtn of an vector? i.e. a[i]=x[i]/x[i-1] -- View this message in context: http://n4.nabble.com/Deltas-or-changes-tp1585960p1585960.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] Deltas or changes
try this: x - runif(100) a - x[-1] / x[-length(x)] a I hope it helps. Best, Dimitris On 3/9/2010 2:37 PM, ManInMoon wrote: How can I generate a vector of differences between each elemtn of an vector? i.e. a[i]=x[i]/x[i-1] -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] Removing Zeros from matrix
On 3/9/2010 1:36 PM, Paul Hiemstra wrote: Dimitris Rizopoulos wrote: one approach is the following: mat - matrix(rnorm(100*45), 100, 45) mat[sample(100*45, 50)] - 0 index - rowMeans(mat == 0) == 0 mat[index, ] Dimitris, You use quite a complicated syntax to get the index. I think the following syntax using apply is more easy to understand: well, this way is much more efficient to compute, especially if you have many rows. Compare the following to see the difference: mat - matrix(rnorm(2*1e06), 1e06, 2) mat[sample(2*1e06, 50)] - 0 system.time(index1 - !apply(mat == 0, MARGIN = 1, any)) system.time(index2 - rowMeans(mat == 0) == 0 ) all.equal(index1, index2) Best, Dimitris # Note, MARGIN equal to 1 means loop over rows # If any member of a row is zero index = apply(mat == 0, MARGIN = 1, any) # If all members of a row are zero index = apply(mat == 0, MARGIN = 1, all) cheers and hope it helps, Paul I hope it helps. Best, Dimitris On 3/9/2010 11:05 AM, ogbos okike wrote: Hi Everybody, I have a matrix of about 45 columns. Some of the rows contain zeros. Using data1-data[complete.cases(data),], I can remove the NA rows. But I am unable to tackle that of zeros. Can anybody give me an idea of how to remove rows containing zeros in a matrix. Thanks so much Best Ogbos [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] is there an inverse method for table()?
rep() is your friend. HTH, Thierry x - c(86, 90, 94, 98, 102, 106, 110, 114, 118, 122, 126, 130, 134, 138, 142, 146, 150, 154, 158, 162, 166, 170, 174) y - c(2, 5, 10, 17, 26, 60, 94, 128, 137, 128, 77, 68, 65, 60, 51, 26, 17, 9, 5, 2, 3, 7, 3) rep(x, y) [1] 86 86 90 90 90 90 90 94 94 94 94 94 94 94 94 94 94 98 [19] 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 102 102 [37] 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 [55] 102 102 102 102 102 102 106 106 106 106 106 106 106 106 106 106 106 106 [73] 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 [91] 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 106 [109] 106 106 106 106 106 106 106 106 106 106 106 106 110 110 110 110 110 110 [127] 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 [145] 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 [163] 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 [181] 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 [199] 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 110 114 114 [217] 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 [235] 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 [253] 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 [271] 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 [289] 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 [307] 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 [325] 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 114 [343] 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 [361] 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 [379] 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 [397] 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 [415] 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 [433] 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 [451] 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 118 [469] 118 118 118 118 118 118 118 118 118 118 118 122 122 122 122 122 122 122 [487] 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 [505] 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 [523] 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 [541] 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 [559] 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 [577] 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 122 [595] 122 122 122 122 122 122 122 122 122 122 122 122 122 126 126 126 126 126 [613] 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 [631] 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 [649] 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 [667] 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 126 [685] 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 [703] 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 [721] 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 130 [739] 130 130 130 130 130 130 130 130 130 130 130 130 130 130 134 134 134 134 [757] 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 [775] 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 [793] 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 134 [811] 134 134 134 134 134 134 134 138 138 138 138 138 138 138 138 138 138 138 [829] 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 [847] 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 138 [865] 138 138 138 138 138 138 138 138 138 138 138 138 138 142 142 142 142 142 [883] 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 [901] 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 [919] 142 142 142 142 142 142 142 142 142 142 146 146 146 146 146 146 146 146 [937] 146 146 146 146 146 146 146 146 146 146 146 146 146 146 146 146 146 146 [955] 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 154 [973] 154 154 154 154 154 154 154 154 158 158 158 158 158 162 162 166 166 166 [991] 170 170 170 170 170 170 170 174 174 174 ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. +
Re: [R] is there an inverse method for table()?
Try as.data.frame.table(mytable) On Tue, Mar 9, 2010 at 10:58 AM, vincent laperriere vincent_laperri...@yahoo.fr wrote: Hi, In R, I know the method table(), which builds a contingency table of the counts y at each level for the factor x. But I would like to know what is the inverse method of table(), if it exists, to obtain the vector z, from the two vectors x and y? x - (86, 90, 94, 98, 102, 106, 110, 114, 118, 122, 126, 130, 134, 138, 142, 146, 150, 154, 158, 162, 166, 170, 174) y - c(2, 5, 10, 17, 26, 60, 94, 128, 137, 128, 77, 68, 65, 60, 51, 26, 17, 9, 5, 2, 3, 7, 3) z [1] 86 86 90 90 90 90 90 94 94 94 94 94 94 94 94 94 94 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 98 102 102 102 102 102 [40] 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102 102... [976] ...170 170 170 170 170 170 170 174 174 174 If such a method does not exist, what code should I type to obtain the complete series quickly? Thank you for your help. I use version 2.10-1 2009-08-24 for Mac OS. Vincent Laperrière. [[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] A list of data.frames merged together
Hello,
I have for a long list of data.frames that I would like to get merged.
Each data.frame have two columns with the same names (Date and Value).
What I would like is for the objects in the list to be merged on Only
date with the column header being the name in the list.
For example
A - data.frame(Date=c(03/15/10,04/15/10,05/15/10),
Value=c(1,2,3))
B - data.frame(Date=c(03/15/10,04/15/10,06/15/10),
Value=c(5,5,5))
...
yoda - list(A=A,B=B,...)
Result:
DateA B C
03/15/101 5 ...
04/15/102 5
05/15/103 NA
06/15/10NA 5
Any ideas? I have been fiddling around with plyr and reshape without success
Thanks
Dan
--
**
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom
Tel: +44 (0) 20 8722 4109
**
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the a...{{dropped:2}}
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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] penalized maximum likelihood estimation and logistf
Hi, I got two questions and would really appreciate any help from here. First, is the penalized maximum likelihood estimation(Firth Type Estimation) only fit for binary response (0,1 or TRUE, FALSE)? Can it be applied to multinomial logistic regression? If yes, what's the formula for LL and U(beta_i)? Can someone point me to the right reference? Second, when I used *logistf *on a dataset with binary response, I got the following error msg: Error in if (mx 1) delta - delta/mx : missing value where TRUE/FALSE needed What does this msg mean? does it mean the dataset includes missing response? I checked my dataset several times and didn't find anything other than TRUE or FALSE for the response. Please shed light on this. Thanks, Xiaoyan [[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] ncdf installation
Friends, I tried to install ncdf package in ubuntu with the following command. R CMD INSTALL --configure-args=-with-netcdf_incdir=/apps/netcdf/4.0.1/gcc/include -with-netcdf_libdir=/apps/netcdf/4.0.1/gcc/lib ncdf_1.6.tar.gz The installation was stopped throwing the following error. I tried to google it but didnt find any solution. someone kindly write me what is going wrong. ** libs gcc -std=gnu99 -I/usr/share/R/include -I/apps/netcdf/4.0.1/gcc/include -fpic -g -O2 -c ncdf.c -o ncdf.o ncdf.c: In function R_nc_get_vara_double: ncdf.c:196: warning: format %u expects type unsigned int, but argument 3 has type size_t ncdf.c:202: warning: format %u expects type unsigned int, but argument 3 has type size_t ncdf.c: In function R_nc_get_vara_int: ncdf.c:239: warning: format %u expects type unsigned int, but argument 3 has type size_t ncdf.c:245: warning: format %u expects type unsigned int, but argument 3 has type size_t ncdf.c: In function R_nc_get_vara_text: ncdf.c:296: warning: format %u expects type unsigned int, but argument 3 has type size_t ncdf.c:302: warning: format %u expects type unsigned int, but argument 3 has type size_t ncdf.c: In function R_nc_ttc_to_nctype: ncdf.c:424: warning: implicit declaration of function exit ncdf.c:424: warning: incompatible implicit declaration of built-in function exit ncdf.c: In function R_nc_put_vara_double: ncdf.c:582: warning: format %d expects type int, but argument 3 has type size_t ncdf.c:585: warning: format %d expects type int, but argument 3 has type size_t gcc -std=gnu99 -I/usr/share/R/include -I/apps/netcdf/4.0.1/gcc/include -fpic -g -O2 -c ncdf2.c -o ncdf2.o gcc -std=gnu99 -I/usr/share/R/include -I/apps/netcdf/4.0.1/gcc/include -fpic -g -O2 -c ncdf3.c -o ncdf3.o ncdf3.c: In function R_nc_get_vara_charvarid: ncdf3.c:221: warning: assignment discards qualifiers from pointer target type ncdf3.c: In function R_nc_get_vara_numvarid: ncdf3.c:267: warning: assignment discards qualifiers from pointer target type gcc -std=gnu99 -shared -o ncdf.so ncdf.o ncdf2.o ncdf3.o -L/apps/netcdf/4.0.1/gcc/lib -lnetcdf -L/usr/lib64/R/lib -lR /usr/bin/ld: /apps/netcdf/4.0.1/gcc/lib/libnetcdf.a(attr.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /apps/netcdf/4.0.1/gcc/lib/libnetcdf.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [ncdf.so] Errore 1 ERROR: compilation failed for package ncdf * Removing /usr/local/lib/R/site-library/ncdf [[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] rcom package
rcom allows you to access the full object model of any COM server. The object browser in Excel allows you to investigate Excel's object model. It also tells you which properties are accessible. There are a few hundreds of them. On 3/9/2010 4:35 PM, Albert-Jan Roskam wrote: Hi, I would like to make a program that reads excel files, and writes the cells of which contents is not a formula to another file. I don't think this is possible with RODBC, but it may be possible with rcom. I read the documentation of the rcom package, but I was hoping somebody knows a good web resource for more eleborate info. I tried Googling, but alas (did you know rcom also is a kind of egg incubator? ;-). In particular, I would like to have a list of the possible values for the 'property' argument. Thanks in advance! Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ [[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. -- Erich Neuwirth, University of Vienna Faculty of Computer Science Computer Supported Didactics Working Group Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-39464 Fax: +43-1-4277-39459 __ 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] A list of data.frames merged together
This will do it:
merge(A, B, by = 1, all = TRUE)
Date Value.x Value.y
1 03/15/10 1 5
2 04/15/10 2 5
3 05/15/10 3 NA
4 06/15/10 NA 5
but you probably really want to be using time series for this so that
you can easily perform other operations too. See ?merge.zoo and the
three zoo vignettes for more.
library(zoo)
library(chron)
za - zoo(A$Value, chron(as.character(A$Date)))
zb - zoo(B$Value, chron(as.character(B$Date)))
merge(za, zb)
za zb
03/15/10 1 5
04/15/10 2 5
05/15/10 3 NA
06/15/10 NA 5
zm - merge(za, zb)
# convert to data frame
cbind(Date = time(zm), as.data.frame(zm))
Date za zb
03/15/10 03/15/10 1 5
04/15/10 04/15/10 2 5
05/15/10 05/15/10 3 NA
06/15/10 06/15/10 NA 5
# handle more than two at a time
merge(za, za2 = za, zb)
za za2 zb
03/15/10 1 1 5
04/15/10 2 2 5
05/15/10 3 3 NA
06/15/10 NA NA 5
# same but series are in a list
do.call(merge, list(za = za, za2 = za, zb = zb))
za za2 zb
03/15/10 1 1 5
04/15/10 2 2 5
05/15/10 3 3 NA
06/15/10 NA NA 5
On Tue, Mar 9, 2010 at 11:21 AM, Daniel Brewer daniel.bre...@icr.ac.uk wrote:
Hello,
I have for a long list of data.frames that I would like to get merged.
Each data.frame have two columns with the same names (Date and Value).
What I would like is for the objects in the list to be merged on Only
date with the column header being the name in the list.
For example
A - data.frame(Date=c(03/15/10,04/15/10,05/15/10),
Value=c(1,2,3))
B - data.frame(Date=c(03/15/10,04/15/10,06/15/10),
Value=c(5,5,5))
...
yoda - list(A=A,B=B,...)
Result:
Date A B C
03/15/10 1 5 ...
04/15/10 2 5
05/15/10 3 NA
06/15/10 NA 5
Any ideas? I have been fiddling around with plyr and reshape without success
Thanks
Dan
--
**
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom
Tel: +44 (0) 20 8722 4109
**
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the a...{{dropped:2}}
__
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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
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[R] R package pdf files
Dear all, the examples in the pdf files that are automatically built from the examples in package help files are poorly formatted; they frequently do not wrap to the next line and are cut off. While there is an easy work around by looking at the examples in the corresponding help files, I do wonder if there is a way to ensure proper line wrappiong when creating a package. Thanks, Markus [[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 with adding points to allEffects plot
Thanks in advance for any help. I am attempting to add points to a plot using the allEffects command in the effects package. When I try to add the points I get the following error message: Error in plot.xy(xy.coords(x, y), type = type, ...) : plot.new has not been called yet Strangely, using the code I've pasted below this has worked for me in the past however figuring out what has changed has proved to be beyond me. Cheers, Grant y-c(1,3,2,4,5) x-c(1,2,3,4,5) GSMOD-lm(y~x) plot(allEffects(GSMOD), ask=F) points(y, x) Error in plot.xy(xy.coords(x, y), type = type, ...) : plot.new has not been called yet [[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] MASS package not on CRAN ?
The MASS package is listed on the CRAN web site ( http://cran.r-project.org/web/packages/MASS/index.html) but I am unable to install it via install.packages(). The error is that the package is unavailable. When I manually download the source tar ball and try to install it on a Linux machine, installation fails because it is not a valid package. Do I need to search different repositories ? Thanks, Markus [[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] Possible error in anova.lm?
Perhaps those more in the know than I could clarify some confusion. In the
ANOVA 'R' code I see:
mss - sum(if (is.null(w)) object$fitted.values^2 else w *
object$fitted.values^2)
if (ssr 1e-10 * mss)
warning(ANOVA F-tests on an essentially perfect fit are unreliable)
But in the summary.lm I see:
mss - if (attr(z$terms, intercept))
sum((f - mean(f))^2)
else sum(f^2)
or
mss - if (attr(z$terms, intercept)) {
m - sum(w * f/sum(w))
sum(w * (f - m)^2)
}
At the very least the ANOVA code seems to be inefficient to calculate mss then
only use it for a warning. But it seems that it is being calculated
incorrectly. It is hard to tell since it is only used to issue the warning. But
it may be that the warning is incorrect in some cases if mss is not calculated
correctly. Ideas?
Kevin
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Re: [R] A list of data.frames merged together
Daniel -
Reduce may be handy here:
ans = Reduce(function(a,b)merge(a,b,by=1),yoda)
names(ans)[2:ncol(ans)] = names(yoda)
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Tue, 9 Mar 2010, Daniel Brewer wrote:
Hello,
I have for a long list of data.frames that I would like to get merged.
Each data.frame have two columns with the same names (Date and Value).
What I would like is for the objects in the list to be merged on Only
date with the column header being the name in the list.
For example
A - data.frame(Date=c(03/15/10,04/15/10,05/15/10),
Value=c(1,2,3))
B - data.frame(Date=c(03/15/10,04/15/10,06/15/10),
Value=c(5,5,5))
...
yoda - list(A=A,B=B,...)
Result:
DateA B C
03/15/101 5 ...
04/15/102 5
05/15/103 NA
06/15/10NA 5
Any ideas? I have been fiddling around with plyr and reshape without success
Thanks
Dan
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Re: [R] Deltas or changes
On Tue, 9 Mar 2010 05:37:52 -0800 (PST) ManInMoon xmoon2000 @googlemail.com wrote: How can I generate a vector of differences between each elemtn of an vector? diff(x) -- Karl Ove Hufthammer __ 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] IMPORTANT - To remove the null elements from a vector
Welcome to R Barbara. Its quite an incredible community from all walks of life. Your beginner questions are answered in the manual. See Introduction to R. Please read the posting guide again because it contains lots of good advice for you. Some people read it three times before posting because they have so much respect for the community. Sometimes they trip up over themselves to show they have read it. Btw - just to let you know that starting your subject lines with IMPORTANT is considered by some people a demanding tone for free help. Not everyone, but some people. Two posts starting IMPORTANT within 5 minutes is another thing that a very large number of people around the world may have just seen you do. I'm just letting you know, in case you were not aware of this. You received answers from four people who clearly don't mind, and you have your answers. Was that your only goal in posting? Did you consider there might be downsides? This is a public list read by many people and one thing the posting guide says is that your questions are saved in the archives forever. Just checking you knew that. I wouldn't want you to reduce your reputation accidentally. A future employer (it might be a company, or it might be a university) anywhere in the world might do a simple search on your name, and thats why you might not get an interview, because you had showed (in their minds) that you didn't have respect for guidlines. I would hate for something like that to happen, all just because you didn't know you were supposed to read the posting guide, it wouldn't be fair on you. So it would be very unfair of me to know that, and suspect that you don't, but not tell you about the posting guide, wouldn't it ? I hope this information helps you. It is entirely up to you. r-help is a great way to increase your reputation, but it can reduce your reputation too. By asking great questions, or even contributing, you can proudly put that on your CV and increase your chances of getting that interview, or getting that position. I have seen on several CVs from students the text please search for my name on r-help. Just like everything you do in public, r-help is very similar. What you write, you write in the public domain, and you write it free of charge, and free of restriction. All this applies to all us. When asking for help, and when giving help. Matthew barbara.r...@uniroma1.it wrote in message news:of1a8063a1.fc14f5ff-onc12576e1.00466053-c12576e1.00466...@uniroma1.it... I have a vector that have null elements. How to remove these elements? For example: x=[10 0 30 40 0 0] I want the vector y=[10 30 40] Thanks [[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] Computation of AIC for gls models
Miguel Angel Rodríguez-Gironés Arbolí rgirones at eeza.csic.es writes: Dear Colleagues, We are using the phylog.gls.fit() function from the R package PHYLOGR (Diaz-Uriarte R, Garland T: PHYLOGR: Functions for phylogenetically based statistical analyses. 2007. [snip] ... we would want to use AIC values for model selection. We can obtain these values directly with the function AIC(), or from the log-likelihood obtained with the logLik() function. (The two methods give the same results.) We have two questions concerning this procedure: 1. Does anybody know whether the output we obtain from the AIC() and logLik() functions is reliable? Does the algorithm used for calculating the model likelihood and AIC take into account the non-independence of data points? Or are the log-likelihood and AIC calculated using some standard R algorithm that is not valid for phylog.gls models or gls? Looking at the guts of phylog.gls.fit, I see that it is using lm() on transformed data (haven't read the paper referenced in the documentation, or at least not recently), so I doubt it is OK. 2. Is the logLik extracted from phylog.gls suitable for a type-III log-likelhood ratio test? What is a type III log-likelihood ratio test? I suggest that you send this query to r-sig-ph...@r-project.org instead; that is the special-interest list for phylogenetic and comparative methods ... Ted Garland even reads that list sometimes. __ 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] Deltas or changes
Henrique Dallazuanna wwwhsd at gmail.com writes: Reduce(/, as.data.frame(embed(x, 2))) ManInMoon xmoon2000 at googlemail.com wrote: How can I generate a vector of differences between each elemtn of an vector? (you mean ratios, right?) i.e. a[i]=x[i]/x[i-1] x[-1]/x[-length(x)] might be a little easier to understand. exp(diff(log(x))) should work too (although a big waste of computational power ...) __ 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] penalized maximum likelihood estimation and logistf
Let us look at a piece of the relevant code from logistf package: iter - iter + 1 XW2 - crossprod(x, diag(pi * (1 - pi))^0.5) Fisher - crossprod(t(XW2)) covs - solve(Fisher) H - crossprod(XW2, covs) %*% XW2 if (firth) U.star - crossprod(x, y - pi + diag(H) * (0.5 - pi)) else U.star - crossprod(x, y - pi) delta - as.vector(covs %*% U.star) mx - max(abs(delta))/maxstep if (mx 1) delta - delta/mx First, note that this is inside an iterative loop. The Fisher information matrix is first formed, and then it is inverted to get `covs'. This is where it can get troublesome. It is very likely in your case that the `Fisher' information matrix is ill-conditioned, and hence `covs' cannot be computed. Consequently, the steplength `delta' for the Newton method cannot be determined. Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: xiaoyan yu xiaoyan...@gmail.com Date: Tuesday, March 9, 2010 11:26 am Subject: [R] penalized maximum likelihood estimation and logistf To: r-help@r-project.org Hi, I got two questions and would really appreciate any help from here. First, is the penalized maximum likelihood estimation(Firth Type Estimation) only fit for binary response (0,1 or TRUE, FALSE)? Can it be applied to multinomial logistic regression? If yes, what's the formula for LL and U(beta_i)? Can someone point me to the right reference? Second, when I used *logistf *on a dataset with binary response, I got the following error msg: Error in if (mx 1) delta - delta/mx : missing value where TRUE/FALSE needed What does this msg mean? does it mean the dataset includes missing response? I checked my dataset several times and didn't find anything other than TRUE or FALSE for the response. Please shed light on this. Thanks, Xiaoyan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list PLEASE do read the posting guide 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] using near-zero probabilities in optimization
Benedikt Gehr benedikt.gehr at ieu.uzh.ch writes: Hi there I am using mle2 for a multinomial likelihood optimization problem. My function works fine when I'm using simulated data, however my cell probabilities of the true data for the multinomial likelihood are sometimes very small (in some cases 0.00...) and the estimated point estimates fit the true vlaues quite poorly. Is there a way how to handle near zero probabilities in maximum likelihood optimization? Hard to say without more detail. Can you send a reproducible example (your data, or a small subset of your data, or some way of simulating the data that *does* create the problem)? Since you're using log-likelihoods already (within mle2) the problem is unlikely (?) to be numerical -- R doesn't have any problem with very large negative log-likelihoods. Do your likelihood profiles look reasonable? If so then the problem is more likely that your model doesn't fit the data well than that you are having convergence problems. Have you considered the possibility of overdispersion (non-homogeneity/non-independence), e.g. via a Dirichlet-multinomial model? __ 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] Help with adding points to allEffects plot
As you can see on ?effects help page, plot.eff() uses lattice graphics. You can't mix those with traditional graphics commands. This should work: plot(allEffects(GSMOD), ask=FALSE) trellis.focus(panel, 1, 1) panel.points(y, x) trellis.unfocus() -Peter Ehlers On 2010-03-09 9:37, Grant Gillis wrote: Thanks in advance for any help. I am attempting to add points to a plot using the allEffects command in the effects package. When I try to add the points I get the following error message: Error in plot.xy(xy.coords(x, y), type = type, ...) : plot.new has not been called yet Strangely, using the code I've pasted below this has worked for me in the past however figuring out what has changed has proved to be beyond me. Cheers, Grant y-c(1,3,2,4,5) x-c(1,2,3,4,5) GSMOD-lm(y~x) plot(allEffects(GSMOD), ask=F) points(y, x) Error in plot.xy(xy.coords(x, y), type = type, ...) : plot.new has not been called yet [[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. -- Peter Ehlers University of Calgary __ 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 package pdf files
On 09/03/2010 9:28 AM, Markus Loecher wrote: Dear all, the examples in the pdf files that are automatically built from the examples in package help files are poorly formatted; they frequently do not wrap to the next line and are cut off. While there is an easy work around by looking at the examples in the corresponding help files, I do wonder if there is a way to ensure proper line wrappiong when creating a package. R will keep whatever formatting the package author puts in the source, so the author simply needs to format the source code nicely. I imagine there are automatic tools to do that (e.g. in ESS or Eclipse). Perhaps the manuals could say how many characters fit on a line on A4 paper. (North Americans get slightly more width on letter-sized paper). It looks to me as though the limit is around 68 characters, though it's still readable if it extends into the margin a little. I tend to set my margins to 70 characters. Duncan Murdoch Thanks, Markus [[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] Cox Calibration regression test double graphs
Dear All, How can i do the bootstrap and calibration plot after surival analysis , i don't know how to do it after that please help me. Thanks here is my syntex library(survival) mfit - survfit(Surv(days, status == 1)~drug, data = melanom) #how can i do the bootstra #Cox Calibration regression test #and the calibration plot paaveen _ [[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] error in a function
Print out the 'str' of the two objects and look at it. Are the matrices the
appropriate sizes to do the operation? The error message indicates they are
not. This is an opportunity to learn how to debug a function. Look at the
'debug' package.
On Tue, Mar 9, 2010 at 5:59 AM, weltbewohnerin1
franziska.schu...@wiwi.hu-berlin.de wrote:
Hallo!
I have the following function:
cLL_beta - function(beta){
sumterm=0
a=1
b=0
S=I_n-lambda*w
R=I_n-rho*w
det_R=det(S)
det_S=det(R)
for (i in 1:t){
b=i*n
y_ausgew=y_tilde[a:b]#y_ausgew ist numeric
y_aus=matrix(y_ausgew)#Typen anpassen
X_ausgew=X[a:b,]#X_ausgew ist eine Matrix
x_tilde=X_ausgew-1/t*x_t #x_tilde ist auch eine Matrix
X_aus=matrix(X_ausgew)
V1=R%*%(S%*%y_aus-x_tilde%*%beta)
V11=t(V1)
V2=V11%*%J_n
V_tilde=V2%*%V1
sumterm=sumterm+V_tilde
a=b+1
}
-((n*t)/2)*log(2*pi*sigm_sq)+t*(log(det_S)+log(det_R))-1/(2*sigm_sq)*sumterm
}
where beta is a matrix (2x1), X is a matrix (n*tx1) and y is numeric with
length nt.
My error message is: X_ausgew%*%beta - non-conformable arguments
Can anybody help me?
THANKS
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What is the problem that you are trying to solve?
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[R] sorting data whilst ignoring NA's
Hello, I am very new to R and have hit my first main problem that I hope someone can easily resolve. I have some data that looks like this (there are 20,000 rows): qdata day month yearflow [1,] 210 1945 NA [2,] 310 1945 NA [3,] 410 1945 NA [4,] 510 1945 NA [5,] 610 1945 2.973 [6,] 710 1945 NA [7,] 810 1945 NA [8,] 910 1945 2.973 [9,] 1010 1945 NA [10,] 1110 1945 NA [11,] 1210 1945 NA [12,] 1310 1945 NA [13,] 1410 1945 2.973 [14,] 1510 1945 NA I want to sort the data in descending order by flow but with all the NA results sent to the bottom. I have managed to sort the data using: topflows - qdata[order(-flow, na.last=TRUE),] But this sorts the data by flow value and then year I think giving: day month year flow [1,] 14 3 1947 222.40 [2,] 15 3 1947 NA [3,] 18 3 1947 NA [4,] 17 3 1947 NA [5,] 19 3 1947 NA [6,] 12 3 1947 NA [7,] 13 3 1947 NA [8,] 16 3 1947 NA [9,] 20 3 1947 NA [10,] 3011 1946 106.50 [11,] 30 3 1947 105.60 [12,] 2911 1946 NA [13,] 11 3 1947 NA [14,] 2211 1946 99.96 [15,] 2111 1946 NA I want my data to come out like this: [1,] 14 3 1947 222.3 [2,] 30 11 1946 106.50 [3,] 30 3 1947 105.60 [4,] 22 11 1946 99.96 and so on... Any help would be greatly valued. Thanks Emma -- View this message in context: http://n4.nabble.com/sorting-data-whilst-ignoring-NA-s-tp1586277p1586277.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! I need to use R to calculate a recursive function!
hi,all Z(i)=0.05X(i)+0.95Z(i-1), where i = 1.32, and X's are given data, the question is how to use r to get the 32 values of Z. I couldn't do this in R and wish somebody can help me. thanks in regards -- View this message in context: http://n4.nabble.com/Help-I-need-to-use-R-to-calculate-a-recursive-function-tp1586189p1586189.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is it possible to recursively update a function?
Thanks for the input, Uwe. Unfortunately, I need to iteratively update
functions from f1 to f25. Seems I have no choice but set each one
manually.
On Mar 6, 11:45 am, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
It is not obvious to me if you can calculate f1, ..., f4, ...
automatically or have to set them manually. Looks like you need to do it
manually. In that case I'd suggest to write something along the lines:
dose - c(-1.47, -1.1, -0.69, -0.42, 0.0, 0.42)
f1 - function(x) exp(-x)
f2 - function(x) f1(x) * (1 - 0.2^x)
f3 - function(x) f2(x) * (1 - 0.3^x)
f4 - function(x) f3(x) * 0.3^x
calcid - function(f, dose){
denom - integrate(f, 0, 100)$value
alpha - integrate(function(x) x * f(x), 0, 100)$value / denom
which.min(abs(-0.5 * log(0.2^(-1/alpha) - 1) - dose))
}
calcid(f2, dose)
calcid(f3, dose)
calcid(f4, dose)
If the hierarchy becomes deeper (i.e. 10 functions or so, it might make
sense to reduce the number of hierarchical calls for efficiency, but
that is not necessary for the current setup.
Uwe Ligges
On 05.03.2010 17:34, Ming Zhong wrote:
I was trying to replicate one CRM simulation. The following code works but
seems redundant so I want to create a loop.
O'Quigley CRM example 1#
f1-function(x) exp(-x)
dose-c(-1.47,-1.1,-.69,-.42,0.0,.42)
p-c(0.05,0.1,0.2,0.3,0.5,0.7)
y-c(0,0,1,0,1,1,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,1,1)
f2-function(x) f1(x)*(1-0.2^x)
denom2-integrate(f2,0,100)$value
alpha2-integrate(function(x) x*f2(x),0,100)$value/denom2
id-which.min(abs(-.5*log(0.2^(-1/alpha2)-1)-dose)) ### id is used to
locate the next prob.
f3-function(x) f2(x)*(1-.3^x)
denom3-integrate(f3,0,100)$value
alpha3-integrate(function(x) x*f3(x),0,100)$value/denom3
id-which.min(abs(-.5*log(0.2^(-1/alpha3)-1)-dose))
f4-function(x) f3(x)*.3^x
denom4-integrate(f4,0,100)$value
alpha4-integrate(function(x) x*f4(x),0,100)$value/denom4
id-which.min(abs(-.5*log(0.2^(-1/alpha4)-1)-dose))
2010/3/5 Uwe Liggeslig...@statistik.tu-dortmund.de
On 05.03.2010 01:40, Carl Witthoft wrote:
My foolish move for this week: I'm going to go way out on a limb and
guess what the OP wanted was something like this.
i=1, foo = x*exp(-x)
i=2, foo= x^2*exp(-x)
i=3, foo = x^3*exp(-x)
.
.
.
In which case he really should create a vector bar-rep(na,5) ,
and then inside the loop,
bar[i]-x^i*foo(x)
Since in this case foo(x) is independent of i, you are wasting resources.
Moreover you could calculate it for a whole matrix at once. Say you want to
calculate this for i=1, ..., n with n=5 for some (here pseudo random x),
then you could do it simpler after defining some data as in:
set.seed(123)
x- rnorm(10)
n- 5
using the single and probably most efficient line:
outer(x, 1:n, ^) * exp(-x)
or if x is a length 1 vector then even simpler:
set.seed(123)
x- rnorm(1)
n- 5
x^(1:5) * exp(-x)
But we still do not know if this is really the question ...
Uwe Ligges
Carl
quoted material:
Date: Thu, 04 Mar 2010 11:37:23 -0800 (PST)
I need to update posterior dist function upon the coming results and
find the posterior mean each time.
On Mar 4, 1:31 pm, jim holtmanjholt..._at_gmail.com wrote:
What exactly are you trying to do? 'foo' calls 'foo' calls 'foo'
How did you expect it to stop the recursive calls?
On Thu, Mar 4, 2010 at 2:08 PM, Seekerzhongm..._at_gmail.com
wrote:
Here is the test code.
foo-function(x) exp(-x)
for (i in 1:5)
{
foo-function(x) foo(x)*x
foo(2)
}
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Re: [R] Monetary support to the R-project (Was: Re: Executable for Production Use)
I would have become a member a long time ago if the money transfer process was more standard. I am not comfortable sending the details of my credit card via snail-mail or fax. Perhaps you could set up a proper Internet service or give people the chance to pay by paypal? I realize that could mean some initial outlay, but maybe it would be worth your while? jarek p Henrik Bengtsson wrote: On Mon, Mar 8, 2010 at 8:46 PM, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: On Mon, Mar 8, 2010 at 6:44 PM, Ma Ismail - NewYork-MEAG-NY i...@meag-ny.com wrote: Hi, A few of the developers on our Quant team are using R for data calculation and to generate a [snip] I've noticed a lot of financial corporates getting into R and getting free help from R-help. From now on, I'm charging $50 per email to answer questions from anyone advertising as a 'quant'. Who do I invoice? For companies and others wondering how to give something back, it is possible to support R and the R Foundation either through a donation: http://www.r-project.org/ - Foundation - Donations [http://www.r-project.org/foundation/donations.html] or via a membership: http://www.r-project.org/ - Foundation - Membership [http://www.r-project.org/foundation/membership.html] or both. /Henrik 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. __ 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] penalized maximum likelihood estimation and logistf
Thanks for your help. I can follow your explanation. Have you tried logistf and met the same problem? Are there any ways to locate which part of data causes the failure or other R code to build the model from the data? Thanks Xiaoyan On Tue, Mar 9, 2010 at 12:22 PM, Ravi Varadhan rvarad...@jhmi.edu wrote: Let us look at a piece of the relevant code from logistf package: iter - iter + 1 XW2 - crossprod(x, diag(pi * (1 - pi))^0.5) Fisher - crossprod(t(XW2)) covs - solve(Fisher) H - crossprod(XW2, covs) %*% XW2 if (firth) U.star - crossprod(x, y - pi + diag(H) * (0.5 - pi)) else U.star - crossprod(x, y - pi) delta - as.vector(covs %*% U.star) mx - max(abs(delta))/maxstep if (mx 1) delta - delta/mx First, note that this is inside an iterative loop. The Fisher information matrix is first formed, and then it is inverted to get `covs'. This is where it can get troublesome. It is very likely in your case that the `Fisher' information matrix is ill-conditioned, and hence `covs' cannot be computed. Consequently, the steplength `delta' for the Newton method cannot be determined. Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: xiaoyan yu xiaoyan...@gmail.com Date: Tuesday, March 9, 2010 11:26 am Subject: [R] penalized maximum likelihood estimation and logistf To: r-help@r-project.org Hi, I got two questions and would really appreciate any help from here. First, is the penalized maximum likelihood estimation(Firth Type Estimation) only fit for binary response (0,1 or TRUE, FALSE)? Can it be applied to multinomial logistic regression? If yes, what's the formula for LL and U(beta_i)? Can someone point me to the right reference? Second, when I used *logistf *on a dataset with binary response, I got the following error msg: Error in if (mx 1) delta - delta/mx : missing value where TRUE/FALSE needed What does this msg mean? does it mean the dataset includes missing response? I checked my dataset several times and didn't find anything other than TRUE or FALSE for the response. Please shed light on this. Thanks, Xiaoyan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotlmer graphics/x-axis and legend options
Hi, I am Using R.2.9.2 and I am trying to make nicer some graphics, which are constructed with plotmer.fnc. In particular, I have two questions: 1. Is is a way to decide in which order we want the labels on the x-axis. For now, the reference value label is the first one, and the other labels appear in the alphabetical order. I would like them to be sorted in the ascending way. Here is my code: plotLMER.fnc(idtt_lmer7bis, xlabel =, xlabs =NA, ylabel = Reaction time (ms), fun = NA, pred = Condition, n = 100, , mcmcMat = NA, lockYlim = TRUE, addlines = TRUE, withList = FALSE, cexsize = 0.7, lwd=2, font=2, cex.lab=1.25, tcl=-0.5, las=2, cex.axis=0.7) 2. In the plotlmer graphic with an interaction, is it possible to remove the legend of the interacted factor? Again here is my code: plotLMER.fnc(idbase_lmer22bis, xlabel = Competence in L2, xlabs = NA, ylabel = Reaction time (ms), ylimit =c(300,1300), fun = NA, pred = Groupe, n = 100, intr=list(Lexical_status, c(Word, PseudoWord), end, list(c(red, blue), lty=c(1,4), rep(1,2))), mcmcMat = NA, lockYlim = TRUE, addlines = TRUE, withList = FALSE, cexsize = 1, lwd=2, font=2, cex.lab=1.25, tcl=-0.5). Sorry if these questions are trivial, but I am been looking for an answer for two entire days now, and I would really appreciate your help!! Sandra Schwab * Sandra Schwab Chargée d'enseignement Université de Genève ELCF/LATL Uni Bastions 5, rue de Candolle 1211 Genève 4 http://www.unige.ch/lettres/elcf/contact/Pageenseignants/Schwab.html __ 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] Help! I need to use R to calculate a recursive function!
On Tue, Mar 9, 2010 at 4:01 PM, anan1986 ayc_...@hotmail.com wrote: hi,all Z(i)=0.05X(i)+0.95Z(i-1), where i = 1.32, and X's are given data, the question is how to use r to get the 32 values of Z. I couldn't do this in R and wish somebody can help me. Can you do anything in R? Have you tried? Have you read any of the introductory R tutorials? All this needs is a for() loop and some vector indexing. You'll do it if you read the first five pages of any introductory R guide. 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.
[R] data frame select max group by like function
Hi, I have a data frame with 3 columns: ID, year and score. How can I select for each unique ID, the year that has the max score? For example, for data frame ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 2000, 97 tom, 1998, 60 mary, 1998,100 I shall have ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 1998,100 Thanks, Richard [[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] Cox Calibration regression test double graphs
A) Please do not highjack threads. Post new topics for new questions. B) Calibration plots are very easy for either logistic regression or Cox models when using the calibrate function in either Harrell's rms or Design packages. (Not sure about how well they play with survfit objects, but you ought to be able to apply the same methods.) -- David. On Mar 9, 2010, at 12:52 PM, paaventhan jeyaganth wrote: Dear All, How can i do the bootstrap and calibration plot after surival analysis , i don't know how to do it after that please help me. Thanks here is my syntex library(survival) mfit - survfit(Surv(days, status == 1)~drug, data = melanom) #how can i do the bootstra #Cox Calibration regression test #and the calibration plot paaveen _ [[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. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sorting data whilst ignoring NA's
On Mar 9, 2010, at 11:57 AM, emwater wrote: Hello, I am very new to R and have hit my first main problem that I hope someone can easily resolve. I have some data that looks like this (there are 20,000 rows): qdata day month yearflow [1,] 210 1945 NA [2,] 310 1945 NA [3,] 410 1945 NA [4,] 510 1945 NA [5,] 610 1945 2.973 [6,] 710 1945 NA [7,] 810 1945 NA [8,] 910 1945 2.973 [9,] 1010 1945 NA [10,] 1110 1945 NA [11,] 1210 1945 NA [12,] 1310 1945 NA [13,] 1410 1945 2.973 [14,] 1510 1945 NA I want to sort the data in descending order by flow but with all the NA results sent to the bottom. I have managed to sort the data using: topflows - qdata[order(-flow, na.last=TRUE),] Try (untested): topflows - qdata[order(-qdata$flow, na.last=TRUE),] But this sorts the data by flow value and then year I think giving: day month year flow [1,] 14 3 1947 222.40 [2,] 15 3 1947 NA [3,] 18 3 1947 NA [4,] 17 3 1947 NA [5,] 19 3 1947 NA [6,] 12 3 1947 NA [7,] 13 3 1947 NA [8,] 16 3 1947 NA [9,] 20 3 1947 NA [10,] 3011 1946 106.50 [11,] 30 3 1947 105.60 [12,] 2911 1946 NA [13,] 11 3 1947 NA [14,] 2211 1946 99.96 [15,] 2111 1946 NA I want my data to come out like this: [1,] 14 3 1947 222.3 [2,] 30 11 1946 106.50 [3,] 30 3 1947 105.60 [4,] 22 11 1946 99.96 and so on... Any help would be greatly valued. Thanks Emma -- View this message in context: http://n4.nabble.com/sorting-data-whilst-ignoring-NA-s-tp1586277p1586277.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sorting data whilst ignoring NA's
On 2010-03-09 9:57, emwater wrote: Hello, I am very new to R and have hit my first main problem that I hope someone can easily resolve. I have some data that looks like this (there are 20,000 rows): qdata day month yearflow [1,] 210 1945 NA [2,] 310 1945 NA [3,] 410 1945 NA [4,] 510 1945 NA [5,] 610 1945 2.973 [6,] 710 1945 NA [7,] 810 1945 NA [8,] 910 1945 2.973 [9,] 1010 1945 NA [10,] 1110 1945 NA [11,] 1210 1945 NA [12,] 1310 1945 NA [13,] 1410 1945 2.973 [14,] 1510 1945 NA I want to sort the data in descending order by flow but with all the NA results sent to the bottom. I have managed to sort the data using: topflows- qdata[order(-flow, na.last=TRUE),] Am I missing something? Or do you just want: qdata[order(qdata$flow, decreasing=TRUE), ] -Peter Ehlers But this sorts the data by flow value and then year I think giving: day month year flow [1,] 14 3 1947 222.40 [2,] 15 3 1947 NA [3,] 18 3 1947 NA [4,] 17 3 1947 NA [5,] 19 3 1947 NA [6,] 12 3 1947 NA [7,] 13 3 1947 NA [8,] 16 3 1947 NA [9,] 20 3 1947 NA [10,] 3011 1946 106.50 [11,] 30 3 1947 105.60 [12,] 2911 1946 NA [13,] 11 3 1947 NA [14,] 2211 1946 99.96 [15,] 2111 1946 NA I want my data to come out like this: [1,] 14 3 1947 222.3 [2,] 30 11 1946 106.50 [3,] 30 3 1947 105.60 [4,] 22 11 1946 99.96 and so on... Any help would be greatly valued. Thanks Emma -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data frame select max group by like function
Try this: library(sqldf) sqldf(SELECT ID, Year, MAX(score) FROM DF GROUP BY ID) Or do.call(rbind, lapply(split(DF - DF[order(DF$score),], DF$ID), tail, 1)) On Tue, Mar 9, 2010 at 3:35 PM, Tan, Richard r...@panagora.com wrote: Hi, I have a data frame with 3 columns: ID, year and score. How can I select for each unique ID, the year that has the max score? For example, for data frame ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 2000, 97 tom, 1998, 60 mary, 1998,100 I shall have ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 1998,100 Thanks, Richard [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data frame select max group by like function
Hi Richard, There are probably better ways, but here is one approach: Dat - read.table(textConnection(ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 2000, 97 tom, 1998, 60 mary, 1998,100), header=TRUE, sep=,) MaxScore - aggregate(Dat$score, list(Dat$ID), max) names(MaxScore) - c(ID, score) MaxYear - merge(Dat, MaxScore) Best, Ista On Tue, Mar 9, 2010 at 1:35 PM, Tan, Richard r...@panagora.com wrote: Hi, I have a data frame with 3 columns: ID, year and score. How can I select for each unique ID, the year that has the max score? For example, for data frame ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 2000, 97 tom, 1998, 60 mary, 1998,100 I shall have ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 1998,100 Thanks, Richard [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data frame select max group by like function
I find ddply() in package plyr handy for this sort of thing: library(plyr) f - function(x) x[which.max( x[[score]] ), ] ## x will be a subset of Dat according to ID ddply(Dat, ID, f) -Peter Ehlers On 2010-03-09 11:59, Ista Zahn wrote: Hi Richard, There are probably better ways, but here is one approach: Dat- read.table(textConnection(ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 2000, 97 tom, 1998, 60 mary, 1998,100), header=TRUE, sep=,) MaxScore- aggregate(Dat$score, list(Dat$ID), max) names(MaxScore)- c(ID, score) MaxYear- merge(Dat, MaxScore) Best, Ista On Tue, Mar 9, 2010 at 1:35 PM, Tan, Richardr...@panagora.com wrote: Hi, I have a data frame with 3 columns: ID, year and score. How can I select for each unique ID, the year that has the max score? For example, for data frame ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 2000, 97 tom, 1998, 60 mary, 1998,100 I shall have ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 1998,100 Thanks, Richard [[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. -- Peter Ehlers University of Calgary __ 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] Executable for Production Use
On 08.03.2010 22:13, Stefan wrote: Ma Ismail - NewYork-MEAG-NYimaat meag-ny.com writes: Hi, A few of the developers on our Quant team are using R for data calculation andto generate a resulting CSV file. They have R installed on their workstations. We are interested in having this deployed to user workstations where the users will not have R installed on their workstations. Is there a way to create an executable that the users can just run without R installed on their workstation? Thanks in advance for your help. Ismail Ma Head of IT Applications MEAG New York Corporation Telephone: (212) 583-4850 Fax: (646) 521-7950 E-Mail: imaat meag-ny.commailto:imaat meag-ny.com Maybe I've misunderstood You, but You can manage a single R installation on a central server, and let clients hook up to it from Emacs+ESS or Eclipse+StatET. I've used both solutions, and they work like a charm... The emacs solution uses SSH and Eclipse a Java server thingy. Plz note that I'm from the Linux side of things. So my server is a Debian, and my clients are all Ubuntu. I have no clue how (or even if) these setups work on windows. Yes, they also do work on Windows. Anyway, to answer the question: No, it is not possible to have a single executable that allows to run R code. Best, uwe Ligges __ 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] Shade area under curve
I want to shade the area under the curve of the standard normal density. Specifically color to the left of -2 and on. How might i go about doing this? Thanks -- View this message in context: http://n4.nabble.com/Shade-area-under-curve-tp1586439p1586439.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] How To Display Current/Next Line Using browser()
Hi, I'm running R 2.10 on a Linux console, inserted a call to browser() in an R script that I source() form the R command line. Two quick questions: (1) Once you are in the browser prompt, is there any way to display the current/next line to be executed without executing it? I can issue an n command to view the line, but was wondering if there's a simple display current line command to view the source code before I execute it. (2) Is there any way to exit the browser() prompt to go back to the R prompt without typing c to continue execution? I tried using Ctl-C, but this stays within the browser. I searched for other posts on these but couldn't find anything. Thanks! -- View this message in context: http://n4.nabble.com/How-To-Display-Current-Next-Line-Using-browser-tp1586434p1586434.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] Moving Average Model
Using the forecast package in R, auto.arima returns a model of type (0,0,3) with coefficients. To forecast the value at any point of time t, I can use the coefficients along with the white noise values e(t). How can we get the value for white noise? -- View this message in context: http://n4.nabble.com/Moving-Average-Model-tp1586447p1586447.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] rcom package
Hi Erich and Gabor, Thank you for your replies. I wanted to write *only* non-formulae cells. I have dozens of sheets with a mix of raw input (ie, no formulae) en calculated values. I want to separate this, In a later stage, I want to let R do all the calculations that with the current system are done with xls. So I need to conditionally write the data using something like (pseudocode): if (!IsFormula(cell)) xls.write(rowno, colno, cell) (...see also the vb code below). I have to study this in more detail, but i still don't think this is possible with the rodbc package. I hope I don;t need to, but I may need to dive into COM and the excel object model. Function IsFormula(Cell As Range) As Boolean If Len(Cell.Formula) = 0 Then IsFormula = False Else IsFormula = (Left(Cell.Formula, 1) = =) End If End Function source: http://www.triskele.com/2008/04/26/excels-missing-isformula-function Thanks again! Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ --- On Tue, 3/9/10, Erich Neuwirth erich.neuwi...@univie.ac.at wrote: From: Erich Neuwirth erich.neuwi...@univie.ac.at Subject: Re: [R] rcom package To: r-help@r-project.org Date: Tuesday, March 9, 2010, 5:28 PM rcom allows you to access the full object model of any COM server. The object browser in Excel allows you to investigate Excel's object model. It also tells you which properties are accessible. There are a few hundreds of them. On 3/9/2010 4:35 PM, Albert-Jan Roskam wrote: Hi, I would like to make a program that reads excel files, and writes the cells of which contents is not a formula to another file. I don't think this is possible with RODBC, but it may be possible with rcom. I read the documentation of the rcom package, but I was hoping somebody knows a good web resource for more eleborate info. I tried Googling, but alas (did you know rcom also is a kind of egg incubator? ;-). In particular, I would like to have a list of the possible values for the 'property' argument. Thanks in advance! Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ [[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. -- Erich Neuwirth, University of Vienna Faculty of Computer Science Computer Supported Didactics Working Group Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-39464 Fax: +43-1-4277-39459 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How To Display Current/Next Line Using browser()
On 09/03/2010 1:45 PM, xallanmillerx wrote: Hi, I'm running R 2.10 on a Linux console, inserted a call to browser() in an R script that I source() form the R command line. Two quick questions: (1) Once you are in the browser prompt, is there any way to display the current/next line to be executed without executing it? I can issue an n command to view the line, but was wondering if there's a simple display current line command to view the source code before I execute it. I don't know of a way. If the code was sourced with source references, it may tell you the line number, and you could look it up from that, but I don't think there's any way to just say show me the next line. (2) Is there any way to exit the browser() prompt to go back to the R prompt without typing c to continue execution? I tried using Ctl-C, but this stays within the browser. Q will quit the browser. The ?browser help page gives the full list of commands. Duncan Murdoch I searched for other posts on these but couldn't find anything. 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] data frame select max group by like function
An alternative base R version: ?by by(Dat,Dat$ID,function(frm)frm$year[which.max(frm$score)]) by() is a wrapper for tapply(), one of the base R apply family of functions (lapply, mapply, etc.) for which many find the plyr package provides a simpler and more consistent interface. I'm used to the base R versions, however, and in fact my preferred approach to this is simply: with(Dat, tapply(seq_len(nrow(Dat)),ID,function(i)year[i][which.max(score[i])])) In any case, you should invest the time to learn either (or both) the base R or plyr version of the apply() functions. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ista Zahn Sent: Tuesday, March 09, 2010 11:00 AM To: Tan, Richard Cc: r-help@r-project.org Subject: Re: [R] data frame select max group by like function Hi Richard, There are probably better ways, but here is one approach: sc MaxScore - aggregate(Dat$score, list(Dat$ID), max) names(MaxScore) - c(ID, score) MaxYear - merge(Dat, MaxScore) Best, Ista On Tue, Mar 9, 2010 at 1:35 PM, Tan, Richard r...@panagora.com wrote: Hi, I have a data frame with 3 columns: ID, year and score. How can I select for each unique ID, the year that has the max score? For example, for data frame ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 2000, 97 tom, 1998, 60 mary, 1998,100 I shall have ID, year, score tom, 1995, 88 rick, 1994, 90 mary, 1998,100 Thanks, Richard [[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. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.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. __ 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] Shade area under curve
Hi, use dnorm() for the density and polygon() to shade the area underneath, with suitably many x values so your density looks smooth. HTH, Stephan claytonmccandless schrieb: I want to shade the area under the curve of the standard normal density. Specifically color to the left of -2 and on. How might i go about doing this? 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] Moving Average Model
On Mar 9, 2010, at 1:54 PM, testuser wrote: Using the forecast package in R, auto.arima returns a model of type (0,0,3) with coefficients. To forecast the value at any point of time t, I can use the coefficients along with the white noise values e(t). How can we get the value for white noise? Teach a man to fish: RSiteSearch(shade the area under a curve) A search query has been submitted to http://search.r-project.org The results page should open in your browser shortly -- View this message in context: http://n4.nabble.com/Moving-Average-Model-tp1586447p1586447.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
