[R] Rounding error in seq(...)
Hi, Today I was flabbergasted to see something that looks like a rounding error in the very basic seq function in R. a = seq(0.1,0.9,by=0.1) a [1] 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 a[1] == 0.1 [1] TRUE a[2] == 0.2 [1] TRUE a[3] == 0.3 [1] FALSE It turns out that the alternative a = (1:9)/10 works just fine. Are there any good guides out there on how to deal with issues like this? I am normally aware of rounding errors, but it really surprised me to see that an elementary function like seq would behave in this way. Thanks, Michael Knudsen -- Michael Knudsen micknud...@gmail.com http://sites.google.com/site/micknudsen/ __ 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] Rounding error in seq(...)
On Wed, Sep 30, 2009 at 8:44 PM, Duncan Murdoch murd...@stats.uwo.ca wrote: Why? You asked for an increment of 1 in the second case (which is exactly represented in R), then divided by 10, so you'll get the same as 0.3 gives you. In the seq() case you asked for an increment of a number close to but not equal to 1/10 (because 1/10 is not exactly representable in R), so you got something different. Well, the problem is that I don't know how seq is implemented. I just assumed that it wouldn't behave like this. -- Michael Knudsen micknud...@gmail.com http://sites.google.com/site/micknudsen/ __ 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] Rounding error in seq(...)
On Wed, Sep 30, 2009 at 8:40 PM, Michael Knudsen micknud...@gmail.com wrote: a = seq(0.1,0.9,by=0.1) a [1] 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 a[1] == 0.1 [1] TRUE a[2] == 0.2 [1] TRUE a[3] == 0.3 [1] FALSE A friend of mine just pointed out a possible solution: a=seq(0.1,0.9,by=0.1) a = seq(0.1,0.9,by=0.1) a[3]==0.3 [1] FALSE all.equal(a[3],0.3) [1] TRUE The all.equal function checks if two objects are nearly equal. -- Michael Knudsen micknud...@gmail.com http://sites.google.com/site/micknudsen/ __ 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] Use of R in Schools
On Sat, Sep 19, 2009 at 6:28 AM, John Maindonald john.maindon...@anu.edu.au wrote: I am looking for information on experimentation with the use of R in the teaching of statistics and science in schools. Any leads would be very welcome. I am certain that there is such experimentation. I read this paper http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000482 some days ago. It's quite interesting, and it links to some excellent slides that look great as templates for making your own R course. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] R on Multi Core
On Fri, Sep 11, 2009 at 10:05 PM, Noah Silverman n...@smartmediacorp.com wrote: Is there a version of R that would take advantage of BOTH cores?? Well, if your job is parallelizable, it's actually fairly easy. When I discovered the package 'foreach', I wrote the following piece completely overwhelmed by enthusiasm: http://lifeofknudsen.blogspot.com/2009/07/most-of-work-i-do-in-r-has-to-do-with.html It's very basic, but maybe you'll find it useful. Best, Michael Knudsen -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] how to determine if a variable is already set?
On Fri, Sep 11, 2009 at 7:15 PM, carol white wht_...@yahoo.com wrote: It might be a primitive question but how it is possible to determine if a variable is initialized in an environment? What about this? x %in% ls() [1] FALSE x = 41 x %in% ls() [1] TRUE Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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 matrix calculation
On Sun, Aug 23, 2009 at 8:53 PM, Bogasobogaso.christo...@gmail.com wrote: No no, I actually want following result : 7, 14, 21, 6, 13, 20, 5, 12, 19, How about this? x = c() for (i in 7:1) x = c(x,mat[i,]) Guess that would do the trick. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Package read large file
On Wed, Aug 19, 2009 at 10:51 AM, Mohamed Lajnefmohamed.laj...@inserm.fr wrote: I am looking for packages that could read large files in R? any suggestions are welcome. As already pointed out by Jim, your question is not very specific. My wild guess is that you probably have some memory issues -- if that is the case, maybe the package bigmemory can alleviate your pain. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Plot(x,y)
On Sun, Aug 16, 2009 at 9:19 PM, malcolm Crouchmalcolm.crouc...@gmail.com wrote: plot(V6,V5, col=red) or plot(V6,V5) It seems that V5 and V6 are column names in your data matrix. If your matrix is called data, you should use plot(x$V6,x$V5,col=red) instead. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] graph label greek symbol failure
On Mon, Aug 17, 2009 at 12:51 PM, e-letter inp...@gmail.com wrote: I have tried to add the delta (δ) symbol to the y axis label and the result is D, using the command: ...ylab=δt... Try ylab = expression(delta*t) instead. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Plot(x,y)
On Tue, Aug 18, 2009 at 6:59 PM, David Winsemiusdwinsem...@comcast.net wrote: ITYM: plot(data$V6, data$V5, col=red) Yup! My mistake. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] randomForest question--problem with ntree
On Thu, Aug 13, 2009 at 11:11 PM, Mary Puttmp...@mail.med.upenn.edu wrote: Hi Mary, I would like to use a random Forest model to get an idea about which variables from a dataset may have some prognostic significance in a smallish study. The default for the number of trees seems to be 500. I tried changing the default to ntree=2000 or ntree=200 and the results appear identical. Have changed mtry from mtry=5 to mtry=6 successfully. Have seen same problem on both a Windows machine and our linux system running 2.8 and 2.9. I don't think it's correct to call it a problem; it's more likely a feature! Try to take a look a Breiman's paper (in the Machine Learning journal), where he introduces random forests. I read it recently, and somewhere he explicitly mentions that ntree often may be set very low without lowering the performance. The random forest algorithm is very robust and apparently 500 trees are usually more than enough. Therefore you don't get better results by using 2000 trees, and often it doesn't affect the performance if you use fewer trees (e.g. 200). Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] randomForest question--problem with ntree
On Fri, Aug 14, 2009 at 1:43 PM, Mary Puttmp...@mail.med.upenn.edu wrote: I'm not calling it a problem that the answer converges--i.e. that the algorithm is stable. but if you look at the example even though I've asked for 2000 or 200 tress, ntree=2000 or ntree=200, it still gives me 500 trees according to the output and identical results when you set the seed before the call. While results are expected to be similar they should not be identical if the number of trees was actuallly changed. Oops! You have written n.tree instead of ntree. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Output to screen and file at the same time
Hello! Using the sink function, output from R may be written to a file instead of the screen. I would really like to write my output to a file while running an R script and at the same time view the output live on my screen. Is there are way to do that? Thanks, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Matrix addition function
On Thu, Aug 13, 2009 at 11:35 AM, Lina Rusyteliner...@yahoo.co.uk wrote:
Hi Lina,
What function can I use for matrices addition? I couldn’t find any
information about it in the manual or in the internet.
(A+B suits, when the number of matrixes is small, function sum() doesn’t suit
for matrices addition, because it sums all variables in the matrices and
produces as an answer single number, not a matrix).
I don't know of any function doing that, but you could easily write a
one yourself. Suppese that X is a list of matrices. Then you could
e.g. do as follows:
matrixSum = function(X)
{
N = length(X)
if (N==2) return(X[[1]]+X[[2]])
else return(matrixSum(X[[1:(N-1)]],X[[N]]))
}
I guess that one should do the trick.
Best,
Michael
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http://lifeofknudsen.blogspot.com/
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Re: [R] downsampling
On Fri, Jul 24, 2009 at 9:32 AM, Jan Wienerjan.wie...@tuebingen.mpg.de wrote: x=sample(1:5, 115, replace=TRUE) How do I downsample this vector to 100 entries? Are there any R functions or packages that provide such functionality. What exactly do you mean by downsampling? Do you just want to sample 100 random entries from x? sample(sample(1:5,115,replace=TRUE),100,replace=FALSE)) -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Re placing null values (#NULL!)
On Wed, Jul 22, 2009 at 10:18 PM, Josh Rollj_r...@hotmail.com wrote: In `[-.factor`(`*tmp*`, Props_$pct_vacant == #NULL!, value = 0) : invalid factor level, NAs generated Thats what made me wonder if the #NULL! value was being treated differently than a typical NULL value. Thoughts? I would like to test it myself, but I haven't succeeded in copying your data to a text file readable by R. If you can email it to me, I'll give it a try. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Multi-line comments?
On Wed, Jul 22, 2009 at 4:30 PM, Mark Knechtmarkkne...@gmail.com wrote:
I wanted to comment out 20 lines that I'm moving to a function but
didn't want to delete them. Is there no defined way to get around
using a # on each of the 20 lines?
Just like you, I have been longing for that myself. It seems that the
answer is negative, so I have ended up using
if (1==0)
{
# code goes here
}
although is not really nice to look at.
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http://lifeofknudsen.blogspot.com/
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Re: [R] Multi-line comments?
On Wed, Jul 22, 2009 at 5:27 PM, Erik Iversoneiver...@nmdp.org wrote: What editor are you all using to write R code? Many will have ways of doing what you want, e.g., comment-region (bound by default to M-; through comment-dwim) in Emacs. Cool! I'm using Xcode, and I have just realized that cmd+/ will make a block comment. By default it adds '//' instead of '#', but I guess that it can be fixed somehow. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Find multiple elements in a vector
Hi, Given a vector, say x=sample(0:9,10) x [1] 0 6 3 5 1 9 7 4 8 2 I can find the location of an element by which(x==2) [1] 10 but what if I want to find the location of more than one number? I could do c(which(x==2),which(x==3)) but isn't there something more streamlined? My first guess was y=c(2,3) which(x==y) integer(0) which doesn't work. I haven't found any clue in the R manual. Thanks! -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Find multiple elements in a vector
On Wed, Jul 22, 2009 at 9:37 PM, Chuck Clelandcclel...@optonline.net wrote: How about this? which(x %in% c(2,3)) Thanks to you all! I had never thought about using %% in this context. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] heatmap plot
2009/7/21 Markus Mühlbacher muehli...@yahoo.com: So just that I understand right. x and y are the scalings of the x and y axis and the matrix represents the color of the points at each gridpoint? Precisely! Try ?image for more details. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Merging lot of zoo objects
On Tue, Jul 21, 2009 at 9:07 AM, RON70ron_michae...@yahoo.com wrote: I have 100 price data series like price1, price2, price3, . All are zoo objects. Now I want to merge all them together. Obviously I can do this using merge(price1, price2, price3, ). However as I have lot of price series (almost 1000) above systax is very tiresome. Is there any other way on doing to in one-go? How did you get the names price1, price2, ..., price_100 in the first place? Did you make 100 lines of code? If you had stored the objects in a list, such that priceN = list_of_prices[[N]] you could easily define a recursive function to do the job for you. Would it difficult for you to read the data into a list? When dealing with only a few sets, numbering objects as you do is no problem, but for many objects it can become very cumbersome. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] writte file doubt
On Tue, Jul 21, 2009 at 2:28 PM, Jose Narillos de Santosnarillosdesan...@gmail.com wrote: Hi I wrotte this function but when I get the tmp.xls file it shows data in a rare way. I mean not appears a matrix with 2000 rows and 100 columns. Can anyone help me, guide me? Short answer: ?write write(tmp,file=tmp.xls) You have to add an ncolumns option like write(tmp,file=tmp.xls,ncolumns=100). The default is five columns. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] heatmap plot
2009/7/21 Markus Mühlbacher muehli...@yahoo.com: I tried to add white to the colors, but this did not change my problem. Still the values of the diagonal seem to be different from those occurring in the matrix. Or in other words all squares of the diagonal should have to SAME color! If you can send me the matrix as a text file -- ready to import in R -- I can give it a try. Best, Michael -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Building a big.matrix using foreach
On Sun, Jul 19, 2009 at 2:29 PM, Jay Emersonjayemer...@gmail.com wrote:
Hi Jay!
foreach(i=1:nrow(x),.combine=c) %dopar% f(x[i,])
That was also my first guess, but it doesn't seem to work. Here is a
trivial example using a regular matrix instead of a big.matrix. The
outcome is the same.
m = matrix(0,nrow=5,ncol=5)
foreach (i=1:5) %dopar% { m[i,] = rnorm(5) }
Since I didn't include the .combine option, a list containing five
independent rnorm(5) is returned. However, the matrix m is not
changed. If I replace %dopar% with %do%, everything works fine (but
not in parallel, of course).
Another thing is: The reason why I want to use big.matrix is, of
course, that my data set is too big to store in a regular matrix.
However, it seems that no matter how you run foreach, it will always
return something (a list, a vector, or...), and that will end up
having the same dimension as the big.matrix. If the returned object
can't be a big.matrix, I'm bound to run out of memory anyway.
should work, essentially applying the functin f() to the rows of x? But
perhaps I misunderstand you. Please feel free to email me or Mike
(michael.k...@yale.edu) directoy with questions about bigmemory, we are very
interested in applications of it to real problems.
My acutal problem is the following: I have a big data set of
observations, and I have a distance measure on this set. I would like
to calculate all pairwise distances and store them in a big.matrix. My
hope was to be able to build the matrix row by row in a parallel way.
Best,
Michael
--
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.com/
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Re: [R] Building a big.matrix using foreach
On Sun, Jul 19, 2009 at 4:02 PM, Michael Kanekaneplusp...@gmail.com wrote:
Hi Mike,
desc = describe(x)
foreach (i=1:nrow(x), .combine=c, .packages='bigmemory') %dopar%
{
x = attach.big.matrix(desc)
f(x[i,])
}
Thanks! The shared.big.matrix was exactly what I needed. It still
remains for me, though, to check if I run into memory problems anyway.
It doesn't seem as if there's a don't return anything option in the
foreach function (also mentioned in my previous post in this thread).
Best,
Michael
--
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.com/
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Re: [R] Building a big.matrix using foreach
On Mon, Jul 20, 2009 at 10:23 AM, Michael Knudsenmicknud...@gmail.com wrote:
Thanks! The shared.big.matrix was exactly what I needed. It still
remains for me, though, to check if I run into memory problems anyway.
It doesn't seem as if there's a don't return anything option in the
foreach function (also mentioned in my previous post in this thread).
Oops! The following code made R go bananas and left the system dead
for fifteen minutes. Trying a simple 'ls' in a terminal resulted in
something like Segmentation fault. Too many files open.
distances =
shared.big.matrix(nrow=length(x),ncol=length(x),type=double,init=0)
desc = describe(distances)
foreach (i=1:(length(x)-1)) %dopar%
{
first_x = x[[i]]
these_distances = numeric(length(x))
for (j in (i+1):length(x))
{
second_x = x[[j]]
these_distances[j] = as.numeric(ks.test(first_x,second_x)$statistic)
}
y = attach.big.matrix(desc)
y[i,] = these_distances
}
The error message from R was:
*** caught segfault ***
address (nil), cause 'memory not mapped'
/Michael
--
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http://lifeofknudsen.blogspot.com/
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Re: [R] what is meaning of the bubbles in boxplots?
On Mon, Jul 20, 2009 at 5:18 AM, Jie TANGtotang...@gmail.com wrote: Can anyone tell me what the correct meaning of these bubbles?and how to remove it? Have a look at the Wikipedia entry on box plots: http://en.wikipedia.org/wiki/Boxplot Why do you want to remove the bubbles? They are outliers and part of your data. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] I might be dumb : a simple question about foreach
On Mon, Jul 20, 2009 at 2:48 PM, Olivier
ETERRADOSSIolivier.eterrado...@ema.fr wrote:
x - foreach(i = 1:3) %do% sqrt(i)
and get :
Erreur dans sqrt(i) : indice hors limites ( i.e. error in sqrt(i) : index
out of bounds)
I once got similar errors because I didn't encapsulate the part af
%do% or %dopar% in curly brackets. Try
x - foreach(i = 1:3) %do% { sqrt(i) }
I should say, however, that in this particular case, your original
code evaluates without errors on my computer (Mac OSX 10.5.7 with R
2.9.1).
By the way, remember to use %dopar% instead of %do%, if you want to
take advantage of multiple cores. While being totally ecstatic after
discovering foreach, I wrote the following (very simple) guide:
http://lifeofknudsen.blogspot.com/2009/07/most-of-work-i-do-in-r-has-to-do-with.html
Maybe you'll find it useful, maybe not.
--
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Re: [R] I might be dumb : a simple question about foreach
On Mon, Jul 20, 2009 at 3:14 PM, Olivier ETERRADOSSIolivier.eterrado...@ema.fr wrote: Do you suggest some Windows related behaviour ? I haven't used Windows for more than ten years, so unfortunately I have no clue whatsoever. Maybe there are some Windows experts here who can help you. America is slowly waking up now, so cross your fingers :-) -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] mahalanobis distance
On Mon, Jul 20, 2009 at 3:08 PM, ekinakoglue...@ims.metu.edu.tr wrote: Error in solve.default(cov, ...) : system is computationally singular: reciprocal condition number = 1.65972e-18 Try calculating the determinant of the S matrix: det(S) [1] 2.825397e-06 It's very close to zero, and I guess that the matrix is therefore considered non-invertible by R. Recall that S must be invertible http://en.wikipedia.org/wiki/Mahalanobis_distance to work as a covarinace matrix in the definition of the Mahalanobis distance. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] heatmap plot
2009/7/20 Markus Mühlbacher muehli...@yahoo.com: What is my mistake? I don't know about the heatmap function, but I have often used 'image' with 'heat.colors' without any problems. There is a nice example here: http://addictedtor.free.fr/graphiques/graphcode.php?graph=20 It should be fairly easy to fit your data into that one. I guess that this should work: x = 1:length(activity.matrix) y = 1:length(activity.matrix) image(x, y, activity.matrix, col=heat.colors(100)) -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] heatmap plot
2009/7/20 Markus Mühlbacher muehli...@yahoo.com: Gives the attached image. Again I am missing the white diagonal. Is there some kind of sorting that I do not consider? Maybe col=c(white,heat.colors(100)) will do the trick? -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] kmeans.big.matrix
Hi, I'm playing around with the 'bigmemory' package, and I have finally managed to create some really big matrices. However, only now I realize that there may not be functions made for what I want to do with the matrices... I would like to perform a cluster analysis based on a big.matrix. Googling around I have found indications that a certain kmeans.big.matrix() function should exist. It is mentioned, among other places, in this document: http://www.stat.yale.edu/~jay/662/bm-nojss.pdf Unfortunately, on my computer the following happens: require(bigmemory) Loading required package: bigmemory kmeans.big.matrix Error: object 'kmeans.big.matrix' not found Does anybody know how to get the kmeans.big.matrix() function? Are there other cluster algorithms out there ready to accept a big.matrix as input? Thanks! -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] mahalanobis distance
On Mon, Jul 20, 2009 at 9:37 PM, ekinakoglue...@ims.metu.edu.tr wrote: Could you please help me with a pseudo matrix of 4x4 that is gonna work with mahalanobis? Hmmm ... I have been trying some different matrices myself now, but I keep getting the same error. Even if det(S) is very far from zero. Maybe I just don't get the point of the mahalanobis() function in R. It looks quite weird to me :-( -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Re placing null values (#NULL!)
On Fri, Jul 17, 2009 at 10:37 PM, PDXRuggerj_r...@hotmail.com wrote: So i need to replace the the #NULL! with 0. I have tried: Props_pct_vacant-Props_pct_vacant[Props_$pct_vacant !=#NULL!] Try this instead: Props_$pct_vacant[which(Props_$pct_vacant==#NULL!)] = 0 -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Building a big.matrix using foreach
Hi there! I have become a big fan of the 'foreach' package allowing me to do a lot of stuff in parallel. For example, evaluating the function f on all elements in a vector x is easily accomplished: foreach(i=1:length(x),.combine=c) %dopar% f(x[i]) Here the .combine=c option tells foreach to combine output using the c()-function. That is, to return it as a vector. Today I discovered the 'bigmemory' package, and I would like to contruct a big.matrix in a parralel fashion row by row. To use foreach I see no other way than to come up with a substitute for c in the .combine option. I have checked out the big.matrix manual, but I can't find a function suitable for just that. Actually, I wouldn't even know how to do it for a usual matrix. Any clues? Thanks! -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Transformation of data!
On Fri, Jul 17, 2009 at 10:29 AM, Andriy Fetsunfet...@googlemail.com wrote: I want to perform some sort of transformation on all the elements in the matrix I have posted and that I have only presented those 3 elements as an example of how the transformation will affect those 3 elements. Do you see the problem now? Hmmm ... I don't think to. If you have a function f, you can apply it to all elements in a vector x by simply typing f(x). If you want to arrange it in two columns as you suggest, you could do cbind(1:length(x),f(x)), but I really can't see why you would ever want to do that. Here the proposed by R-guy solution mydata - data.frame(W21) Where is your function, and what is W21? -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] dot plot with several points for 2 categories
On Fri, Jul 17, 2009 at 7:17 PM, jaregisuck...@mpi-cbg.de wrote: I'm trying to wean myself off the very limited capabilities of Excel and Oo. Currently, I am trying to make a plot showing several values for 2 categories in a dot blot (see http://www.nabble.com/file/p24538360/Picture%2B1.png Picture+1.png except that the x axis should contain the category not a number, which was the only way to coax Excel into displaying a plot like this). Let y1 be a vector containing the values in the first category, and let y2 contain those of the second. The you could do like this: x1 = rep(1,times=length(y1)) x2 = rep(2,times=length(y2)) plot(c(x1,x2),c(y1,y2),xaxt=n) axis(side=1,at=c(1,2),labels=c(label1,label2)) It looks like a hack, but it should work. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] loading a file in R in mac OS X
On Thu, Jul 16, 2009 at 1:32 PM, caballojamespi...@hotmail.com wrote: Error in file(file, r) : cannot open the connection In addition: Warning message: In file(file, r) : cannot open file 'c:\harddrivename\users\username\desktop\schools.txt': No such file or directory. I'm guessing that there's a different way to enter the path name on a macintosh? There is no such thing as a c-drive on a Mac. Try this location instead: ~/Desktop/schools.txt and note that Mac is case-sensitive. The tilde (~) refers to your home directory. Alternatively you could write: /Users/username/Desktop/schools.txt -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] loading a file in R in mac OS X
On Thu, Jul 16, 2009 at 3:04 PM, Marc Schwartzmarc_schwa...@me.com wrote: Actually, by default, the OSX HFS+ file system is not case sensitive: Sorry. I just took that for granted, as Mac (at least in a terminal) is very similar to Linux. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] loading a file in R in mac OS X
On Thu, Jul 16, 2009 at 2:44 PM, Marc Schwartzmarc_schwa...@me.com wrote: If you are using the OSX GUI (R.app) you may also want to review the OSX FAQ: If you use the GUI, you may also just want to hit cmd+d and browse to your preferred working directory. If you set the working directory to Desktop, you can just type read.table(school.txt,...) I would, however, suggest that you move your files to a directory specifically dedicated to your R project in order not to clutter up your desktop. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Transformation of data!
On Thu, Jul 16, 2009 at 10:09 PM, Andriy Fetsun fet...@googlemail.com wrote: [1] 0.00e+00 1.89e-04 3.933000e-05 1.701501e-04 2.040456e-04 [6] 3.119242e-04 2.545665e-04 1.893930e-03 1.303112e-03 9.880183e-04 [11] 1.504378e-03 1.549246e-03 5.877690e-04 4.771359e-04 8.528219e-04 That it a vector of length 15. How is it possible to transform the data to get a vector as following 10 0.017511063 11 0.017819918 12 0.017944472 That looks like a 3x2 matrix. How do you get that from the vector above? -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] The greatest common divisor between more than two integers
On Wed, Jul 15, 2009 at 8:55 AM, Atte Tenkanenatte...@utu.fi wrote:
Do somebody know if there is a function in R which computes the greatest
common divisor between several (more than two) integers?
Is there a function for computing the greatest common divisor of *two*
numbers? I can't find one, but assume that there is such a function,
and call it gcd. Then you could define a recursive function to do the
job. Something like
new_gcd = function(v)
{
if (length(v)==2) return(gcd(v))
else return (new_gcd(v[1],new_gcd(v[2:length(v)]))
}
where v is a vector containing the numbers you want to calculate the
greatest common divisor of.
--
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.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] Nested for loops
On Tue, Jul 14, 2009 at 8:03 AM, Moshe Olshanskym_olshan...@yahoo.com wrote: Make it for (i in 1:9) Thanks. That's also how I solved the problem myself. I just somehow think it makes my code look rather clumsy and opaque. Maybe I just have to get used to this kind of nasty tricks. This is not the general solution, (...) What do you mean? It looks a like a very general solution to me. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Nested for loops
On Tue, Jul 14, 2009 at 8:20 AM, Michael Knudsenmicknud...@gmail.com wrote: What do you mean? It looks a like a very general solution to me. Just got an email suggesting using the functions col and row. For example temp = matrix(c(1:36),nrow=6) which(col(temp)row(temp)) This gives the indices (in the matrix viewed as a vector) of the above-diagonal entries. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Nested for loops
On Tue, Jul 14, 2009 at 1:56 PM, David Winsemiusdwinsem...@comcast.net wrote: temp[ upper.tri(temp) ] [1] 7 13 14 19 20 21 25 26 27 28 31 32 33 34 35 Thanks! I didn't know about that function; it certainly makes things a lot easier. For example, until now I have used the following, homemade expression (1:N^2)[which((1:N^2)!=seq(0,(N-1)*N,by=N)+(1:N))] to get the indices of the non-diagonal entries of a matrix :-) -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Nested for loops
On Tue, Jul 14, 2009 at 2:29 PM, Gabor Grothendieckggrothendi...@gmail.com wrote: seq. - function(from, to) seq(from = from, length = max(0, to - from + 1)) Really nice! Thank you! -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Combine two matricies
On Mon, Jul 13, 2009 at 11:31 AM, Tom Liptrot tomlipt...@hotmail.com wrote: I wish to combine these two into one matrix using the values from x where x has values, and values from a where x has NA's, giving a new matrix which would look like this: This should do the trick: x[which(is.na(x))]=a[which(is.na(x))] -- Michael Knudsen micknud...@gmail.com http://www.google.com/profiles/micknudsen __ 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] graph: axis label font
On Mon, Jul 13, 2009 at 5:31 PM, serbringbracard...@email.it wrote: excuse me for my english, i am using R on windows and i have to do several graphs with axis labels and the axis text thicks has a specified font type, (Arial) and a specified font size. How can i do these? Thank you in advance Interesting question, I didn't know the answer to, so I tried to look it up. There might be some help towards the bottom of this page: http://www.statmethods.net/advgraphs/parameters.html It seems to be specific for Windows, so I can't test it myself. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.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] Nested for loops
Hi,
I have spent some time locating a quite subtle (at least in my
opinion) bug in my code. I want two nested for loops traversing the
above-diagonal part of a square matrix. In pseudo code it would
something like
for i = 1 to 10
{
for j = i+1 to 10
{
// do something
}
}
However, trying to do the same in R, my first try was
for (i in 1:10)
{
for (j in (i+1):10)
{
// do something
}
}
but there's a problem here. For i=10, the last for loop is over 11:10.
Usually programming laguages would regard what corresponds to 11:10 as
empty, but A:B with A bigger than B is in R interpreted as the numbers
from B to A in reverse order.
Is there a clever way to make nested loops like the one above in R?
--
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.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.
