Re: [R] I'd like to request that my R CRAN package is not tested on Solaris OS

Just to add my personal cent to this: I've had similar issues with an R package some time ago, which kept crashing somewhat unpredictably in the Solaris tests. Debugging was hard because it only happened on Solaris, but in the end it turned out to be due to serious bugs in the code that only

Re: [R] Beginner problem - using mod function to print odd numbers

> > I don't understand. -- > > 7%%2=1 > 9%%2=1 > 11%%2=1 > > What aren't these numbers printing ? > > num<-0 > for (i in 1:100){ > num<-num+i > if (num%%2 != 0) > print(num) > } Your code tests the numbers 1, 3, 6, 10, 15, 21, 28, 36, 45, 55, 66, … and correctly prints the odd

Re: [R] Printing upon calling a function

> On 30 Nov 2020, at 10:41, Steven Yen wrote: > > Thanks. I know, my point was on why I get something printed by simply doing > line 1 below and at other occasions had to do line 2. > > me.probit(obj) That means the return value of me.probit() has been marked as invisible, so it won't

Re: [R] Question about PERL lookahead construct in regex's

> On 10 Aug 2020, at 18:36, Bert Gunter wrote: > > But this appears to be imprecise (it confused me, anyway). The usual sense > of "matching" in regex's is "match the pattern somewhere in the string > going forward." But in the perl lookahead construct it apparently must > **exactly** match

Re: [R] how to calculate odd ratios with R?

fisher.test() computes exact confidence intervals for the odds ratio. > On 6 Jul 2020, at 15:01, Luigi Marongiu wrote: > > Is there a simple function from some package that can also add a > p-value to this test? Or how can I calculate the p-value on my own?

Re: [R] Ubuntu 18.04 R repo bionic-cran35 seems to be broken

> On 28 Apr 2020, at 05:59, Yakov Goldberg wrote: > > I have not mispelled it. > That's how repo is added for Ubuntu. > The problem is: there is no Release file in that folder. But there is: https://cloud.r-project.org/bin/linux/ubuntu/bionic-cran35/Release So the problem must be

Re: [R] regex - optional part isn't considered in replacement with gsub

> On 27 Aug 2017, at 18:18, Omar André Gonzáles Díaz > wrote: > > 3.- If I make the 2 first letter optional with: > > ecommerce$sku <- > gsub("(.*)([a-zA-Z]?{2}[0-9]{2}[a-zA-Z]{1,2}[0-9]{2,4})(.*)", "\\2", > ecommerce$producto) > > "49MU6300" is capture, but again

Re: [R] Flummoxed by gsub().

> On 23 Aug 2017, at 07:45, Rolf Turner wrote: > > My reading of ?regex led me to believe that > >gsub("[:alpha:]","",x) > > should give the result that I want. That's looking for any of the characters a, l, p, h, : . What you meant to say was

Re: [R] Sparse (dgCMatrix) Matrix row-wise normalization

> On 4 May 2017, at 20:13, Murat Tasan wrote: > > The only semi-efficient method I've found around this is to `apply` across > rows (more accurately through blocks of rows coerced into dense > sub-matrices of P), but I'd like to try to remove the looping logic from my >

Re: [R] Using R and Python together

> On 30 Mar 2017, at 23:37, Kankana Shukla wrote: > > I have searched for examples using R and Python together, and rpy2 seems > like the way to go, but is there another (easier) way to do it? Rpy2 would seem to be a very easy and convenient solution. What do you need

Re: [R] fisher.test function error

> On 30 Mar 2017, at 11:51, Eshi Vaz wrote: > > When trying to computer a fisher’s exact test using the fisher.test function > from the gmodels() package, < The problem seems to be with a different fisher.test() function from the gmodels package, not with

Re: [R] multiplying a matrix by a vector

> On 4 Nov 2016, at 17:35, peter dalgaard wrote: > > Notice though, that Bert loses (or _should_ lose) for larger values of N, > since that method involves O(N^3) operations whereas the other two are > O(N^2). I am a bit surprised that sweep() is so inefficient even at

Re: [R] Resample with replacement to produce many rarefaction curves with same number of samples

> On 8 Sep 2016, at 16:25, David L Carlson wrote: > > Sampling without replacement treats the sample as the population for the > purposes of estimating the outcomes at smaller sample sizes. Sampling with > replacement (the same as bootstrapping) treats the sample as one

Re: [R] Resample with replacement to produce many rarefaction curves with same number of samples

> On 7 Sep 2016, at 00:07, Nick Pardikes wrote: > > Is there any way to use rarecurve to resample a community (row) with > replacement the same number of times for all 50 communities? With > replacement is important because the communities differ greatly in their > size

Re: [R] strange behavior of lchoose in combinatorics problem

Dear Gonçalo, thanks for the additional information – I think I get now what you're trying to do. > On 27 Jun 2016, at 06:35, Gonçalo Ferraz wrote: > > probabilities in lpvec should be <=1, but it is not. The sum is something on > the order of 1.48e-13.” > It is

Re: [R] strange behavior of lchoose in combinatorics problem

Why do you want to do this? Why not simply use Fisher's exact test? N <- 2178 N1 <- 165 N2 <- 331 J <- 97 ct <- rbind(c(J, N1-J), c(N2-J, N-N1-N2+J)) fisher.test(ct) Background explanation: - Your formula computes the log hypergeometric probability for a contingency table as ct above, but

Re: [R] Scaling rows of a large Matrix::sparseMatrix()

> On 13 Jan 2016, at 02:50, tomdhar...@gmail.com wrote: > > So my question is: How can the rows of a large sparse matrix be > efficiently scaled? If you're not picky about the particular storage format, the "wordspace" package http://wordspace.r-forge.r-project.org/ has an efficient

Re: [R] RGL Problem

> On 24 Nov 2015, at 13:32, Duncan Murdoch wrote: > >> Perhaps it would make sense always to use the well-known standard XQuartz >> paths on Mac and only consider other locations if explicitly asked for by >> the user? > > If rgl is using non-standard features in

Re: [R] RGL Problem

> On 23 Nov 2015, at 11:50, Duncan Murdoch wrote: > > The OSX binary version of rgl on CRAN is ancient. You'll need to reinstall > it from source for a current one. Since you bring up this point: any chance of getting Mac binaries from CRAN again? Rgl is a

Re: [R] package implementing continuous binomial?

I don't think Benjamin should use the zipfR package just for these functions [and even the zipfR package help page on these can be read as saying so .. ] Exactly. They are simply there because it's much easier to write and read code with wrappers that parametrize the incomplete Beta and

Re: [R] Two-tailed exact binomial test with binom.test and sum(dbinom(...))

If your null hypothesis is that the probability of a success is 0.6, i.e. H0: p=0.6, then those (a) Let's also assume we have an H1 that there are more than 6 successes (b) Now let's assume we have an H1 that there are fewer than 6 successes (1). My understanding would be that, if we

Re: [R] Finding unique elements faster

On 8 Dec 2014, at 21:21, apeshifter ch_k...@gmx.de wrote: The last relic of the afore-mentioned for-loop that goes through all the word pairs and tries to calculate some statistics on them is the following line of code: typefreq.after1[i]-length(unique(word2[which(word1==word1[i])])) (where

Re: [R] R write strange behavior in huge file

You probably told R to write out the file as a single long line with fields separated alternately by 380 TABs and one newline � that�s what the ncol argument does (write is just a small wrapper around cat()). cat() doesn�t print lines that are longer than 2 GiB, so it will insert an extra \n

Re: [R] Fast way to populate a sparse matrix

On 24 Apr 2014, at 23:56, Greg Snow 538...@gmail.com wrote: library(Matrix) adjM - Matrix(0,nrow=10,ncol=10) locs - cbind( sample(1:10), sample(1:10) ) vals - rnorm(10) adjM[ locs ] - vals ... and once you've got your data in this format, why not construct the sparse matrix

Re: [R] GotoBLAS2 with multiple cores

Your report sounds somewhat similar to problems I encountered with OpenBLAS on Ubuntu Linux (which is a maintained version of GotoBLAS; I couldn't get the latter to compile properly). OpenBLAS uses OpenMP for parallelization. Once linked into R, other OpenMP-based code would only use a single

Re: [R] Small p from binomial probability function.

Sounds like you want a 95% binomial confidence interval: binom.test(N, P) will compute this for you, and you can get the bounds directly with binom.test(N, P)$conf.int Actually, binom.test computes a two-sided confidence interval, which corresponds roughly to 2.5 and 97.5

Re: [R] Random Projection

On 3 Oct 2013, at 22:39, Monaghan, David dmonag...@gc.cuny.edu wrote: I was wondering, has anyone has encountered an R package that performs random projection/random mapping? RP is a procedure that is akin to Principal Components Analysis in that it accomplishes dimensionality reduction,

Re: [R] SVD on very large data matrix

On 8 Apr 2013, at 23:21, Andy Cooper andy_coope...@yahoo.co.uk wrote: So, no one has direct experience running irlba on a data matrix as large as 500,000 x 1,000 or larger? I haven't used irlba in production code, but ran a few benchmarks on much smaller matrices. My impression was (also

Re: [R] Package check using --as-cran

sh: de: command not found ERREUR : loading failed for ‘i386’, ‘x86_64’ * removing ‘/Users/marcgirondot/Documents/Espace de travail R/Phenology/Source fit/Phenology Package/phenology.Rcheck/phenology’ Looks to me like it might be an issue with whitespace in the directory path. In

Re: [R] Any better way of optimizing time for calculating distances in the mentioned scenario??

On 12 Oct 2012, at 09:46, Purna chander wrote: 4) scenario4: x-read.table(query.vec) v-read.table(query.vec2) v-as.matrix(v) d-dist(rbind(v,x),method=manhattan) m-as.matrix(d) m2-m[1:nrow(v),(nrow(v)+1):nrow(x)] print(m2[1,1:10]) time taken for running the code: real0m0.445s

Re: [R] Efficient distance calculation on big matrix

It so happens I have been looking at very similar changes, as well as adding multi-threading support for dist(); these should make it into R-devel later this summer. That's good to hear! I was thinking about giving OpenMP a try in my package, but am not sure whether it's worth the overhead

Re: [R] Efficient distance calculation on big matrix

I'm working on analyzing a large data set, lets asume that dim(Data)=c(1000,8700). I want to calculate the canberra distance between the columns of this matrix, and using a toy example ('test' is a matrix filled with random numbers 0-1): system.time(d-as.matrix(dist(t(test), method =

Re: [R] Inf and lazy evaluation

Oh, what is this world coming to when you can't count on laziness to be lazy. ;) I should probably stop reading about Haskell and their lazy way of doing things. Haskell would still have to check an infinite number of potential files on your hard disk, because it can't now when it's seen

Re: [R] Fast version of Fisher's Exact Test

Is anyone aware of a fast way of doing fisher's exact test for a series of 2 x 2 tables in R? The fisher.test is really slow if n1=1000 and n2 = 1000. If you don't require exact two-sided p-values (determined according to a likelihood criterion as in fisher.test), you can use the vectorised

Re: [R] Speed up sum of outer products?

), but vecLib BLAS beats CUDA by a factor of 2. Kudos to the gputools developers: despite what the README says, the package compiles out of the box on Mac OS X 10.6, 64-bit R 2.12.1, with CUDA release 3.2. Thanks for this convenient package! Best regards, Stefan Evert [ stefan.ev...@uos.de

Re: [R] create a pairwise coocurrence matrix

If I understood you correctly, you have this matrix of indicator variables for occurrences of terms in documents: A - matrix(c(1,1,0,0,1,1,1,0,1,1,1,0,0,0,1), nrow=3, byrow=TRUE, dimnames=list(paste(doc,1:3), paste(term,1:5))) A and want to determine co-occurrence counts for pairs of

Re: [R] plotting Zipf and Zipf-Mandelbrot curves in R

Hi! Using R, I plotted a log-log plot of the frequencies in the Brown Corpus using plot(sort(file.tfl$f, decreasing=TRUE), xlab=rank, ylab=frequency, log=x,y) However, I would also like to add lines showing the curves for a Zipfian distribution and for Zipf-Mandelbrot. It's fairly

[R] unz() ignores encoding argument

rev52157 language R version.string R version 2.11.1 (2010-05-31) but have been looking at the current R-devel source code, so I suspect my problem won't just go away with the next release. Best regards, Stefan Evert

Re: [R] 3D stariway plot

On 24 Aug 2010, at 02:20, Ben Bolker wrote: Please, is there an R function /package that allows for 3D stairway plots like the attached one ? In addition, how can I overlay a parametric grid plot?? Not exactly, that I know of, but maybe you can adapt library(rgl) demo(hist3d) to

Re: [R] Layering multiple persp plots

On 30 Jul 2010, at 19:22, Ian Bentley wrote: I've got two persp plots with Identical X and Y's, and I'd like to plot them on the same graph, so that it is obvious where one plot is above the other. I can't find any mention of this anywhere. Do I need to use wireframe? You can do it with

Re: [R] regularised incomplete beta function

On 16 Dec 2009, at 21:40, Ravi Varadhan wrote: ?pbeta And the zipfR package wraps these in terms of the usual terminology for incomplete/regularised upper/lower Beta functions (see ?Rbeta there), for people like me who can't get their head around the equivalence between the Beta

Re: [R] Regularized gamma function/ incomplete gamma function

Indeed, it seems that the author of zipfR has neither been aware that the (scaled / aka regularized) incomplete gamma (and beta, for that matter!) functions have been part of R all along. ... ... well , inspecting his code reveals he did know it. But why then on earth provide all the

Re: [R] Regularized gamma function/ incomplete gamma function

I would be very grateful if you could help me with: Given the regularized gamma function Reg=int_0^r (x^(k-1)e^(-x))dx/ int_0^Inf (x^(k-1)e^(-x))dx ; 0rInf (which is eventually the ratio of the Incomplete gamma function by the gamma function), does anyone know of a package in R that would

Re: [R] python

Sure, badly written R code does not perform as well as well written python code or C code. On the other hand badly written python code does not perform as well as well written R code. What happens when you try one of these : sum - sum( 1:N ) R runs out of memory and crashes. :-) I didn't

Re: [R] python

My hunch is that Python and R run at about the same speed, and both use C libraries for speedups (Python primarily via the numpy package). That's not necessarily true. There can be enormous differences between interpreted languages, and R appears to be a particularly slow one (which

Re: [R] sorting table output

I would like to have the output sorted in descending order by height or frequency. But when I do the following: rev(table(xx)) xx T G C A 15 10 12 13 Err, I guess you meant to write sort(table(xx)) here? Cheers, Stefan __

Re: [R] reference on fisher.test()

, Author = {Agresti, Alan}, Journal = {Statistical Science}, Number = 1, Pages = {131--153}, Source = {JSTOR}, Title = {A Survey of Exact Inference for Contingency Tables}, Volume = 7, Year = 1992} Best regards, Stefan Evert [ stefan.ev

Re: [R] image() generates many border lines in pdf, not on screen (quartz) - R 2.9.1 GUI 1.28 Tiger build 32-bit (5444) - OS X 10.5.8

On 23 Aug 2009, at 20:26, Uwe Ligges wrote: Since it looks like nobody answered so far: Your code is not reproducible, we do not have rfc, y, zVals nor NoCols. It's much easier to reproduce: just type in the first example from the image help page x - y - seq(-4*pi, 4*pi,

Re: [R] image() generates many border lines in pdf, not on screen (quartz) - R 2.9.1 GUI 1.28 Tiger build 32-bit (5444) - OS X 10.5.8

Your code is not reproducible, we do not have rfc, y, zVals nor NoCols. It's much easier to reproduce: just type in the first example from the image help page x - y - seq(-4*pi, 4*pi, len=27) r - sqrt(outer(x^2, y^2, +)) image(z = z - cos(r^2)*exp(-r/6), col=gray((0:32)/32)) then

Re: [R] RSPerl and Statistics::R

(see http://www.rforge.net/Rserve/) . Best, Stefan Evert [ stefan.ev...@uos.de | http://purl.org/stefan.evert ] __ 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

Re: [R] Newbie R question PART2

the little r comes from littler [1]. it doesn't claim to be larger than it is. [1] http://dirk.eddelbuettel.com/code/littler.html Unless you're working on a Mac or Windows (if I'm not mistaken about case handling there), where it will just overwrite the standard R interpreter. :-(

Re: [R] R interpreter not recognized

Dear Maria, this is quite probably my faul, in some way. The UCS software has been abandoned a bit recently, as I'm planning to rewrite it into a pure R package. On the other hand, I still use the software occasionally, so it should work with recent R versions. I am trying to install

Re: [R] statistical significance of accuracy increase in classification

On 26 Feb 2009, at 14:14, Max Kuhn wrote: Do you know about any good reference that discusses kappa for classification and maybe CI for kappa??? You might also want to take a look at this survey article on kappa and its alternatives: Artstein, Ron and Poesio, Massimo (2008). Survey

Re: [R] [Rd] Semantics of sequences in R

can you please stop repeating this nonsense? I don't think anybody ever claimed that vectors can be considered list. yes, it is nonsense. yes, there is one person who repeatedly made this claim. please read the archives; specifically, [1]. note this statement: Note that any

Re: [R] Alternate to for-loop

I ran into a similar issue with a simple benchmark the other day, where a plain loop in Lua was faster than vectorised code in R ... hmm, would you be saying that r's vectorised performance is overhyped? or is it just that non-vectorised code in r is slow? What I meant, I guess, was

Re: [R] Alternate to for-loop

(f.rep(10, 100)) user system elapsed 4.109 0.028 4.172 system.time(f.pat(10, 100)) user system elapsed 1.580 0.134 1.739 Best regards, Stefan Evert [ stefan.ev...@uos.de | http://purl.org/stefan.evert ] PS: Don't feed trolls who say that Lua is better than R

Re: [R] How to handle large numbers?

to know which of the numbers are large in order to do this right ... Best regards, Stefan Evert [ stefan.ev...@uos.de | http://purl.org/stefan.evert ] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Mac OS X / preview.app / fullrefman.pdf

when reading R's fullrefman.pdf (available from http://cran.r-project.org/doc/manuals/fullrefman.pdf) in Mac OS X's preview.app (version 4.1, on Mac OS 10.5.x), if i try to do a keyword search within the document, the indexing step freezes about 2/3 the way through the progress bar. this

Re: [R] Using optim with exponential power distribution

it even smaller if the fitted function is much larger than the actual y values, so all differences are negative). You probably wanted to minimise the squared errors: sum((y - b/(2*pi*a^2*gamma(2/b))*exp(-(x/a)^b)))^2) Best regards, Stefan Evert [ stefan.ev...@uos.de | http

Re: [R] Zipf fitting using R

our zipfR package available from CRAN. The tutorial and background materials at http://zipfR.R-Forge.R-project.org/ should help you to get started and will also explain how to calculate the coefficients of Zipf's law from estimates of the model parameters. Best regards, Stefan Evert

Re: [R] Spatial Statistics e-book.

Well, I suppose he might get away with it as long as said *Brian Ripley* doesn't read this list ... ;-) Sorry, couldn't resist, Stefan On 28 Dec 2008, at 21:07, stephen sefick wrote: Is that an appropriate request? On Sun, Dec 28, 2008 at 2:14 PM, Marcus Vinicius mvi...@gmail.com wrote:

Re: [R] Regex: workaround for variable length negative lookbehind

Hi Stefan! :-) From tools where negative lookbehind can involve variable lengths, one would think this would work: grep((?!(?:\\1|^))(.)\\1{1,}$, vec, perl=T) But then R doesn't like it that much ... It's really the PCRE library that doesn't like your regexp, not R. The problem is

Re: [R] Regex: workaround for variable length negative lookbehind

But is there a one-line grep thingy to do this? Can't think of a one-liner, but a three-line solution you can easily enough wrap in a small function: vec-c(, baaa, bbaa, bbba, baamm, aa) idx.1 - grep((.)\\1$, vec) idx.2 - grep(^(.)\\1*$, vec) vec[setdiff(idx.1, idx.2)] Oops, my bad,

Re: [R] More than doubling performance with snow

I'm sorry but I don't quite understand what not running solve() in this process means. I updated the code and it do show that the result from clusterApply() are identical with the result from lapply(). Could you please explain more about this? The point is that a parallel processing framework

Re: [R] Calculating sum of letter values

How about this? as.numeric(factor(unlist(strsplit(ECX, )), levels=LETTERS)) Best regards, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert ] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] how to test for the empty set

(x) == 0 do the trick? Or am I missing something? Best regards, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert ] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] pdf device: rasterize portions of the plot to reduce file size

-line options are: pstoimg -type png -depth 24 -antialias -scale 2 plot.eps Use the -scale option to generate the desired bitmap size. Best regards, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert ] __ R-help@r-project.org

Re: [R] Mathematica now working with Nvidia GPUs -- any plan for R?

in thinking that R only works with double precision?) According to the nVidia Web site, the Tesla architecture is _ten times_ slower for double-precision operations than for single- precision, which makes it seem far less amazing than at first sight. Best regards, Stefan Evert [ [EMAIL PROTECTED

Re: [R] ? extended rep()

On 20 Oct 2008, at 22:57, (Ted Harding) wrote: I'm wondering if there's a compact way to achieve the following. The dream is that one could write rep(c(0,1),times=c(3,4,5,6)) which would produce # [1] 0 0 0 1 1 1 1 0 0 0 0 0 1 1 1 1 1 1 in effect recycling x through 'times'. rep2 -

Re: [R] several postscript problems

will usually mess up your bounding box and revert to a standard page size. Best regards, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert ] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] Bug in is ?

into the same trap more than once, and painfully, myself (often in connection with MySQL). Best wishes, and with a tiny grain of salt, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert ] [[alternative HTML version deleted

Re: [R] fast value replacement in (numeric) vector

elapsed 0.508 0.552 1.054 I suppose that's the fastest you can get because of R's copy-on-write semantics (if I understand the R internals correctly, it's always a bit magical to me ...) Best regards, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert

Re: [R] A question about the hypergeometric distribution and phyper()

(M, beside=TRUE, legend = TRUE) Best regards, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert ] __ 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

Re: [R] instal tar.gz package on windows

regards, Stefan Evert [ [EMAIL PROTECTED] | http://purl.org/stefan.evert ] __ 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

Re: [R] Case statements in R

And you may want to consider using the 'cut' function. In your case, something like veg_mean - cut(veg_mean, breaks=c(0,.1,1,2,5,10,25,50,75,95,100), right=FALSE) should do the trick (see ?cut for more options). Best, Stefan On 28 Jul 2008, at 19:52, Henrik Bengtsson wrote: Use ''