similar to: FW: Optimising code

Hi, Does anyone have any advice on speeding up R functions (short of re-implementing them in C :-) )? I have a function that applies a wilcoxon test to 12 sets of about a quarter of a million pairs (and takes about 3 hours). I've replaced the inner loop I had originally with a function call via mapply, and also considered different approximations of the wilcoxon, rather than that which is

I have a question concerning the Wilcoxon signed-rank test, and specifically, which R subroutine I should use for my particular dataset. There are three different commands in R (that I'm aware of) that calculate the Wilcoxon signed-rank test; wilcox.test, wilcox.exact, and wilcoxsign_test. When I run the three commands on the same dataset, I get different p-values. I'm hoping that

The function 'wilcox.test' in R and S gives (almost) identical results (see below). 'qwilcox' however, does not: > qwilcox(p,5,5) p: 0.025 0.975 -------------------- R> 3 22 S> 18 37 I originally wanted to ask a questions, but then I found the answer. Given the confusion I run into, I wonder if this experience is worth reporting. The

how do I check the rank of a matrix ? say A= 1 0 0 0 1 0 then rank(A)=2 what is this function? thanks I did try help.search("rank"), but all the returned help information seem irrelevant to what I want. I would like to know how people search for help information like this. rank(base) Sample Ranks SignRank(stats) Distribution of the

Hi, I have a data set: > Dataset X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14 X15 X16 X17 1 user1 m 22 19 28 24 12 18 9 7 4 5 4 7 5 7 9 2 user2 f 25 19 23 18 18 15 6 8 6 6 7 10 7 7 7 3 user3 f 28 21 24 18 15 12 10 6 7 9 5 10 5 9 5 4 user4 f 26 19 26 21 12 18 6 6 5 1 3 8 6 5 6 5 user5 m 21 22 26 18 9 6 4 6 1

Help needed! Has anyone access to StatXact? I just hacked exact two-sided p-values for rank tests (for package exactDistr, which will move to CRAN/contrib as exactRankTests soon ;-) and would like to compare the results of my implementation to that of StatXact. Could someone please calculate the exact one-sided (both greater and less) and two-sided p-values? # Data from the StatXact-4 manual,

Hello, I use t.test for normal distributed and wilcox.test for non-normal distributed samples. It is easy to write a function for t.test that calculates the effect size, because all parts of the formula are available from the t.test result: r = sqrt(t*t / (t*t + df)) However, for Wilcoxon tests, the formula for effect sizes is: r = Z / sqrt(N) I wonder how I can calculate the Z-score in R for

Hi. I'm going to introduce the R-package for a group of medical doctors later this week and is a little confused about there use of a test named "willcoxon-pratt" for testing if the clinical and biochemical markers has decreased significantly after the use of some drugs for a group of patients. Looking into the R-functions I would in R recommand using a matched-pairs Wilcoxon

>>>>> Karolis Koncevi?ius >>>>> on Mon, 9 Dec 2019 23:43:36 +0200 writes: > So I tried adding Infinity support for all cases. > And it is (as could be expected) more complicated than I thought. "Of course !" Thank you, Karolis, in any case! > It is easy to add Inf support for the test. The problems start with conf.int=TRUE.

Thank you for a fast response. Nice to see this mailing list being so alive. Regarding Inf issue: I agree with your assessment that Inf should not be removed. The code gave me an impression that Inf values were intentionally removed (since is.finite() was used everywhere, except for paired case). I will try to adjust my patch according to your feedback. One more thing: it seems like you

Hi all, I have a distribution, and take a sample of it. Then I compare that sample with the mean of the population like here in "Wilcoxon signed rank test with continuity correction": > wilcox.test(Sample,mu=mean(All), alt="two.sided") Wilcoxon signed rank test with continuity correction data: AlphaNoteOnsetDists V = 63855, p-value = 0.0002093 alternative hypothesis:

Dear List, after updating the exactRanksumTests package I receive a warning that the package is not developed any further and that one should consider the coin package. I don't find the signed rank test in the coin package, only the Wilcoxon Mann Whitney U-Test. I only found a signed rank test in the stats package (wilcox.test) which is able to calculate the exact pvalues but unfortunately

Dear everyone, I am trying to do a Wilcoxon one-sided test on my gene expression data. These are the data i have in R: data.matrix (matrix, numeric) containing all gene expression data (42 rows=genes, 42 columns=tumors), no column header or row names data.cl (vector, numeric) consisting of 42 0's and 1's to indicate class 0 or class 1 for each column in data.matrix I want to do a

Dear R-ers, I am currently running some Wilcoxon tests in R-64. How do I find the degrees of freedom in the output I am receiving? > wilcox.test(good$TRUE, good$x4a, paired=FALSE) Wilcoxon rank sum test with continuity correction data: good$TRUE and good$x4a W = 2455, p-value < 2.2e-16 alternative hypothesis: true location shift is not equal to 0 Thank you, Stephen.

This is my first post to the mailing list and I guess it's a pretty stupid question but I can't figure it out. I hope this is the right forum for these kind of questions. Before I started using R I was using STATA to run a Wilcoxon signed-rank test on two variables. See data below:

When I use wilcox.test, I get vastly different p-values than the problems from Statistics textbooks. For example: The following problem comes from "Applied Statistics and Probability for Engineers", 2nd Edition, by D. C. Montgomery. Page736, problem 14.7. The problem is to compare the sample data with a population median of 8.5. The book answer is p = 0.25, wilcox.test answer is p =

Hi there, I'm a total newbie to R. I'd like to use a Wilcoxon Rank Sum test to compare two populations of values. Further, I'd like to do this simultaneously for 114 sets of values. The two populations are C and N. The different sets of values have arbitrary names (I'll call them a, b, c etc). The set-up is as follows: a b c d .... C 2 C 3 C 5 C 9 C 4

Por si alguno pudiera ayudarme. Al realizar el t.test para una muestra, junto con el valor de t y el p-valor, la función proporciona la estimación de la media y su INTERVALO DE CONFIANZA. Desde el punto de vista de la estadística de rangos esto se puede hacer mediante: > iris$MEDIANA <- with(iris, 2.95) > median(iris$Sepal.Width - iris$MEDIANA, na.rm=TRUE) # median difference [1]

Dear, I'm using R software to evaluate Wilcoxon Rank Sum Test and I' getting one Warning message as this: > C1dea_com [1] 1.000 0.345 0.200 0.208 0.508 0.480 0.545 0.563 0.451 0.683 0.380 0.913 1.000 0.506 > C1dea_sem [1] 1.000 0.665 0.284 0.394 0.509 0.721 0.545 0.898 0.744 0.683 0.382 0.913 1.000 0.970 > wilcox.test(C1dea_sem,C1dea_com, paired = TRUE, alternative =

Hello, I am hoping someone could shed some light into the Wilcoxon Rank Sum Test for me? In looking through Stats references, the Mann-Whitney U-test and the Wilcoxon Rank Sum Test are statistically equivalent. When using the following dataset: m <- c(2.0863,2.1340,2.1008,1.9565,2.0413,NA,NA) f <- c(1.8938,1.9709,1.8613,2.0836,1.9485,2.0630,1.9143) and the wilcox.test command as