similar to: Permutations

Dear R users, First of all, thanks for the incredibly fast answers and help of Rolf, Marc and Robert. Yes, I noticed that it was a lot of permutacions, but my intention was to make this process automatic and take only 5.000 - 10.000 permutations. Therefore, I wanted only to take that "interesting permutations" with "some information" [inter-block permutations]. The

Dear R users, This is a second summary of the permutation problem I previously posted. This summary restates the problem as well as the solution. First of all thanks to everyone including Erich, Robin, Gabor, Christian, Ingmar and others for your suggestions. With the help of an off-list discussion with Gabor I?m going to summarize. THE PROBLEM We have 12 elements in blocks of 3 : 1 2

J?r?me, As a first attempt, how about the function below. It works (or not) by randomly sorting the rows and columns, then searching the table for "squares" with the corners = matrix(c(1,0,0,1),ncol=2) and subtracting them from 1 to give matrix(c(0,1,1,0),ncol=2) (and vice versa). Randomized matrices can be produced as a chain where each permutation is seeded with the previous one.

Hi- General question: I have written a function that performs a permutation test. I use the function "sample" to randomize my data, then I call on another function I wrote to analyze the randomized data. This process repeats "n" times-- 10, 100 or whatever. The function applied to the randomized data creates a matrix and sometimes the matrix contains NaN's. I would

Hello,   is there a simple way to give all combinations for a given vector:   v<-c("a","b","c")   combination(v,v) becomes "aa","ab","ac","bb","bc","cc'   combination(v,v,v) becomes "aaa","aab","aac","abb",......     [[alternative HTML version deleted]]

Hi list, I tried to load the package SAGx and failed because it complains it's looking for the Biobass which is not there. Then I looked up the package list and Biobass is not found. I'm trying to run the Jonckheere-Terpstra test and from what I see in the R archive, SAGx is the only place it's been implemented. > library(SAGx) Loading required package: multtest Loading required

Dear all, Dose anyone know whether there is a good R packege or program for Mantel's randomization test? Thanks in advance. ------------------------ Takashi Mizuno zoono at sci.osaka-cu.ac.jp Plant Ecology Lab. Osaka City University ------------------------ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

Hi all Consider the classic data below from Darwin on the heights of 15 pairs of zea mays (corn) plants either cross-fertilized or self-fertilized, where the goal is to see if it makes a difference. > head(ZeaMays) pair pot cross self diff 1 1 1 23.500 17.375 6.125 2 2 1 12.000 20.375 -8.375 3 3 1 21.000 20.000 1.000 4 4 2 22.000 20.000 2.000 5 5 2 19.125

Dear R users, I want to perform an exact permutation of multisets. I have looked at the coin package, but it doesn't seem to offer what I am looking for. I want to perform permutations (exact - without duplications) on multisets of scalars (e.g., the multiset 0,0,1,2,2). I want to output all the possible permutations into a data frame so that each multiset permutation occupies a row (or

Dear all, I did a RDA and when I looked to the signification of the test with permutest, the output was non-significant. But when I used the envfit function, some of the vectors are significant. All the test's conditions are respected. What it means? Is it an error in the script? Commands and output: > permutest(rda.ind, perm=999, first=TRUE) Permutation test for rda  Call:

Dear R Programmers, I am trying to run a Poisson regression on all pairs of variables in a data set and obtain the permutation distribution. The number of pairs is around 100000. It seems my code will take weeks to run, unless I try something else. Could you give me any suggestions on how to improve the speed of the code below, or any general suggestions on how I may accomplish this task. Thanks

Hi I am using verion 2.0.10 of Shorewall. My configuration is as follows: Eth1 dmz1 ------------| __________ | | | Eth2 dmz2 | FIREWALL |------| INTERNET | ----------| | _______ | |__________| | |---------| |

Hello everybody, I have a question. I would like to get a correlation between constitutive and induced plant defence which I messured on 30 plant species. So I have table with Species, Induced defence (ID), and constitutive defence (CD). Since Induced and constitutive defence are not independant (so called spurious correlation) I should do a randomisation test. I have a syntax of my

Hi, I have a little problem that puzzles me about contradictory results returned by a bootstraped t-test (as in MASS 3rd ed p. 146) versus a permutation t-test (as in MASS 3rd ed, p 147). Data are measurements done on 100 cells in 9 slides of fish blood. With one method, cells are randomly sampled, and with the other method, the operator selects cells arbitrarily (in a way it is done usually

Apropos the question about permutation tests in multiple regression: We do have perm.test in package ExactRankTests, but it does one- and two-sample tests, as in t.test, wilcox.test, etc. There doesn't seem to be an exact version of the permutation test for correlations, i.e., the one that could be estimated using replicate(10000, cor(x,sample(y))) # or other values of 10000 or, of course,

Dear R users, I am trying to perform a hypothesis test on a marked point pattern. I would like to calculate the mean of the absolute value of the difference of marks between nearest neigbours, randomize the marks among points, then calculate this mean again. Ideally, I would test whether random mean values smaller than the observed mean value occur less than 5% of the time. I suppose 1000

Hello, I am using logistic discriminant analysis to check whether a known classification Yobs can be predicted by few continuous variables X. What I do is to predict class probabilities with multinom() in nnet(), obtaining a predicted classification Ypred and then compute the percentage P(obs) of objects classified the same in Yobs and Ypred. My problem now is to figure out whether P(obs) is

The gregmisc package contains a function 'perumutations' which generates all permutations of n choose r. It also contains 'combinations' which generates all combinations, and which appears to match your example: > library(gregmisc) Loading required package: MASS Attaching package `gregmisc': The following object(s) are masked from package:base :

Hi, I have a complex-valued vector X in C^n. Given another complex-valued vector Y in C^n, I want to find a permutation of Y, say, Y*, that minimizes ||X - Y*||, the distance between X and Y*. Note that this problem can be trivially solved for "Real" vectors, since real numbers possess the ordering property. Complex numbers, however, do not possess this property. Hence the

Hi, Is there a way to convert a matrix into a vector representing all permutations of values and column/row headings with native R functions? I did this with 2 nested for loops and it took about 25 minutes to run on a ~700x700 matrix. I'm assuming there must be a smarter way to do this with R's vector commands, but being new to R, I'm having trouble making it work. Thanks,