search for: hypergeometric

Dear R Users, There exists a non-central hypergeometric distribution function in the (MCMCpack) package, and a hypergeometric distribution function in the (stats) package. Is there a function for sampling from an extended hypergeometric distribution? Thanks, Narcyz This message is intended for the addressee named and may con...{{dropped}}

Hi, I hope somebody can help me on how to use the hypergeometric function. I did read through the R documentation on hypergeometric but not really sure what it means. I would like to evaluate the hypergeometric function as follows: F((2*alpha+1)/2, (2*alpha+2)/2 , alpha+1/2, betasq/etasq). I'm not sure which function should be used- either phyper or...

I have been reading, in various sources, that a poisson distribution is related to binomial, extending the idea to include numbers of events in a given period of time. In my case, the hypergeometric distribution seems more appropriate, but I need a temporal dimension to the distribution. I have weekly samples of two kinds of events: call them A and B. I have a count of A events. These change dramatically from one week to the next. I also have weekly counts of B events that I can relate to...

Is there any way to know how the "dmvt" function computes the hypergeometric function needed in the calculation for the density of multivariate t distribution? -- View this message in context: http://r.789695.n4.nabble.com/hypergeometric-function-in-mvtnorm-tp4483730p4483730.html Sent from the R help mailing list archive at Nabble.com.

...to estimate the likelihood that the number of genes overlapping between 2 different lists of genes is due to chance. This appears to work appropriately. Now i want to try this with 3 lists of genes which phyper() does not appear to support. Some googling suggests i can utilize the Multivariate hypergeometric distribution to achieve this. eg.: http://en.wikipedia.org/wiki/Hypergeometric_distribution But when i try to do this manually using the choose() function (see attempt below example with just two gene lists) i'm unable to perform the calculations- the numbers hit infinity before getting an...

For those who are interested, I have made available a R function for noncentral hypergeometric distribution at http://www.geocities.com/jg_liao/software/Hypergeometric/hypergeometric_in_R.txt The paper that describes the algorithm will appear in The American Statistician. The function does not run on S-plus as the R's scoping rule is used. Here is how the function can be used: &g...

Dear All, I am looking for an implementation in R of the Appell Hypergeometric function. Any suggestions will be more than appreciated! GP -- dr. Giovanni Parrinello External Lecturer Medical Statistics Unit Department of Biomedical Sciences Viale Europa, 11 - 25123 Brescia Italy Tel: +390303717528 Fax: +390303717488 email: parrinel at med.unibs.it

Hello. Somebody knows how to compute generalized hypergeometric series in R? (see http://functions.wolfram.com/HypergeometricFunctions/HypergeometricPFQ/02/ to understand what I mean) Thanks in advance, Arnau.

...7 and then I tried this command: (fisher.test(matrix(c(17,449,181,19551),2,2), alternative='greater'))$p.value [1] 3.693347e-06 Shouldn't be identical the results of the two commands ? What is the difference ? Thx a lot -- View this message in context: http://r.789695.n4.nabble.com/hypergeometric-vs-fisher-test-tp2324223p2324223.html Sent from the R help mailing list archive at Nabble.com.

I'd like to fit the (1-displaced) negative hypergeometric distribution to data samples such as the following:- x <- c(370, 311, 299, 266, 265, 232, 197, 198, 170, 154, 133, 123, 120, 103, 80, 72, 69, 67, 67, 50, 36, 35, 26, 23, 15, 11, 9, 6, 5, 3, 3, 2, 2, 2) i.e., I want to estimate the parameter values of K and M (with my data, n would usually be t...

A cut and paste typo has crept in and is rendering all values returned for the hypergeometric distribution incorrect. The problem is in src/main/arithmetic.c in the function "math4". The lines PROTECT(sy = allocVector(REALSXP, n)); a = REAL(sa); b = REAL(sb); c = REAL(sc); d = REAL(sc); /* <-- change this line */ y = REAL(sy);...

"help" We want to estimate the number of caribou in Jasper. We recently conducted an aerial survey and saw 70 uncollared caribou and 8 of 11 collared caribou. We want to estimate the number of caribou in this population with 95% confidence limits. Gary White uses the hypergeometric distribution and determines the population estimates using maximum likelihood and 95%CL as -2LogLikelihoods. Below, I determined the population estimate using dhyper(x,m,n,k) and maximizing the density value as a function of n, but do not know how I should calculate MLE with this distribution. x...

...l the four cases have to consider and so the resultant change of red balls will become 48.45 to 51.54 So my problem is, is there any convenient built-in function that helps extract this 95% confidence interval-like data? -- View this message in context: http://r.789695.n4.nabble.com/Retrieve-hypergeometric-results-in-large-scale-tp4644683.html Sent from the R help mailing list archive at Nabble.com.

In both versions of R to which I currently have access (R-0.16.1 and R-0.61.1), "phyper" stops returning correct cumulative probabilities as the parameters of the hypergeometric distribution get large. For example, when N1=1345, N2=1055, and n=1330, phyper returns either 0 or 1, and nothing in between. Looking at phyper.c, it's clear what's happening. First a term (called "term") is computed: term = exp(lfastchoose(NR, xr) + lfastchoose(NB, xb)...

Hi, I'm an R newbie and I've got a question regarding a certain function in R. I need to calculate values of the hypergeometric 2f1 function (hyp2f1 in cephes math library, Hypergeometric2f1 in Mathematica) and I'm wondering if anyone has tried to implement it in R or S-Plus. If not, what would be the prefered way to do so? Should I rather try to use an external C module or implement it in R directly? Thanks for any h...

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Dear list, I have performed several tests for the hypergeometric distribution using phyper() for some gene annotation categories as follows >phyper(26,830,31042,337, lower.tail=F) >phyper(16,387,31042,337, lower.tail=F) . . . I am only running some selected categories but I would like to correct this value for multiple testing since I have 3121 pos...

Dear All I have a question about the hypergeomteric distribution. Example 1: I have a universe of 6187 objects, and 164 have a particular attribute, therefore 6187-164 do not have that attribute. I sample 249 of those objects, and find that 19 have that attribute. I get a p-value here (looking at just over-representation): phyper(19, 164, 6187-164, 249, lower.tail=FALSE) [1] 7.816235e-06

...le being of size 'n = sum(x)'." The last paragraph suggests that in the goodness-of-fit case, if p gives the expected probability for each cell, this random sampling is multinomial. Unfortunately, as the following examples reveal, the sampling model is neither multinomial nor hypergeometric - at least when it is applied to a 4-fold table. This is rather sad as some people assume that R's chisq.test function can perform a Monte Carlo test of X-squared, employing a multinomial model - in other words, assuming that your data are a single random sample. ### Example 1. > x=mat...

Hello! I use R-version 1.0.0 To get the 0.95 quantile of the hypergeometric distribution with the parameters m=45000,n=5000 and k=600 I use the R-command > qhyper(0.95,45000,5000,600). The value obtained is 600. However, the true value is 552. The latter can be obtained for example by calling the corresponding distribution function with the R commands > x<-...