similar to: dhyper, phyper (PR#10853)

This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---1936847065-1111238301-1101309010=:193006 Content-Type: TEXT/PLAIN; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE On Wed, 24 Nov 2004 Erik.Jorgensen@agrsci.dk wrote: > > dhyper() does not allow non-integer

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

Full_Name: Utz J. Pape Version: 2.2.0 OS: linux Submission from: (NULL) (141.14.23.12) If I use phyper and set parameter x equal to k (meaning that all balls I draw are white) phyper returns 1 which is not (always) correct: pape at xxx:~> R2.2.0 --vanilla R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.0 (2005-10-06 r35749) ISBN 3-900051-07-0 R is free software

Last night I sent the bug report below to r-help. I have since then looked at dhyper.c and found: if (NR < 0 || NB < 0 || n <= 0 || n > N) DOMAIN_ERROR; I changed 'n <= 0' to 'n < 0' and then dhyper worked as I wanted. Am I introducing some potentially dangerous behaviour by this change? Goran

Hi, I am attempting to use phyper to test the significance of two overlapping lists. I keep getting a zero and wondered if that was determining non-significance of my overlap or a p-value too small to calculate? overlap = 524 lista = 2784 totalpop = 54675 listb = 1296 phyper(overlap, lista, totalpop, listb,lower.tail = FALSE, log.p=F) [1] 0 If I plug in some different values I get a p-value but

Full_Name: Morten Welinder Version: snapshot OS: Submission from: (NULL) (65.213.85.218) Time to kick phyper's tires... The current version has very serious cancellation issues. For example, if you ask for a small right-tail you are likely to get total cancellation. For example phyper(59, 150, 150, 60, FALSE, FALSE) gives 6.372680161e-14. The right answer is dhyper(0, 150, 150, 60,

Dear R-users, In R 2.5.1 on Windows XP, SP2 the call to phyper(0,0,74,3,lower.tail=FALSE) returns -4.195862e-17. This does not happen with R2.5.1 on Linux, 0 is returned. Is this a bug (and should be reported as such), since phyper should not return negative values, or is this considered as one of the annoyances of finite precision arithmetic. I tend to think of this as a bug since it breaks the

Dear R Users, I employed the phyper() function 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.:

There is a problem with `rpois'. It does seem to take care about the order of the arguments. This is an example: > rpois(n=1,lambda=2) [1] 3 > rpois(lambda=2,n=1) [1] 2 0 It obviously uses the first argument as the number of samples to be drawn, which is wrong. I used Version 0.49 Beta (April 23, 1997). Fredrik

There is a problem with `rpois'. It does seem to take care about the order of the arguments. This is an example: > rpois(n=1,lambda=2) [1] 3 > rpois(lambda=2,n=1) [1] 2 0 It obviously uses the first argument as the number of samples to be drawn, which is wrong. I used Version 0.49 Beta (April 23, 1997). Fredrik

Hi all, I have tried to compute a p-value for a hypergeometric distribution as: dhyper(x,k,l,n) + phyper(x,k,l,n,lower.tail=FALSE) and sometimes obtained negative values. Do you know if it is because a round error or am I doing something wrong? Thanks in advance, Aurora

lgamma(x) and lfactorial(x) are defined to return ln|Gamma(x)| {= log(abs(gamma(x)))} or ln|Gamma(x+1)| respectively. Unfortunately, we haven't chosen the analogous definition for lchoose(). So, currently > lchoose(1/2, 1:10) [1] -0.6931472 -2.0794415 NaN -3.2425924 NaN -3.8869494 [7] NaN -4.3357508 NaN -4.6805913 Warning message: In

(1) ...need to speed up a monte-carlo sampling...any suggestions about how I can get R to use all 8 cores of a mac pro would be most useful and very appreciated... (2) spent the last few hours trying to get pnmath to compile under os- x 10.5.4... using gcc version 4.2.1 (Apple Inc. build 5553) as downloaded from CRAN, xcode 3.0... ...xcode 3.1 installed over top of above after

>From: Sundar Dorai-Raj <sundar.dorai-raj at PDF.COM> >Reply-To: sundar.dorai-raj at PDF.COM >To: Zhen Pang <nusbj at hotmail.com> >CC: r-help at stat.math.ethz.ch >Subject: Vectorising and loop (was Re: [R] optim "a log-likelihood >function") >Date: Wed, 29 Sep 2004 18:21:17 -0700 > > > >Zhen Pang wrote: > >> >>I also use

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 qhyper or dhyper Where

Hello I have a time-comsuming program which need to simplify, I have tested the annotated program as follow: > #define function which will be call > calsta <- function(c, n=100000) + { + i <- seq(from=0, length=c) + logx <- lchoose(NT-n, CT-i) + lchoose(n, i) + logmax <- max(logx) + logmax + log(sum(exp(logx - logmax))) + } > CT=6000 #assignment to CT >

Hello, I've come across the following situation in R-1.8.1 (compile + running under RedHat 7.1): > phyper(24, 514, 5961-514, 53, lower.tail=T) [1] 1 > phyper(24, 514, 5961-514, 53, lower.tail=F) [1] -1.037310e-11 I'd expect the later to be 0 or some very small positive number. Is this a number under-flow of the calculation? Do you think I'm safe if I just set the result to 0

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

Dear R team, I have a simple question. I tried this command: phyper(17,449,19551,181, FALSE) [1] 1.47295e-07 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:

Hello T I want to order some calculation "result", there will be lots of "result" that need to calculate and order PS: the "result" is just a intermediate varible and ordering them is the very aim # problem: # For fixed NT and CT, and some pair (c,n). order the pair by corresponding result # c and n are both random variable CT<-6000 #assignment to CT