Displaying 20 results from an estimated 1000 matches similar to: "A question about the hypergeometric distribution and phyper()"
2008 Feb 27
1
dhyper, phyper (PR#10853)
Aloha all,
I know too little about what I'm about to write and hope I'm not
wasting your time.
For a class I'm teaching in archaeological data analysis, I'm trying
to put together a routine that calculates the so-called Petersen
index and, especially, confidence intervals for the index. This was
introduced to archaeologists by N.R.J. Fieller and A. Turner in an
article
2008 Dec 03
1
hypergeometric
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
2010 Mar 30
1
Multivariate hypergeometric distribution version of phyper()
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.:
2006 Jan 18
1
phyper returns 1 if x==k (PR#8499)
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
2003 Nov 14
2
Round error?
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
1998 Apr 03
1
R-beta: Bug in dhyper (and phyper) (fwd)
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
1998 Feb 23
0
R-beta: Hypergeometric Probabilities
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
2010 Aug 13
1
hypergeometric vs fisher.test
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:
2000 Mar 24
3
quantiles of the hypergeometric distribution (PR#502)
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<-540:580
>
2013 Mar 15
2
phyper returning zero
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
2004 Apr 15
0
phyper accuracy and efficiency (PR#6772)
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,
2007 Oct 02
1
phyper returns negative results
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
2012 Oct 01
1
Retrieve hypergeometric results in large scale
I'm going to use
dhyper(x, m, n, k)
to get a 95% coverage. Let me use an example to explain my problem:
Suppose I have a urn containing 90 red and 10 black balls.
Now I wanna remove 3 from the urn. By the following codes:
m<-90;n<-10;k<-3;
x<-0:3
dhyper(x,m,n,k)
I can obtain the probability that 0,1,2,3 red balls will be removed.
0.000742115 0.025046382 0.247680891
2008 Jan 15
0
FDR for hypergeometric tests
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 possible tests according to 3121
2004 Nov 24
1
(PR#7393) Re: dhyper() does not allow non-integer values for
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
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On Wed, 24 Nov 2004 Erik.Jorgensen@agrsci.dk wrote:
>
> dhyper() does not allow non-integer
2008 Aug 21
1
pnmath compilation failure; dylib issue?
(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
1997 Jul 09
1
R-beta: Problem with `rpois'
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
1997 Jul 09
1
R-beta: Problem with `rpois'
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
2003 Oct 01
1
hypergeometric & population estimates
"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
2004 Jul 07
1
negative p-value from fisher.test() (PR#7064)
Full_Name: Anja von Heydebreck
Version: 1.9.1
OS: Linux
Submission from: (NULL) (155.250.128.25)
I obtained a negative p-value from the fisher.test() function:
> fisher.test(matrix(c(14576,3023,89,68),2), alternative="g")$p.value
[1] -8.426593e-13
With R 1.8.1, I got a p-value of -6.239231e-12 for this example.
Anja von Heydebreck