similar to: Does R implement Hypergeometric test?

Dear r-users, I want to use the Cox's ph model to analyze survival data set. How can I extract the model coefs. and Wald test p-value or Score? For example: I use the data set melanom in iSwR package. > library(survival) > data(melanom) > attach(melanom) > cox.model <- coxph(Surv(days,status==1)~sex) > summary(cox.model) Call: coxph(formula = Surv(days, status == 1) ~

I try to do single proportion test on my category data. Here is my R script: library("ctest") catSignifTest <- function( catFile ) { ############################################################### ## Get the data sets from text file catData <- read.table( catFile ) ncols <- length(catData) nrows <- length(catData[,1]) ncol1 <- ncols - 1 probeNbr

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 qhyper or dhyper Where

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.

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.:

I'm doing prediction of the survival cases using gene expression profiles(Affymetrix chips). Can somebody tell me how to use the Cox PH model to select genes and make a prediction of survival? Thanks. Guangchun

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. 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.

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

"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

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); should

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

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

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

Dear R-users/helpers, Does anyone tell me how to retrieve the data frame column names? I'm working on coxph model to analyze survival data of Affy DNA chips. I get the coxph coef p-value for each probe and want output the probe name with the p-value. The probe names are the data frame column names. How can I do this? Thanks for your help. Guangchun

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 >

Dear All, I am trying to fiugre out how install packages on the base system. The "FAQ" tells me that more details can be obtained by typing "help(install.packages)", but my R system gives me an error message when I did that. I also tried "help(PACKAGES)", "help(install.packages())", but none worked. Anybody can help? I am running R 1.1.1 on WinNT 4.

[this message needed manual improvement by the mailing list administrator since it was `HTMLified' .. ``please do not''] Apologies for bothering you about a fairly trivial matter. I have been getting some inconsistencies with the display digits in R V1.5. I have been using the hypergeometric distribution function, and have found that when printing out the results from this

Hi, Who should I ask about my package Rigroup_0.83 being moved to Archive status on CRAN and no longer available via install.package? I have no problems with the move if this was simply because of low demand. However, if there was a build issue with the newest releases that caused problems, I would be happy to address it. I'll just ask my students to install it from my own locally hosted