similar to: using R source as a library (a) for our own C++ code

Hi folks, I'm trying to call an R function (fisher.test) in my program for like a billion times! Though my program is in Python and I feel that using rpy2 to interface R to python doesn't give me satisfactory performance. So I looked into R code and found out that fisher.test is actually a wrapper around another function called fexact which is implemented in C. Using Cython I managed to

This is a bad bug as reported by Robin Hankin, it is still in "R-patched" ... ##- From: Robin Hankin <r.hankin@auckland.ac.nz> ##- To: r-help@stat.math.ethz.ch ##- Subject: [R] possum sleeping: thanks and fisher.test() FEXACT error ##- Date: Thu, 13 Jun 2002 16:46:26 +1200 ## ..... ## Example slighlty modified (MM) d4 <- matrix(c(0, 0, 0, 0, 0, 0, 3, 0, 1, 0, 0, 0, 0, 0,

(CC'ed to R-bugs ``for the record'') >>>>> "BDR" == Prof Brian D Ripley <ripley@stats.ox.ac.uk> writes: BDR> On Thu, 13 Jun 2002, Martin Maechler wrote: >> >>>>> "MM" == Martin Maechler >> <maechler@stat.math.ethz.ch> writes: >> >> >>>>> "BDR" ==

Dear all, I’m having an awkward problem in R. When I write the command Fisher.test(school.data,workspace=2e+07), where school.data is the matrix corresponding to the data set, I get the error message: FEXACT error 7. LDSTP is too small for this problem. Try increasing the size of the workspace. Increasing the workspace: Fisher.test(school.data,workspace=1e+10), I

Hello, I'm using R to apply Fishers exact test to a whole pile of contingency tables, and I've run into the bug shown below. regards, Francis -- > dat1 = matrix(c(0,1,0,1,0,0,1,0,0,0,1,0,1,0,0,1,0,0,0,1,0,1,0,0,1,0,0,0,0, 1,1,0,0,1,0,0,1,0,0,1,0,0,3,0,0,2,0,0,1,0,0,0,1,0,0,2,0,0, 2,0,0,1,0,1,0,0,3,0,0,2,0,0,0,1,0,5,0,0,0,1,0,1,0,0), nrow=3) >

Hi! I am Marta Colombo, student in Mathematical Engineering at "Politecnico di Milano". For my master degree thesis I have to analyze some categorical data. My dataset is composed by 327 individuals and 16 variables. I am using Fisher exact test to test independence on IxJ contingency tables, but I have a problem with one variable. R gives me this error message: FEXACT error 7.

Dear helplist Many many thanks to everyone who helped me. The trick was to use tabulate() or, better, tab <- rep(0,50) names(tab) <- 1:50 tab[names(table(sleeps))] <- table(c) My original dataset was a list of 50 trees and a length 12 vector recording which tree a certain possum slept in on 12 nights. As Professor Ripley points out, a Monte-Carlo simulation is easy to set up, and it

Hello, I have an error message that doesn't seem to make sense in that having read the R documentation I was under the impression that R was able to grab as much memory as it needed, and has been able to do so for some time, so the advice given below about increasing the size of the workspace is redundant. If I'm right, does anyone have a solution to the problem of the size of

I posted this last night but I think I figured out the problem. I checked on the underlying equation for the Fisher Exact Test for tables greater than 2X2. It looks like I have an insane amount of factorials to be multiplied. Is that problem? Is it an overflow issue? Jeff Last night’s post: I just a ran a fisher.test on a 9x5 table and received the following message

The hybrid feature in fisher.test looks to me like an excellent way to analyze my two-way tables. The only problem is that it does not seem to be implemented. Am I right about this? An example is pasted below. I note that I get the warning message only when I shouldn't: for a 2x2 table hybrid seems to be ignored without warning. In no case does fisher.test seem to be checking Cochran

Hi, I want to analyse a contigency table (3 x 12) with a fisher.test beacause there are cells that are less than 5. ?mmen Anken Baf Belchen H?chi Hof Porti R?m Schmutz Sch?n Sissa Tann class14 7 26 150 2 46 68 126 66 3 31 7 61 class24 7 6 55 5 49 71 93 90 1 18 16 79 class34 1 1 4 3 19 8 29 61

Hello out there, my first try to install a package (e.g. ctest from CRAN) didn't succeed; looking at the error messages I think it must be a configuration problem of my machine, but as I'm not very experienced I would be glad if someone could give me a hint ... R's version is 0.63.0, my i386-Linux is kernel 2.0.35. I hadn't had problems to compile R, and R itself seems to work.

Prof Brian D Ripley wrote: > > On Thu, 24 Aug 2000, Emmanuel Paradis wrote: > > > Dear All, > > > > We encountered an unexpected crash with R under Windows when running > > fisher.test(). We had this problem only under this OS and only with the > > following data: > > > > > T > > [,1] [,2] > > [1,] 2 1 > > [2,]

I want to ascertain the basis of the table ranking, i.e. the meaning of "extreme", in Fisher's Exact Test as implemented in 'fisher.test', when applied to RxC tables which are larger than 2x2. One can summarise a strategy for the test as 1) For each table compatible with the margins of the observed table, compute the probability of this table conditional on the

Dear all, I have a dataset with qualitative variables (factors) and I want to test the null hypothesis of independance between two variables for each pair by using appropriate tests on contingency tables. I first applied chisq.test and obtained dependance in almost all cases with extremely small p-values and warning messages. > chisq.test(table(data$ins.f, data$ins.st))$p.val [1]

I just a ran a fisher.test on a 9x5 table and received the following message Error in fisher.test(apaslg.t) : FEXACT error 30. Stack length exceeded in f3xact. This problem should not occur. I agree. The problem should not occur. I did some searching but only found other reports of the problem. Does anyone know of a fix? Jeff Internal Virus Database is out-of-date.

Dear All, I am using fexact.c on a C++ program I wrote. To minimize dependencies on other files (e.g., to not need to include R.h and ctest.h ---now I only include the R files Boolean.h, Constants.h, and Memory.h), I have re-written all declarations of Sints as ints and, what is potentially more serious, I have re-written the line (lines 329 and 330, in fexact.c on R-1.6.1) /* IMAX is the

I tried to build R-1.1.1 on my HP-UX 10.20 box. For this I installed gcc 2.95.2 and built g77 (version 2.95.2 19991024 (release)). Making R runs to the point, where shared libs are linked. There it reports: make[4]: Entering directory `/disk4/hoffmann/Work/rwork/src/library/ctest/src' gcc -I../../../../include -I/usr/local/include -fPIC -g -O2 -c

Sorry for leaving this one in my mail box for so long, but - well, I suppose you know what I mean. (I'm shifting it over to r-devel, so I'll include all your original text) Kurt Hornik <hornik@ci.tuwien.ac.at> writes: > Well, ctest is not making progress as quickly as I wanted it ... > Anyway, here are a few questions/remarks. > > * I am still a bit confused about

"Michael S. Tsirkin" <mst at redhat.com> writes: > Memory allocation for vhost-net now supports fallback on vmalloc (same > as for vhost-scsi) this makes it possible to create the device on > systems where memory is very fragmented, with slightly lower > performance. Thanks Michael, I'm glad to see that this change made its way into mainline after all! Would you