As a follow up, I found out the proc freq in SAS can perform the exact permutation trend test.
Hanna 2016-01-08 9:30 GMT-05:00 li li <hannah....@gmail.com>: > Thanks Bert. > > > 2016-01-07 13:39 GMT-05:00 Bert Gunter <bgunter.4...@gmail.com>: > >> Sorry -- neglected to reply to the list. -- Bert >> >> >> >> ---------- Forwarded message ---------- >> From: Bert Gunter <bgunter.4...@gmail.com> >> Date: Thu, Jan 7, 2016 at 10:38 AM >> Subject: Re: [R] exact trend test (enumerate all possible contingency >> tables with fixed row and column margins) >> To: li li <hannah....@gmail.com> >> >> >> I do not know whether there is any package to do what you want. >> >> I **do** know that the algorithms required to do this are very >> sophisticated and that with more than a few groups, all possible >> enumerations are out of the question so that approximating shortcuts >> must be used. See http://www.cytel.com/software-solutions/statxact for >> some background. >> >> I **suspect** that you have no need to do what you have requested and >> **suggest** that you consult a local statistician or >> stats.stackexchange.com for another approach to whatever your >> underlying issue is. >> >> Cheers, >> Bert >> Bert Gunter >> >> "The trouble with having an open mind is that people keep coming along >> and sticking things into it." >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >> >> >> On Thu, Jan 7, 2016 at 10:18 AM, li li <hannah....@gmail.com> wrote: >> > I did check the coin package before. I did not see a function in that >> > package that can be used to list all the possible contingency tables >> with >> > fixed margins. >> > Of course I googled "exact trend test using R". There is not enough help >> > there. >> > For up to three groups, I can easily enumerate all the contingency table >> > with fixed margins, but with 5 groups it is not that easy. >> > But as mentioned before, this is done implicitly and routinely in >> > fisher.test function in R. So if anyone who have done this in R before, >> > please help. >> > Thanks. >> > Hanna >> > >> > >> > 2016-01-07 12:20 GMT-05:00 Michael Dewey <li...@dewey.myzen.co.uk>: >> > >> >> You received a number of suggestions about where to look and packages >> that >> >> might be suitable. Did you do that? If you did which ones did you look >> at >> >> and why did you reject them? >> >> >> >> >> >> On 07/01/2016 16:29, li li wrote: >> >> >> >>> Thanks for all the reply. Below is the data in a better format. >> >>> >> >>> addmargins(dat) >> >>>> >> >>> >> >>> dose 0 dose 0.15 dose 0.5 dose 1.5 dose 5 Sum >> >>> >> >>> yes 4 3 4 5 8 24 >> >>> >> >>> no 4 5 4 3 0 16 >> >>> >> >>> Sum 8 8 8 8 8 40 >> >>> >> >>> I think it is easier and better that I rephrase my question. I would >> like >> >>> to enumerate all possible >> >>> contingency tables with the row margins and column margins fixed as >> in the >> >>> above table. Yes. In fisher's exact test, this should have been done >> >>> internally. But I need explicitly find all such tables. Need some >> help on >> >>> this and thanks very much in advance. >> >>> >> >>> Hanna >> >>> >> >>> >> >>> 2016-01-07 7:15 GMT-05:00 peter dalgaard <pda...@gmail.com>: >> >>> >> >>> >> >>>> On 07 Jan 2016, at 08:31 , David Winsemius <dwinsem...@comcast.net> >> >>>> wrote: >> >>>> >> >>>> >> >>>>>> On Jan 6, 2016, at 8:16 PM, li li <hannah....@gmail.com> wrote: >> >>>>>> >> >>>>>> Hi all, >> >>>>>> Is there an R function that does exact randomization trend test? >> >>>>>> For example, consider the 2 by 5 contingency table below: >> >>>>>> >> >>>>>> dose0 dose 0.15 dose 0.5 dose 1.5 dose 5 >> >>>>>> row >> >>>>>> margin >> >>>>>> Yes 4 3 4 5 >> >>>>>> 8 24 >> >>>>>> No 4 5 4 3 >> >>>>>> 0 16 >> >>>>>> col sum 8 8 8 8 >> >>>>>> 8 40 >> >>>>>> >> >>>>> >> >>>>> Your data presentation has been distorted by your failure to post in >> >>>>> >> >>>> plain text. Surely you have been asked in the past to correct this >> issue? >> >>>> >> >>>>> >> >>>>> >> >>>>>> To do the exact trend test, we need to enumerate all the >> contingency >> >>>>>> >> >>>>> table >> >>>> >> >>>>> with the >> >>>>>> row and column margins fixed. >> >>>>>> >> >>>>> >> >>>>> Er, how should that be done? A trend test? What is described above >> would >> >>>>> >> >>>> be a general test of no association rather than a trend test. Please >> use >> >>>> clear language and be as specific as possible if you choose to >> respond. >> >>>> >> >>>>> >> >>>>> Find the probability corresponding to >> >>>>>> obtaining >> >>>>>> the corresponding contingency tables based on the multivariate >> >>>>>> hypergeometric distribution. Finally the pvalue is obtained by >> adding >> >>>>>> relevant probabilities. >> >>>>>> >> >>>>> >> >>>>> If there is a trend under consideration, then I do not understand >> such a >> >>>>> >> >>>> trend would be modeled under a hypergeometric distribution? A >> >>>> hypergeometic >> >>>> distribution would suggest no trend, at least to my current >> >>>> understanding. >> >>>> >> >>>> I'd expect that there is such a beast as a noncentral multivariate >> >>>> hypergeometric (for the 2x2 case that is what we use to get the CI >> for >> >>>> the >> >>>> odds ratio), but usually, one just wants the null distribution of the >> >>>> test >> >>>> statistic. >> >>>> >> >>>> >> >>>> >> >>>>> >> >>>>>> Is there an R function that does this? if not, I am wondering >> whether >> >>>>>> >> >>>>> it is >> >>>> >> >>>>> possible to >> >>>>>> enumerate all possible contingency tables that has column sun and >> row >> >>>>>> >> >>>>> sum >> >>>> >> >>>>> fixed? >> >>>>>> >> >>>>> >> >>>>> Wel, yes, that is possible and routinely done with `fisher.test`, >> but it >> >>>>> >> >>>> is up to you to describe how that activity leads to a trend test. >> >>>> >> >>>>> >> >>>>> If you assume Poisson distributed errors a trend test is fairly >> easy to >> >>>>> >> >>>> construct with glm. >> >>>> >> >>>>> >> >>>>> >> >>>> Or, more to the point, there is prop.trend.test(). Neither are exact >> >>>> tests, though. >> >>>> >> >>>> I think package "coin" may something relevant. >> >>>> >> >>>> -pd >> >>>> >> >>>> >> >>>> -- >> >>>>> David. >> >>>>> >> >>>>>> >> >>>>>> Thanks very much!! >> >>>>>> >> >>>>>> Hanna >> >>>>>> >> >>>>>> [[alternative HTML version deleted]] >> >>>>>> >> >>>>>> ______________________________________________ >> >>>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-help >> >>>>>> PLEASE do read the posting guide >> >>>>>> >> >>>>> http://www.R-project.org/posting-guide.html >> >>>> >> >>>>> and provide commented, minimal, self-contained, reproducible code. >> >>>>>> >> >>>>> >> >>>>> David Winsemius >> >>>>> Alameda, CA, USA >> >>>>> >> >>>>> ______________________________________________ >> >>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> >>>>> https://stat.ethz.ch/mailman/listinfo/r-help >> >>>>> PLEASE do read the posting guide >> >>>>> >> >>>> http://www.R-project.org/posting-guide.html >> >>>> >> >>>>> and provide commented, minimal, self-contained, reproducible code. >> >>>>> >> >>>> >> >>>> -- >> >>>> Peter Dalgaard, Professor, >> >>>> Center for Statistics, Copenhagen Business School >> >>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >> >>>> Phone: (+45)38153501 >> >>>> Office: A 4.23 >> >>>> Email: pd....@cbs.dk Priv: pda...@gmail.com >> >>>> >> >>>> >> >>>> >> >>> [[alternative HTML version deleted]] >> >>> >> >>> ______________________________________________ >> >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> >>> https://stat.ethz.ch/mailman/listinfo/r-help >> >>> PLEASE do read the posting guide >> >>> http://www.R-project.org/posting-guide.html >> >>> and provide commented, minimal, self-contained, reproducible code. >> >>> >> >>> >> >> -- >> >> Michael >> >> http://www.dewey.myzen.co.uk/home.html >> >> >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> > https://stat.ethz.ch/mailman/listinfo/r-help >> > PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> > and provide commented, minimal, self-contained, reproducible code. >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.