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.
