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.
