[R] Fwd: exact trend test (enumerate all possible contingency tables with fixed row and column margins)

li li hannah.hlx at gmail.com
Fri Jan 8 15:30:10 CET 2016


Thanks Bert.


2016-01-07 13:39 GMT-05:00 Bert Gunter <bgunter.4567 at gmail.com>:

> Sorry -- neglected to reply to the list. -- Bert
>
>
>
> ---------- Forwarded message ----------
> From: Bert Gunter <bgunter.4567 at 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.hlx at 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.hlx at 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 <lists at 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 <pdalgd at gmail.com>:
> >>>
> >>>
> >>>> On 07 Jan 2016, at 08:31 , David Winsemius <dwinsemius at comcast.net>
> >>>> wrote:
> >>>>
> >>>>
> >>>>>> On Jan 6, 2016, at 8:16 PM, li li <hannah.hlx at 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 at 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 at 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.mes at cbs.dk  Priv: PDalgd at gmail.com
> >>>>
> >>>>
> >>>>
> >>>         [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-help at 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 at 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 at 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.
>

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