[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 22:10:19 CET 2016
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.hlx at gmail.com>:
> 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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