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
To do the exact trend test, we need to enumerate all the contingency table
with the
row and column margins fixed. 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.
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?
Thanks very much!!
Hanna
[[alternative HTML version deleted]]
> 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 40Your 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.> > 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. -- 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
On 07/01/2016 2:31 AM, David Winsemius 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.Under (one version of) the null hypothesis of no trend, the distribution should show no association. The difference from the Fisher's test is in the statistic: rather than a measure of lack of association, you want a measure of trend. It's been a long time since I worked on this kind of thing, but I believe Tarone's test gives an appropriate statistic. I don't know which package calculates its permutation distribution with fixed margins, but there's probably one out there somewhere. Duncan Murdoch>> 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. > >> >> 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. >
Have you tried Google? exact randomisation trend test r finds what look like clearly relevant packages On 07/01/2016 04:16, li li 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 > > To do the exact trend test, we need to enumerate all the contingency table > with the > row and column margins fixed. 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. > > 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? > > 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. >-- Michael http://www.dewey.myzen.co.uk/home.html
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