Re: [R] correlation between categorical data
comment inline David Winsemius wrote on 24.01.2015 21:08: On Jan 23, 2015, at 5:54 PM, JohnDee wrote: Heinz Tuechler wrote At 07:40 21.06.2009, J Dougherty wrote: [...] There are other ways of regarding the FET. Since it is precisely what it says - an exact test - you can argue that you should avoid carrying over any conclusions drawn about the small population the test was applied to and employing them in a broader context. In so far as the test is concerned, the sample data and the contingency table it is arrayed in are the entire universe. In that sense, the FET can't be conservative or liberal. It isn't actually a hypothesis test and should not be thought of as one or used in the place of one. JDougherty Could you give some reference, supporting this, for me, surprising view? I don't see a necessary connection between an exact test and the idea that it does not test a hypothesis. Thanks, Heinz Fisher's Exact Test is a nonparametric test. It tests the distribution in the contingency table against the total possible arrangements and gives you the precise likelihood of that many items being arranged in that manner. That's not the way I understand the construction of the result. The statistic gives rather the ratio of the number of permutations as extreme or more extreme (as measured by the odds ratio) while holding the marginals constant which is then divided by the total number of possible permutations of the data. No more and no less. You could argue about the greater population from which your sample is drawn, but FET makes no assumptions at all about any greater sample universe. It is conditional on the margins, so that is the description of the universe. Also, since the population being used in FET is strictly limited to the members of the contingency table, the results are a subset of a finite group of possible results that are relevant to that specific arrangement of data. You are not estimating parameters of a parent population or making any assumptions about the parent distribution. You can designate a p value such as 0.05 as a level of significance, but there is no error term in the FET result. Fisher stated that the test DOES assume a null hypothesis of independence to a hypergeometric distribution of the cell members. But that creates other issues if you are attempting to use the results in conjunction with assumptions about a broader sample universe than that in the test. For instance you have to carry the assumption of a hypergeometric distribution over in to the land of reality your sample is drawn from and you then have to justify that. In this respect I agree. A real world situation with a universe of fixed margins seems unusual to me. And this is off-topic on Rhelp . Sorry for asking a question off-topic more than five years ago. A nice surprise to get an answer. Thanks, Heinz -- View this message in context: http://r.789695.n4.nabble.com/correlation-between-categorical-data-tp888975p4702235.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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.
Re: [R] correlation between categorical data
On Jan 23, 2015, at 5:54 PM, JohnDee wrote: Heinz Tuechler wrote At 07:40 21.06.2009, J Dougherty wrote: [...] There are other ways of regarding the FET. Since it is precisely what it says - an exact test - you can argue that you should avoid carrying over any conclusions drawn about the small population the test was applied to and employing them in a broader context. In so far as the test is concerned, the sample data and the contingency table it is arrayed in are the entire universe. In that sense, the FET can't be conservative or liberal. It isn't actually a hypothesis test and should not be thought of as one or used in the place of one. JDougherty Could you give some reference, supporting this, for me, surprising view? I don't see a necessary connection between an exact test and the idea that it does not test a hypothesis. Thanks, Heinz Fisher's Exact Test is a nonparametric test. It tests the distribution in the contingency table against the total possible arrangements and gives you the precise likelihood of that many items being arranged in that manner. That's not the way I understand the construction of the result. The statistic gives rather the ratio of the number of permutations as extreme or more extreme (as measured by the odds ratio) while holding the marginals constant which is then divided by the total number of possible permutations of the data. No more and no less. You could argue about the greater population from which your sample is drawn, but FET makes no assumptions at all about any greater sample universe. It is conditional on the margins, so that is the description of the universe. Also, since the population being used in FET is strictly limited to the members of the contingency table, the results are a subset of a finite group of possible results that are relevant to that specific arrangement of data. You are not estimating parameters of a parent population or making any assumptions about the parent distribution. You can designate a p value such as 0.05 as a level of significance, but there is no error term in the FET result. Fisher stated that the test DOES assume a null hypothesis of independence to a hypergeometric distribution of the cell members. But that creates other issues if you are attempting to use the results in conjunction with assumptions about a broader sample universe than that in the test. For instance you have to carry the assumption of a hypergeometric distribution over in to the land of reality your sample is drawn from and you then have to justify that. And this is off-topic on Rhelp . -- View this message in context: http://r.789695.n4.nabble.com/correlation-between-categorical-data-tp888975p4702235.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] correlation between categorical data
Heinz Tuechler wrote At 07:40 21.06.2009, J Dougherty wrote: [...] There are other ways of regarding the FET. Since it is precisely what it says - an exact test - you can argue that you should avoid carrying over any conclusions drawn about the small population the test was applied to and employing them in a broader context. In so far as the test is concerned, the sample data and the contingency table it is arrayed in are the entire universe. In that sense, the FET can't be conservative or liberal. It isn't actually a hypothesis test and should not be thought of as one or used in the place of one. JDougherty Could you give some reference, supporting this, for me, surprising view? I don't see a necessary connection between an exact test and the idea that it does not test a hypothesis. Thanks, Heinz __ R-help@ mailing list 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. Fisher's Exact Test is a nonparametric test. It tests the distribution in the contingency table against the total possible arrangements and gives you the precise likelihood of that many items being arranged in that manner. No more and no less. You could argue about the greater population from which your sample is drawn, but FET makes no assumptions at all about any greater sample universe. Also, since the population being used in FET is strictly limited to the members of the contingency table, the results are a subset of a finite group of possible results that are relevant to that specific arrangement of data. You are not estimating parameters of a parent population or making any assumptions about the parent distribution. You can designate a p value such as 0.05 as a level of significance, but there is no error term in the FET result. Fisher stated that the test DOES assume a null hypothesis of independence to a hypergeometric distribution of the cell members. But that creates other issues if you are attempting to use the results in conjunction with assumptions about a broader sample universe than that in the test. For instance you have to carry the assumption of a hypergeometric distribution over in to the land of reality your sample is drawn from and you then have to justify that. -- View this message in context: http://r.789695.n4.nabble.com/correlation-between-categorical-data-tp888975p4702235.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] correlation between categorical data
At 07:40 21.06.2009, J Dougherty wrote: [...] There are other ways of regarding the FET. Since it is precisely what it says - an exact test - you can argue that you should avoid carrying over any conclusions drawn about the small population the test was applied to and employing them in a broader context. In so far as the test is concerned, the sample data and the contingency table it is arrayed in are the entire universe. In that sense, the FET can't be conservative or liberal. It isn't actually a hypothesis test and should not be thought of as one or used in the place of one. JDougherty Could you give some reference, supporting this, for me, surprising view? I don't see a necessary connection between an exact test and the idea that it does not test a hypothesis. Thanks, Heinz __ R-help@r-project.org mailing list 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.
Re: [R] correlation between categorical data
For measures of association between two variables with two values each,
Cramer's V and Yule's Q are useful statistics. Look into this thread, for
example: http://markmail.org/message/sjd53z2dv2pb5nd6
To get a grasp from plotting (sometimes), you may use the jitter function in
the plot...
e=rnorm(n,0,1)
y=x+e
xprob=exp(x)/(1+exp(x))
yprob=exp(y)/(1+exp(y))
xcat=rbinom(n,1,xprob)
ycat=rbinom(n,1,yprob)
plot(ycat~xcat) #totally useless
plot(jitter(ycat)~jitter(xcat)) #can be somewhat useful
table(ycat,xcat) # interesting
#A measure of correlation between nominal variables
yule.Q=function(x,y){(table(x,y)[1,1]*table(x,y)[2,2]-table(x,y)[1,2]*table(
x,y)[2,1])/(table(x,y)[1,1]*table(x,y)[2,2]+table(x,y)[1,2]*table(x,y)[2,1])
}
yule.Q(ycat,xcat)
Best,
Daniel
-
cuncta stricte discussurus
-
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im
Auftrag von Marc Schwartz
Gesendet: Saturday, June 20, 2009 7:37 PM
An: Jason Morgan
Cc: r-help
Betreff: Re: [R] correlation between categorical data
On Jun 20, 2009, at 2:05 PM, Jason Morgan wrote:
On 2009.06.19 14:04:59, Michael wrote:
Hi all,
In a data-frame, I have two columns of data that are categorical.
How do I form some sort of measure of correlation between these two
columns?
For numerical data, I just need to regress one to the other, or do
some pairs plot.
But for categorical data, how do I find and/or visualize correlation
between the two columns of data?
As Dylan mentioned, using crosstabs may be the easiest way. Also, a
simple correlation between the two variables may be informative. If
each variable is ordinal, you can use Kendall's tau-b (square table)
or tau-c (rectangular table). The former you can calculate with ?cor
(set method=kendall), the latter you may have to hack something
together yourself, there is code on the Internet to do this. If the
data are nominal, then a simple chi-squared test (large-n) or Fisher's
exact test (small-n) may be more appropriate. There are rules about
which to use when one variable is ordinal and one is nominal, but I
don't have my notes in front of me. Maybe someone else can provide
more assistance (and correct me if I'm wrong :).
I would be cautious in recommending the Fisher Exact Test based upon small
samples sizes, as the FET has been shown to be overly conservative. This
also applies to the use of the continuity correction for the chi-square test
(which replicates the behavior of the FET).
For more information see:
Chi-squared and Fisher-Irwin tests of two-by-two tables with small sample
recommendations Ian Campbell Stat in Med 26:3661-3675; 2007
http://www3.interscience.wiley.com/journal/114125487/abstract
and:
How conservative is Fisher's exact test?
A quantitative evaluation of the two-sample comparative binomial trial
Gerald G. Crans, Jonathan J. Shuster Stat Med. 2008 Aug 15;27(18):3598-611.
http://www3.interscience.wiley.com/journal/117929459/abstract
Frank also has some comments here (bottom of the page):
http://biostat.mc.vanderbilt.edu/wiki/Main/DataAnalysisDisc#Some_Important_P
oints_about_Cont
More generally, Agresti's Categorical Data Analysis is typically the first
reference in this domain to reach for. There is also a document written by
Laura Thompson which provides for a nice R companion to Agresti. It is
available from:
https://home.comcast.net/~lthompson221/Splusdiscrete2.pdf
HTH,
Marc Schwartz
__
R-help@r-project.org mailing list
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
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.
Re: [R] correlation between categorical data
On Jun 20, 2009, at 2:05 PM, Jason Morgan wrote: On 2009.06.19 14:04:59, Michael wrote: Hi all, In a data-frame, I have two columns of data that are categorical. How do I form some sort of measure of correlation between these two columns? For numerical data, I just need to regress one to the other, or do some pairs plot. But for categorical data, how do I find and/or visualize correlation between the two columns of data? As Dylan mentioned, using crosstabs may be the easiest way. Also, a simple correlation between the two variables may be informative. If each variable is ordinal, you can use Kendall's tau-b (square table) or tau-c (rectangular table). The former you can calculate with ?cor (set method=kendall), the latter you may have to hack something together yourself, there is code on the Internet to do this. If the data are nominal, then a simple chi-squared test (large-n) or Fisher's exact test (small-n) may be more appropriate. There are rules about which to use when one variable is ordinal and one is nominal, but I don't have my notes in front of me. Maybe someone else can provide more assistance (and correct me if I'm wrong :). I would be cautious in recommending the Fisher Exact Test based upon small samples sizes, as the FET has been shown to be overly conservative. This also applies to the use of the continuity correction for the chi-square test (which replicates the behavior of the FET). For more information see: Chi-squared and Fisher-Irwin tests of two-by-two tables with small sample recommendations Ian Campbell Stat in Med 26:3661-3675; 2007 http://www3.interscience.wiley.com/journal/114125487/abstract and: How conservative is Fisher's exact test? A quantitative evaluation of the two-sample comparative binomial trial Gerald G. Crans, Jonathan J. Shuster Stat Med. 2008 Aug 15;27(18):3598-611. http://www3.interscience.wiley.com/journal/117929459/abstract Frank also has some comments here (bottom of the page): http://biostat.mc.vanderbilt.edu/wiki/Main/DataAnalysisDisc#Some_Important_Points_about_Cont More generally, Agresti's Categorical Data Analysis is typically the first reference in this domain to reach for. There is also a document written by Laura Thompson which provides for a nice R companion to Agresti. It is available from: https://home.comcast.net/~lthompson221/Splusdiscrete2.pdf HTH, Marc Schwartz __ R-help@r-project.org mailing list 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.
Re: [R] correlation between categorical data
On Saturday 20 June 2009 04:36:55 pm Marc Schwartz wrote: On Jun 20, 2009, at 2:05 PM, Jason Morgan wrote: On 2009.06.19 14:04:59, Michael wrote: Hi all, In a data-frame, I have two columns of data that are categorical. How do I form some sort of measure of correlation between these two columns? For numerical data, I just need to regress one to the other, or do some pairs plot. But for categorical data, how do I find and/or visualize correlation between the two columns of data? As Dylan mentioned, using crosstabs may be the easiest way. Also, a simple correlation between the two variables may be informative. If each variable is ordinal, you can use Kendall's tau-b (square table) or tau-c (rectangular table). The former you can calculate with ?cor (set method=kendall), the latter you may have to hack something together yourself, there is code on the Internet to do this. If the data are nominal, then a simple chi-squared test (large-n) or Fisher's exact test (small-n) may be more appropriate. There are rules about which to use when one variable is ordinal and one is nominal, but I don't have my notes in front of me. Maybe someone else can provide more assistance (and correct me if I'm wrong :). I would be cautious in recommending the Fisher Exact Test based upon small samples sizes, as the FET has been shown to be overly conservative. . . . There are other ways of regarding the FET. Since it is precisely what it says - an exact test - you can argue that you should avoid carrying over any conclusions drawn about the small population the test was applied to and employing them in a broader context. In so far as the test is concerned, the sample data and the contingency table it is arrayed in are the entire universe. In that sense, the FET can't be conservative or liberal. It isn't actually a hypothesis test and should not be thought of as one or used in the place of one. JDougherty [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] correlation between categorical data
Hi all, In a data-frame, I have two columns of data that are categorical. How do I form some sort of measure of correlation between these two columns? For numerical data, I just need to regress one to the other, or do some pairs plot. But for categorical data, how do I find and/or visualize correlation between the two columns of data? Thanks! __ R-help@r-project.org mailing list 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.
Re: [R] correlation between categorical data
Not an expert, but I would try some of the following: # tabulate joint frequencies ?table ?xtabs # plotting mosaicplot(Titanic, main = Survival on the Titanic, color = TRUE, shade=TRUE) # log-linear models check the library for more ideas. Cheers, Dylan On Fri, Jun 19, 2009 at 2:04 PM, Michaelcomtech@gmail.com wrote: Hi all, In a data-frame, I have two columns of data that are categorical. How do I form some sort of measure of correlation between these two columns? For numerical data, I just need to regress one to the other, or do some pairs plot. But for categorical data, how do I find and/or visualize correlation between the two columns of data? Thanks! __ R-help@r-project.org mailing list 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 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.
