I'm using fisher.exact on a 4x2 table and it seems to work. Does anyone know exactly what is going on? I thought fisher.exact is only for 2x2 tables. Note: I can't use chi-squared because I have a couple of cells with 0 and < 5 observations. -- View this message in context: http://r.789695.n4.nabble.com/fisher-exact-for-2x2-table-tp3481979p3481979.html Sent from the R help mailing list archive at Nabble.com.
fisher exact for > 2x2 table
13 messages · viostorm, David Winsemius, Thomas Lumley +3 more
On Apr 28, 2011, at 3:45 PM, viostorm wrote:
I'm using fisher.exact on a 4x2 table and it seems to work. Does anyone know exactly what is going on? I thought fisher.exact is only for 2x2 tables.
Have you read the help page?
David Winsemius, MD West Hartford, CT
On Thu, 28 Apr 2011, viostorm wrote:
I'm using fisher.exact on a 4x2 table and it seems to work. Does anyone know exactly what is going on? I thought fisher.exact is only for 2x2 tables.
You were wrong. I'm sure there's nothing wrong with the program. You will find that with bigger tables and larger sample sizes the computational cost becomes quite enormous. Mike
On Fri, Apr 29, 2011 at 8:01 AM, Mike Miller <mbmiller+l at gmail.com> wrote:
On Thu, 28 Apr 2011, viostorm wrote:
I'm using fisher.exact on a 4x2 table and it seems to work. Does anyone know exactly what is going on? ?I thought fisher.exact is only for 2x2 tables.
You were wrong. ?I'm sure there's nothing wrong with the program. ?You will find that with bigger tables and larger sample sizes the computational cost becomes quite enormous.
In fact, with large tables, roundoff error becomes significant before
computational cost becomes prohibitive.
-thomas
Thomas Lumley Professor of Biostatistics University of Auckland
I have read the help page, or at least ?fisher.exact I looked a bit on the Internet I guess it is applicable to > 2x2. I had spoken to a biostatistician here who is quite excellent and was adamant with me I could not do > 2x2. I found this: http://mathworld.wolfram.com/FishersExactTest.html Does anyone know specifically how R is calculating this? -- View this message in context: http://r.789695.n4.nabble.com/fisher-exact-for-2x2-table-tp3481979p3482102.html Sent from the R help mailing list archive at Nabble.com.
On Apr 28, 2011, at 4:23 PM, viostorm wrote:
I have read the help page, or at least ?fisher.exact
Then it should have been clear that more than 2x2 tables can be used.
I looked a bit on the Internet I guess it is applicable to > 2x2. I had spoken to a biostatistician here who is quite excellent and was adamant with me I could not do > 2x2. I found this: http://mathworld.wolfram.com/FishersExactTest.html Does anyone know specifically how R is calculating this?
The answer to any question like that is ... look at the source. You will see extensive use of phyper() which is calculating that expression for various arguments. ?phyper
David Winsemius, MD West Hartford, CT
On Fri, 29 Apr 2011, Thomas Lumley wrote:
On Fri, Apr 29, 2011 at 8:01 AM, Mike Miller <mbmiller+l at gmail.com> wrote:
On Thu, 28 Apr 2011, viostorm wrote:
I'm using fisher.exact on a 4x2 table and it seems to work. Does anyone know exactly what is going on? ?I thought fisher.exact is only for 2x2 tables.
You were wrong. ?I'm sure there's nothing wrong with the program. ?You will find that with bigger tables and larger sample sizes the computational cost becomes quite enormous.
In fact, with large tables, roundoff error becomes significant before computational cost becomes prohibitive.
To avoid both of these problems one might use Monte Carlo resampling under the null, maybe 10,000 times or more. I think independence_test() in the coin package will do this: http://cran.r-project.org/web/packages/coin/ To estimate very small p-values properly, one must resample many more times. Mike
On Thu, 28 Apr 2011, viostorm wrote:
I have read the help page, or at least ?fisher.exact I looked a bit on the Internet I guess it is applicable to > 2x2. I had spoken to a biostatistician here who is quite excellent and was adamant with me I could not do > 2x2. I found this: http://mathworld.wolfram.com/FishersExactTest.html
That page shows that the Fisher Exact test can be implemented on tables with any numbers of rows and columns (so long as there are at least two rows and two columns). Your biostatistician just didn't happen to know about this, but s/he shouldn't have been adamant when s/he was wrong. Show your biostatistician the MathWorld page. Mike
Thank you all very kindly for your help. -Rob -------------------------------- Robert Schutt III, MD, MCS Resident - Department of Internal Medicine University of Virginia, Charlottesville, Virginia -- View this message in context: http://r.789695.n4.nabble.com/fisher-exact-for-2x2-table-tp3481979p3482351.html Sent from the R help mailing list archive at Nabble.com.
After I shared comments form the forum yesterday with the biostatistician he indicated this: "Fisher's exact test is the non-parametric analog for the Chi-square test for 2x2 comparisons. A version (or extension) of the Fisher's Exact test, known as the Freeman-Halton test applies to comparisons for tables greater than 2x2. SAS can calculate both statistics using the following instructions. proc freq; tables a * b / fisher;" Do people here still stand by position fisher exact test can be used for RxC contingency tables ? Sorry to both you all so much it is just important for a paper I am writing and planning to submit soon. ( I have a 4x2 table but does not meet expected frequencies requirements for chi-squared.) I guess people here have suggested R implements, the following, which unfortunately are unavailable at least easily at my library but at least by the titles indicates it is extending it to RxC Mehta CR, Patel NR. A network algorithm for performing Fisher's exact test in r c contingency tables. Journal of the American Statistical Association 1983;78:427-34. Mehta CR, Patel NR. Algorithm 643: FEXACT: A FORTRAN subroutine for Fisher's exact test on unordered r x c contingency tables. ACM Transactions on Mathematical Software 1986;12:154-61. The only reason I ask again is he is exceptionally clear on this point. Thanks again, -Rob
viostorm wrote:
Thank you all very kindly for your help. -Rob -------------------------------- Robert Schutt III, MD, MCS Resident - Department of Internal Medicine University of Virginia, Charlottesville, Virginia
viostorm wrote:
Thank you all very kindly for your help. -Rob -------------------------------- Robert Schutt III, MD, MCS Resident - Department of Internal Medicine University of Virginia, Charlottesville, Virginia
-- View this message in context: http://r.789695.n4.nabble.com/fisher-exact-for-2x2-table-tp3481979p3484009.html Sent from the R help mailing list archive at Nabble.com.
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Rob-- Your biostatistician has not disagreed with the rest of us about anything except for his preferred name for the test. He wants to call it the Freeman-Halton test, some people call it the Fisher-Freeman-Halton test, but most people call it the Fisher Exact test -- all are the same test. When he was "adamant you could not do > 2x2", what he was being adamant about was the name you should use when referring to the test for tables larger than 2x2. Why he was doing that, I don't know, but I think it is silly -- he confused you and the rest of us. He goes on to tell you that to get the Freeman-Halton test in SAS, you use "tables a * b / fisher". In other words, SAS calls the test "Fisher" instead of calling it Freeman-Halton. R also calls it "Fisher" and not Freeman-Halton. I'm like R and SAS and unlike your biostatistician, but to each his own. You say that he is "exceptionally clear on this point," which may be true, but what is the point? The point is that he prefers a different *name* for the test than the rest of us. Everyone agrees on the math/stat. Mike -- Michael B. Miller, Ph.D. Minnesota Center for Twin and Family Research Department of Psychology University of Minnesota
On Fri, 29 Apr 2011, viostorm wrote:
After I shared comments form the forum yesterday with the biostatistician he indicated this: "Fisher's exact test is the non-parametric analog for the Chi-square test for 2x2 comparisons. A version (or extension) of the Fisher's Exact test, known as the Freeman-Halton test applies to comparisons for tables greater than 2x2. SAS can calculate both statistics using the following instructions. proc freq; tables a * b / fisher;" Do people here still stand by position fisher exact test can be used for RxC contingency tables ? Sorry to both you all so much it is just important for a paper I am writing and planning to submit soon. ( I have a 4x2 table but does not meet expected frequencies requirements for chi-squared.) I guess people here have suggested R implements, the following, which unfortunately are unavailable at least easily at my library but at least by the titles indicates it is extending it to RxC Mehta CR, Patel NR. A network algorithm for performing Fisher's exact test in r c contingency tables. Journal of the American Statistical Association 1983;78:427-34. Mehta CR, Patel NR. Algorithm 643: FEXACT: A FORTRAN subroutine for Fisher's exact test on unordered r x c contingency tables. ACM Transactions on Mathematical Software 1986;12:154-61. The only reason I ask again is he is exceptionally clear on this point. Thanks again, -Rob
On 29 April 2011 08:43, viostorm <rob.schutt at gmail.com> wrote:
After I shared comments form the forum yesterday with the biostatistician he indicated this: "Fisher's exact test is the non-parametric analog for the Chi-square test for 2x2 comparisons. A version (or extension) of the Fisher's Exact test, known as the Freeman-Halton test applies to comparisons for tables greater than 2x2. SAS can calculate both statistics using the following instructions. ?proc freq; tables a * b / fisher;"
SAS documentation says: "Fisher's exact test was extended to general R?C tables by Freeman and Halton (1951), and this test is *also* known as the Freeman-Halton test." Emphasis mine. Jeremy
Jeremy Miles Psychology Research Methods Wiki: www.researchmethodsinpsychology.com