Re: [R] Question about cochran test in R
Hi Luis, (Let's keep R-help in the loop for the benefit of others.) On 2015-05-08 10:25, Luis Fernando García wrote: Thanks a lot for your replies Henry! Your answer was specially a bless! Many thanks this was an issue which was breaking my head. I have another couple of questions, may be you could help me. For post hoc comparison I was planning to run a McNemar test with a bonferroni correction, but wanted to be sure my approach is correct. It's an OK approach, I guess, but you should use the Holm correction rather than Bonferroni. (Holm dominates Bonferroni and is valid under the same arbitrary assumptions.) The classical approach, and as suggested in Cochran (1950), would be to partition the chi-squared statistic into components of interest. In a more general approach, a test of all the post-hoc comparisons is performed simultaneously. This is very efficient, in terms of power, since it takes account of the correlation between the test statistics. Ignoring such dependencies may result in strange results, due to loss of power, where none of the partial null hypotheses are rejected even though the global null hypothesis is rejected. Unfortunately, I'm not aware of any publicly available software that let's you do this. In theory, 'coin' should be able to, and there has even been some work done in this direction, but it's currently unfinished. Henric Winell Sorry if I annoy you with this remaining question. Thanks in advance! 2015-05-07 8:03 GMT-03:00 Henric Winell nilsson.hen...@gmail.com mailto:nilsson.hen...@gmail.com: On 2015-05-07 09:15, Jim Lemon wrote: Hi Luis, Try this page: http://www.r-bloggers.com/cochran-q-test-for-k-related-samples-in-r/ Jim Cochran's Q test is a marginal homogeneity test, and such tests can be performed by the 'mh_test' function in the 'coin' package. The following replicates the result in the blog post library(coin) dta - data.frame( + method= factor(rep(LETTERS[1:4], 6)), + repellent = factor(c(1, 1, 0, 0, + 1, 1, 0, 1, + 1, 0, 0, 0, + 1, 1, 1, 0, + 1, 1, 0, 1, + 1, 1, 0, 1)), + fabric= gl(6, 4, labels = as.roman(1:6)) + ) mh_test(repellent ~ method | fabric, data = dta) Asymptotic Marginal-Homogeneity Test data: repellent by method (A, B, C, D) stratified by fabric chi-squared = 9.3158, df = 3, p-value = 0.02537 and uses the asymptotic approximation to compute the p-value. The 'coin' package also allows you to approximate the exact null distribution using Monte Carlo methods: set.seed(123) mh_test(repellent ~ method | fabric, data = dta, + distribution = approximate(B = 1L)) Approximative Marginal-Homogeneity Test data: repellent by method (A, B, C, D) stratified by fabric chi-squared = 9.3158, p-value = 0.0202 For future reference, 'mh_test' is fairly general and handles both matched pairs or matched sets. So, the well-known tests due McNemar, Cochran, Stuart(-Maxwell) and Madansky are just special cases. For more general symmetry test problems, the 'coin' package offers the 'symmetry_test' function and this can be used to perform, e.g., multivariate marginal homogeneity tests like the multivariate McNemar test (Klingenberg and Agresti, 2006) or the multivariate Friedman test (Gerig, 1969). Henric On Thu, May 7, 2015 at 4:59 PM, Luis Fernando García luysgar...@gmail.com mailto:luysgar...@gmail.com wrote: Dear R Experts, May be this is a basic question for you, but it is something I need really urgently. I need to perform a Chi Square analysis for more than two groups of paired observations. It seems to be ok For Cochran test. Unfortunately I have not found info about this test in R, except for dealing with outliers which is not my aim. I am looking for something like this https://www.medcalc.org/manual/cochranq.php I found a video to perform this analysis in R, but was not specially useful. Does some of you know have some info about how to make this analysis in R? Thanks in advance! [[alternative HTML version deleted]] __ R-help@r-project.org mailto: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
[R] Question about cochran test in R
Dear R Experts, May be this is a basic question for you, but it is something I need really urgently. I need to perform a Chi Square analysis for more than two groups of paired observations. It seems to be ok For Cochran test. Unfortunately I have not found info about this test in R, except for dealing with outliers which is not my aim. I am looking for something like this https://www.medcalc.org/manual/cochranq.php I found a video to perform this analysis in R, but was not specially useful. Does some of you know have some info about how to make this analysis in R? Thanks in advance! [[alternative HTML version deleted]] __ 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] Question about cochran test in R
Hi Luis, Try this page: http://www.r-bloggers.com/cochran-q-test-for-k-related-samples-in-r/ Jim On Thu, May 7, 2015 at 4:59 PM, Luis Fernando García luysgar...@gmail.com wrote: Dear R Experts, May be this is a basic question for you, but it is something I need really urgently. I need to perform a Chi Square analysis for more than two groups of paired observations. It seems to be ok For Cochran test. Unfortunately I have not found info about this test in R, except for dealing with outliers which is not my aim. I am looking for something like this https://www.medcalc.org/manual/cochranq.php I found a video to perform this analysis in R, but was not specially useful. Does some of you know have some info about how to make this analysis in R? Thanks in advance! [[alternative HTML version deleted]] __ 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] Question about cochran test in R
On 2015-05-07 09:15, Jim Lemon wrote: Hi Luis, Try this page: http://www.r-bloggers.com/cochran-q-test-for-k-related-samples-in-r/ Jim Cochran's Q test is a marginal homogeneity test, and such tests can be performed by the 'mh_test' function in the 'coin' package. The following replicates the result in the blog post library(coin) dta - data.frame( + method= factor(rep(LETTERS[1:4], 6)), + repellent = factor(c(1, 1, 0, 0, + 1, 1, 0, 1, + 1, 0, 0, 0, + 1, 1, 1, 0, + 1, 1, 0, 1, + 1, 1, 0, 1)), + fabric= gl(6, 4, labels = as.roman(1:6)) + ) mh_test(repellent ~ method | fabric, data = dta) Asymptotic Marginal-Homogeneity Test data: repellent by method (A, B, C, D) stratified by fabric chi-squared = 9.3158, df = 3, p-value = 0.02537 and uses the asymptotic approximation to compute the p-value. The 'coin' package also allows you to approximate the exact null distribution using Monte Carlo methods: set.seed(123) mh_test(repellent ~ method | fabric, data = dta, + distribution = approximate(B = 1L)) Approximative Marginal-Homogeneity Test data: repellent by method (A, B, C, D) stratified by fabric chi-squared = 9.3158, p-value = 0.0202 For future reference, 'mh_test' is fairly general and handles both matched pairs or matched sets. So, the well-known tests due McNemar, Cochran, Stuart(-Maxwell) and Madansky are just special cases. For more general symmetry test problems, the 'coin' package offers the 'symmetry_test' function and this can be used to perform, e.g., multivariate marginal homogeneity tests like the multivariate McNemar test (Klingenberg and Agresti, 2006) or the multivariate Friedman test (Gerig, 1969). Henric On Thu, May 7, 2015 at 4:59 PM, Luis Fernando García luysgar...@gmail.com wrote: Dear R Experts, May be this is a basic question for you, but it is something I need really urgently. I need to perform a Chi Square analysis for more than two groups of paired observations. It seems to be ok For Cochran test. Unfortunately I have not found info about this test in R, except for dealing with outliers which is not my aim. I am looking for something like this https://www.medcalc.org/manual/cochranq.php I found a video to perform this analysis in R, but was not specially useful. Does some of you know have some info about how to make this analysis in R? Thanks in advance! [[alternative HTML version deleted]] __ 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. __ 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.
