[R] Question about cochran test in R

[Henric Winell]

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.henric at gmail.com
> <mailto:nilsson.henric at 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 = 10000L))
>
>              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
>         <luysgarcia at gmail.com <mailto:luysgarcia at 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]]
>
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>
>         ______________________________________________
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>
>
>