R help - Feb 2009 - R equivalent of SAS Cochran-Mantel-Haenszel tests?

In SAS, for a two-way (or 3-way, stratified) table, the CMH option in 
SAS PROC FREQ gives
3 tests that take ordinality of the factors into account, for both 
variables, just the column variable
or neither.   Is there an equivalent in R?
The mantelhaen.test in stats gives something quite different (a test of 
conditional independence for
*nominal* factors in a 3-way table).

e.g. I'd like to reproduce:
*-- CMH tests;
proc freq data=sexfun order=data;
  weight count;
  tables husband * wife / cmh chisq nocol norow;
  run;

                              The FREQ Procedure
                     Summary Statistics for Husband by Wife
          Cochran-Mantel-Haenszel Statistics (Based on Table Scores)

        Statistic    Alternative Hypothesis    DF       Value      Prob

            1        Nonzero Correlation        1     10.0142    0.0016
            2        Row Mean Scores Differ     3     12.5681    0.0057
            3        General Association        9     16.7689    0.0525

-- 
Michael Friendly     Email: friendly AT yorku DOT ca 
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

Dear Michael,
It sounds as a linear-by-linear loglinear model (and its variants) which 
uses scores for one or more variables in the table.. (see Agresti, 1990, 
Categorical Data Analysis. I do remember the pages and I have not the 
book here..)

If this is the case, you can use standard call to glm(.., 
family=poisson) with score variables in the linear predictor. For 
instance for a two-way table with ordered variables the linear-by-linear 
model is,

glm(freq~factor(x)+factor(y)+I(score.x*score.y), family=poisson)

The CMH test, probably, is the score test of the parameter of 
I(score.x*score.y)..

best,
vito

Michael Friendly ha scritto:
> In SAS, for a two-way (or 3-way, stratified) table, the CMH option in 
> SAS PROC FREQ gives
> 3 tests that take ordinality of the factors into account, for both 
> variables, just the column variable
> or neither.   Is there an equivalent in R?
> The mantelhaen.test in stats gives something quite different (a test of 
> conditional independence for
> *nominal* factors in a 3-way table).
> 
> e.g. I'd like to reproduce:
> *-- CMH tests;
> proc freq data=sexfun order=data;
>  weight count;
>  tables husband * wife / cmh chisq nocol norow;
>  run;
> 
>                              The FREQ Procedure
>                     Summary Statistics for Husband by Wife
>          Cochran-Mantel-Haenszel Statistics (Based on Table Scores)
> 
>        Statistic    Alternative Hypothesis    DF       Value      Prob
> 
>            1        Nonzero Correlation        1     10.0142    0.0016
>            2        Row Mean Scores Differ     3     12.5681    0.0057
>            3        General Association        9     16.7689    0.0525
> 
-- 
===================================Vito M.R. Muggeo
Dip.to Sc Statist e Matem `Vianelli'
Universit? di Palermo
viale delle Scienze, edificio 13
90128 Palermo - ITALY
tel: 091 6626240
fax: 091 485726/485612
http://dssm.unipa.it/vmuggeo

How about 'cmh_test' in the coin package?
>From the PDF: The null hypothesis of the independence of y and x is tested,
block defines an optional factor for stratification. chisq_test implements
Pearson?s chi-squared test, cmh_test the Cochran-Mantel-Haenzsel test and
lbl_test the linear-by-linear association test for ordered data.

David Freedman



Michael Friendly wrote:
> 
> In SAS, for a two-way (or 3-way, stratified) table, the CMH option in 
> SAS PROC FREQ gives
> 3 tests that take ordinality of the factors into account, for both 
> variables, just the column variable
> or neither.   Is there an equivalent in R?
> The mantelhaen.test in stats gives something quite different (a test of 
> conditional independence for
> *nominal* factors in a 3-way table).
> 
> e.g. I'd like to reproduce:
> *-- CMH tests;
> proc freq data=sexfun order=data;
>   weight count;
>   tables husband * wife / cmh chisq nocol norow;
>   run;
> 
>                               The FREQ Procedure
>                      Summary Statistics for Husband by Wife
>           Cochran-Mantel-Haenszel Statistics (Based on Table Scores)
> 
>         Statistic    Alternative Hypothesis    DF       Value      Prob
> 
>             1        Nonzero Correlation        1     10.0142    0.0016
>             2        Row Mean Scores Differ     3     12.5681    0.0057
>             3        General Association        9     16.7689    0.0525
> 
> -- 
> Michael Friendly     Email: friendly AT yorku DOT ca 
> Professor, Psychology Dept.
> York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
> 4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
> Toronto, ONT  M3J 1P3 CANADA
> 
> ______________________________________________
> R-help at 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.
> 
> 
-- 
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