[R] Cochran-Mantel-Haenszel test

[Bert Gunter]

This looks more like a statistics than an R issue. Try posting on
stats.stackexchange.com, a statistics list, instead.

ALternatively, talk to your local statistician (if there is one).

-- Bert

On Tue, Sep 18, 2012 at 3:02 PM, McPhie, Romney
<Romney.McPhie at dfo-mpo.gc.ca> wrote:
> Hello,
>
> I have some satellite tag time-at-depth (TAD) frequency data that I
> would like some help with.
>
> The data was transmitted via satellite as percent time spent in each of
> 7 depth bins (0m, 0-1m, 1-10m, 10-50m etc.), binned over 6-hour
> intervals.  I categorized each row of data corresponding to a date and
> time into summer vs. winter, and day vs. night, and then summed and
> averaged the given % for each depth bin.  My data looks like this (for
> one individual, HG03):
>
> HG03.dat
>    Season  Time Depth    Sum       Avrg
> 1    summ   day     0   17.2  0.1702970
> 2    summ   day     1   23.9  0.2366337
> 3    summ   day    10  868.5  8.5990099
> 4    summ   day    50 2698.2 26.7148515
> 5    summ   day   100  419.7  4.1554455
> 6    summ   day   200  266.1  2.6346535
> 7    summ   day   300 1668.6 16.5207921
> 8    summ   day   500 4138.2 40.9722772
> 9    summ night     0  283.6  5.7877551
> 10   summ night     1  229.1  4.6755102
> 11   summ night    10  479.3  9.7816327
> 12   summ night    50  761.9 15.5489796
> 13   summ night   100  235.8  4.8122449
> 14   summ night   200   40.9  0.8346939
> 15   summ night   300  763.1 15.5734694
> 16   summ night   500 2106.1 42.9816327
> 17   wint   day     0    0.0  0.0000000
> 18   wint   day     1    0.0  0.0000000
> 19   wint   day    10    0.0  0.0000000
> 20   wint   day    50    0.0  0.0000000
> 21   wint   day   100    7.9  1.1285714
> 22   wint   day   200   92.1 13.1571429
> 23   wint   day   300    0.0  0.0000000
> 24   wint   day   500  600.0 85.7142857
> 25   wint night     0   43.9  1.7560000
> 26   wint night     1    0.3  0.0120000
> 27   wint night    10    0.3  0.0120000
> 28   wint night    50    0.8  0.0320000
> 29   wint night   100   10.5  0.4200000
> 30   wint night   200   51.6  2.0640000
> 31   wint night   300  411.4 16.4560000
> 32   wint night   500 1981.2 79.2480000
>
> I wanted to test whether significant differences existed between depth
> in summer vs. winter, and day vs. night, controlling first for season
> and then for time of day.  I carried out a Cochran-Mantel-Haenszel test,
> using Average Frequency (Avrg) as the dependent variable (2x2x8
> contingency table).
>
>> ct<-xtabs(Avrg~Time+Depth+Season,data=HG03.dat)
>> mantelhaen.test(ct)
>
>         Cochran-Mantel-Haenszel test
>
> data:  ct
> Cochran-Mantel-Haenszel M^2 = 28.4548, df = 7, p-value = 0.0001818
>
>> ct<-xtabs(Avrg~Season+Depth+Time,data=HG03.dat)
>> mantelhaen.test(ct)
>
>         Cochran-Mantel-Haenszel test
>
> data:  ct
> Cochran-Mantel-Haenszel M^2 = 111.5986, df = 7, p-value < 2.2e-16
>
> However, I'm not sure if these results are valid, since my raw data is
> already in frequencies, not in counts.  When I used Sum as the dependent
> variable, I obtained different results.
>
> I am at a loss on how to proceed.  If anyone has any ideas, they would
> be greatly appreciated.
>
> Thanks!
> Romney
>
>
>         [[alternative HTML version deleted]]
>
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

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