[R] Manova question.

[knussear]

On Jun 15, 2004, at 10:11 AM, Douglas Bates wrote:

> Jens Schumacher wrote:
>> knussear wrote:
>>> Hi list,
>>>
>>> I'm attempting to re-create a Repeated Measures Compositional 
>>> Analysis as
>>>  described in the work by Aebischer et. al. (Ecology. 1993. 74(5): 
>>> 1313-1325).
>>>
>>> In this paper they describe transitions of data into a log ratio 
>>> difference matrix, from which they obtain two matrices using a 
>>> monova routine.
>>>
>>> I am able to produce the second of the two matrices, but I'm having 
>>> trouble with the first.
>>>
>>> the difference matrix going in is given here.
>>>
>>> Animal    Scrub    Bl wood    Con wood     Grass
>>> 1    0.970    -2.380    -5.154    -9.408
>>> 2    1.217    -0.173    -4.955    -5.521
>>> 3    1.178    -0.248    -4.089    0.338
>>> 4    0.520    0.466    -4.801    -1.946
>>> 5    8.445    9.319    10.753    8.171
>>> 6    8.654    9.327    10.732    8.152
>>> 7    8.429    9.350    10.818    8.141
>>> 8    9.120    9.565    3.813    8.127
>>> 9    9.227    9.882    3.813    7.779
>>> 10    9.423    8.086    3.813    8.539
>>> 11    9.626    9.392    3.813    8.135
>>> 12    9.234    8.302    3.813    8.537
>>> 13    8.672    8.908    9.832    8.416
>>>
>>>
>>> And the first of the matrices is given here, and is "matrix of 
>>> mean-corrected sums of squares and cross products calculated from 
>>> the difference matrix."
>>>
>>>
>>>     Scrub    Bl wood    Con wood     Grass
>>> Scrub    179.52    214.59    244.58    273.75
>>> Bl wood    214.59    268.44    314.35    343.86
>>> Con wood     244.58    314.35    471.09    400.22
>>> Grass    273.75    343.86    400.22    477.78
>>>
>>>
>>> From manova on the data set I can get the diagonal of the matrix, 
>>> but not the others.
>>>
>>> manova(y ~ NULL)
>>>
>>> Terms:
>>>                 Residuals
>>> Scrub            179.5273
>>> Bl.wood          268.4347
>>> Con.wood         471.0845
>>> Grass            477.8014
>>> Deg. of Freedom        12
>>>
>>>
>>> Could anyone offer a suggestion ?
>>>
>>> Thanks
>>>
>>>
>>> Ken
>>>
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>>> PLEASE do read the posting guide! 
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>>>
>>>
>> Let   data.matrix    be the above difference matrix. You obtain the 
>> "raw sums of squares and cross-products matrix" by
>> R2 <- t(data.matrix) %*% data.matrix
>> or even
>> R2 <- crossprod(data.matrix, data.matrix)
>
> or, the preferred form,
>
> R2 <- crossprod(data.matrix)
>
>

I'm not sure if this helps but I get the correct matrices if I use JMP. 
It refers to them as E&H matrices. Is there a way to get R to produce 
these?

Thanks

Ken