[R] Manova question.
knussear
knussear at biodiversity.unr.edu
Tue Jun 15 19:47:56 CEST 2004
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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>>>
>>>
>> 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)
>
Thanks for the help.
Neither of those approaches gives the final matrix with 179.5273 in the
top left position!
Ken
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