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)
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