On Jun 15, 2004, at 10:11 AM, Douglas Bates wrote:
Jens Schumacher wrote:knussear wrote:Let data.matrix be the above difference matrix. You obtain the "raw sums of squares and cross-products matrix" byHi 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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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
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