I'm trying to use the randomTF function from package palaeoSig to
test the significance of a MAT reconstruction with nine analogs and a
WA-PLS reconstruction with four components. I'm probably missing
something obvious here but how do I make sure that randomTF is testing
the reconstruction based on the desired number of analogs / components?
In:
fitmap.wapls = WAPLS( lumapspc, lumap)
sig.wapls = randomTF( spp = sqrt( lumapspc ), env = lumapenv, fos =
sqrt( hcspc ), n = 999, fun = WAPLS, col = 4 )
I assume "col = 4" tells randomTF to test the reconstruction based
on the four component WA-PLS model as that's what the documentation
seems to indicate.
However, in:
fitmap.mat = MAT( lumapspc, lumap, dist.method = "chord", k = 20 )
sig.mat = randomTF( spp = lumapspc, env = lumapenv, fos = hcspc, n =
999, fun = MAT, col = 9 )
it seems that "col = 9" does not tell randomTF to test the
reconstruction based on the 9 analog MAT model. If I give col a value
other than one or two, I get a "subscript out of bounds" error. So I
assume the col argument in this case selects between the mean and
weighted mean predictions.
If I pass additional arguments, k = 9 and dist.method = "chord" to
randomTF, then the values of sig.mat$preds do not match the values
obtained from:
predmap.mat = predict( fitmap.mat, hcspc, k = 9 )
Also, if I give randomTF a k value less than 5, I get the error "k
out of range". So, passing k to randomTF must not be telling randomTF
to use that number of analogs as I would not be able to select a four
analog model.
Jason
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