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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