Closed Max-Bladen closed 1 year ago
Thanks, @Max-Bladen. Great work on spotting and addressing this. I noticed that the checks for consistency of tune(method='spls') and tune.spls are dropped in unit tests. Was there a specific reason for that? Also, why was the RNG specifier removed in unit tests? Thanks
Hi @aljabadi,
This is something I meant to ask you about but forgot. Due to my implementation of bplapply()
, set.seed()
is no longer affecting tune.spls()
. Hence, calling the method twice on the same seed produced different results - the tune()
and tune.spls()
methods couldn't be equated. This is also why the tests currently just assess the class of the output and .mixo_rng()
was removed. How can I make use of bplapply()
without hindering the rng?
Second set of commits on 13/12/2022 reflect initial set of commits, but replicated after the branch was rebased to master following PR #281.
The
tune.spls()
function did not have any form ofBiocParallel
implementation which was quite misleading for users. As this function is likely to be more frequently used, this was a priority to resolve.The main body of the function was adjusted such that now the internal function
iter_keep.vals()
iterates over all pairs ofkeepX
/keepY
. Rather than doing it within each iteration, the functionDetermineOptimalKeepVals()
is called after all measure (cor
,RSS
) calculations. Impossible to iteratively buildmeasure.pred
usingbplapply()
.Old function names and structure was preserved to the best of my ability, though some of it sorely needed a face lift