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Improve function efficiency through matrix algebra #11

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Rekyt opened this issue Dec 15, 2020 · 3 comments
Closed

Improve function efficiency through matrix algebra #11

Rekyt opened this issue Dec 15, 2020 · 3 comments
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enhancement New feature or request

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@Rekyt
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Rekyt commented Dec 15, 2020

I'm pretty sure that the call to apply() in fd_raoq() could be simplified through matrix algebra:
https://github.com/Bisaloo/fundiversity/blob/1e175ba88531e08242ab9c69b9e470b4cee9e759/R/fd_raoq.R#L60-L62
@Rekyt Rekyt added the enhancement New feature or request label Dec 15, 2020
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Bisaloo commented Dec 15, 2020 

diag(sp_com %*% tcrossprod(dist_matrix, sp_com))

Now, an interesting question is trying to understand what values outside of the diagonal mean 🤔

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Bisaloo commented Dec 16, 2020

expr min lq mean median uq max neval
fd_raoq(traits = traits_birds, sp_com = site_sp_birds) 1.119820 1.167955 1.577048 1.207574 1.300485 8.713098 1000
fd_raoq_old(traits = traits_birds, sp_com = site_sp_birds) 2.045435 2.100812 3.159528 2.160546 2.357134 100.263167 1000

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Bisaloo commented Dec 16, 2020

Fixed by 5240f08.

@Bisaloo Bisaloo closed this as completed Dec 16, 2020
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@Rekyt @Bisaloo