Speed improvements for PE, RPE etc #831
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This saves some repeated calculation of the same values per processing group.
This should avoid the need to climb up and down the tree when PD is not needed.
Benchmarking shows it to be faster.
We can grab these once after all the weights have been calculated. This means we do not need to run all the hash mergers and so Data::Recursive and Panda::Lib can be removed from this file.
It avoids repeated calls to the last-if sub by running it all in one, and also assigns as it goes.
A micro-optimisation but otherwise it triggers huge numbers of calls for no real update when analysing large data sets.
… anyway Still has much repeated looping.
Mainly by avoiding recursion in internal methods.
This avoids recursion in delete_cached_values_below.
Returns an array of node names up to and including to the root. This saves time in the Phylo calculations as there is no need to then get the names. The array args variant does all the work.
This reduces the time for one large tree from ~14 s to ~6.5 s. Whether it scales linearly remains to be seen. The commented code in Spatial.pm will be cleaned up in a later commit.
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Includes a few other minor cleanups.