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Speed improvements for PE, RPE etc#831

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shawnlaffan merged 24 commits intomastershawnlaffan/biodiverse:masterfrom faster_RPE2_maybeshawnlaffan/biodiverse:faster_RPE2_maybeCopy head branch name to clipboardOct 24, 2022

+369-161

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Commits on Sep 27, 2022

• Experimental code to see if we can make RPE2 faster

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• Indices: PE: possible faster local range assignment for single element calcs

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• Indices: RPE2: get the equalised branch length as a global precalc

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• Indices: PE: back to slice assign for local ranges

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• Indices: PE: use hash slice assign for global ranges

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• Indices: PE: precalculate the inverse range weighted branch lengths

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• Indices: PE: use a hash of parent names for each node on the tree

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• Indices: PE: go back to the previous approach

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Commits on Oct 6, 2022

• Indices PE: use List::Util::sum instead of a loop

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• Indices PE: simplify global range calcs

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Commits on Oct 22, 2022

• PE: use Biodiverse::Utils 1.08 where available

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• Indices: get_node_range_hash makes fewer progress calls

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• Tree.pm: clone_tree_with_equalised_branch_lengths: clear cache in one call

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• Tree.pm: clone_tree_with_equalised_branch_lengths: shorter length assignment

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• Tree: add method to avoid cloning caches when they are then discarded anyway

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• Tree.pm: use cacheless tree clone in rescale

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• GUI: more efficient tree trimming to basedata

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• use Tree::delete_all_cached_values in more places

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Commits on Oct 23, 2022

• TreeNode.pm: add get_path_name_array_to_root_node methods

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• Another use of Tree::delete_all_cached_values

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• Simplify Tree::get_total_tree_length

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• Spatial.pm: Avoid creating variables we don't use

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• Speed up tree destruction by avoiding recursion

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• clarify a comment

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