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Indices - add phylogenetic abundance #559

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shawnlaffan opened this issue Jul 6, 2015 · 1 comment
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Indices - add phylogenetic abundance #559

shawnlaffan opened this issue Jul 6, 2015 · 1 comment
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enhancement
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Release_1.1

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@shawnlaffan
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It would be useful to calculate PD weighted by the abundance of the terminals, where a branch's abundance is the sum of the abundances of its terminals.

PDA = \sum_{c \in C}(abundance \times l_c)
@shawnlaffan shawnlaffan self-assigned this Jul 6, 2015
@shawnlaffan shawnlaffan added this to the Release_1.01 milestone Jul 6, 2015
shawnlaffan added a commit that referenced this issue Jul 7, 2015
@shawnlaffan
Add calculation for phylogenetic abundance.
453940d 
The abundance of each branch is the sum of its named descendant abundance, multiplied by the branch length.

This is on the basis that PD is feature diversity thus if a branch is 10 units long then it represents 10 features.  If that branch has 5 named descendants, each with unit abundance (=1) then there are 10 * 5 features from that branch in the sample.

Updates issue #559

Signed-off-by: Shawn Laffan <shawnlaffan@gmail.com>
shawnlaffan added a commit that referenced this issue Jul 7, 2015
@shawnlaffan
Use get_path_lengths_to_root_node to take advantage of caching.
bdf455d 
This avoids the need to repeatedly traverse the path to the root node and get the lengths along the way.  The paths are cached so the overall code speed is improved.

Updates issue #559.

Signed-off-by: Shawn Laffan <shawnlaffan@gmail.com>
@shawnlaffan shawnlaffan changed the title Indices - add abundance weighted PD Indices - add phylogenetic abundance Jul 7, 2015
shawnlaffan added a commit that referenced this issue Jul 8, 2015
@shawnlaffan
Avoid "value on reference is experimental" warning.
5acdc6b 
Updates issue #559

Signed-off-by: Shawn Laffan <shawnlaffan@gmail.com>
@shawnlaffan shawnlaffan mentioned this issue Aug 31, 2015
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Mark as fixed.

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