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Indices - implement exact NRI expectations #789

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shawnlaffan opened this issue Apr 30, 2021 · 1 comment
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Indices - implement exact NRI expectations #789

shawnlaffan opened this issue Apr 30, 2021 · 1 comment
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Release_4.0

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Described in Tsirogiannis et al. (2012). https://doi.org/10.1007/978-3-642-33122-0_3

Follow-on from #786
@shawnlaffan shawnlaffan self-assigned this Apr 30, 2021
@shawnlaffan shawnlaffan added this to the Release_4.0 milestone Apr 30, 2021
shawnlaffan added a commit that referenced this issue Apr 30, 2021
@shawnlaffan
NRI/NTI: Add infrastructure to disable MPD calls
81f7b6a 
Preparation for #789
shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
indices: add exact implementation of expected MPD
bf31429 
Updates #789
shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
Implement exact expected SD for NRI calculations
89f4c03 
This is done of the tree object, so move
the expected mean caluclation to there as well.

Commented debug code will be removed in a future commit.

Updates #789
shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
Remove commented code, unused variables
04a456e 
Updates #789
shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
NRI calcs: use exact mean and SD
a8edc13 
Update tests accordingly

Updates #789
shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
NRi exact estimates: cache more constants
558de2d 
Rearrange the cache structure while we are at it.

Also skip root nodes with single children.

Updates #789
shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
NRI exact calcs: test for when tree root is not the LCA
7dee206 
Where LCA is the last common ancestor of all terminals.

Sometimes there are single child nodes immediately below the root.

Updates #789
shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
Add Tsirogiannis et al. (2012) to get_metadata_calc_nri_nti_expected_…
c272263 
…values

Updates #789
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shawnlaffan commented May 5, 2021 •
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All changes now on master branch. Mark as fixed.

@shawnlaffan shawnlaffan mentioned this issue May 5, 2021
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shawnlaffan added a commit that referenced this issue May 5, 2021
@shawnlaffan
NRI SD: throw exception when sample size exceeds tree terminal count
0976fb2 
A late update to #789
shawnlaffan added a commit that referenced this issue May 12, 2021
@shawnlaffan
Add tests for NRI and NTI exact expected values
0f2e044 
Also return 0 for the SD when the requested
sample count equals the number of terminals.

Updates #790, and a late update to #789
This was referenced May 18, 2021
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