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Indices - add MPD and MNTD variance #811

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shawnlaffan opened this issue Jul 9, 2022 · 1 comment
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Indices - add MPD and MNTD variance #811

shawnlaffan opened this issue Jul 9, 2022 · 1 comment
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enhancement indices
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Release_4.0

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@shawnlaffan
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This is an adaptation of Clarke & Warwick (2001) https://dx.doi.org/10.3354/meps216265

It is similar to the RMSD indices but corrects for the sample mean.

See also discussion at https://groups.google.com/g/biodiverse-users/c/vgy0k5GHPeA
@shawnlaffan shawnlaffan added this to the Release_4.0 milestone Jul 9, 2022
@shawnlaffan shawnlaffan self-assigned this Jul 9, 2022
shawnlaffan added a commit that referenced this issue Jul 9, 2022
@shawnlaffan
Add MPD and MNTD variance indices
1e0846e 
Updates #811
shawnlaffan added a commit that referenced this issue Jul 10, 2022
@shawnlaffan
Indices: Set up infrastructure to not skip the MPD variance when needed
6fcae87 
Updates #811
shawnlaffan added a commit that referenced this issue Jul 10, 2022
@shawnlaffan
NRI/NTI: add conditional var for mntd calculations, rename mpd condit…
bfd7eec 
…ional

Preparatory for also doing the variance.

Minor code formatting changes while we are there.

Updates #811
shawnlaffan added a commit that referenced this issue Jul 10, 2022
@shawnlaffan
NRI/NTI: Refactor repeated conditionals
962e8ef 
Related to #811
shawnlaffan added a commit that referenced this issue Jul 10, 2022
@shawnlaffan
Indices: calculate net VPD (variance of phylogenetic distances)
3750ce5 
Still need to double check tests.

Updates #811
shawnlaffan added a commit that referenced this issue Jul 10, 2022
@shawnlaffan
Indices: Only calc VPD when n tips >2
7689a6b 
Updates #811
shawnlaffan added a commit that referenced this issue Jul 10, 2022
@shawnlaffan
Clarify PMPD_VARIANCE description
e815888 
Updates #811
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