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Add CANAPE #819

Closed
3 tasks done
shawnlaffan opened this issue Sep 1, 2022 · 2 comments
Closed
3 tasks done

Add CANAPE #819

shawnlaffan opened this issue Sep 1, 2022 · 2 comments
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@shawnlaffan
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enhancement
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Release_4.0

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@shawnlaffan
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shawnlaffan commented Sep 1, 2022 •
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The CANAPE protocol is one of the things Biodiverse is most used for. CANAPE is a compound method that requires certain indices and a set of randomisations, which is why it has not yet been implemented.

However, it can be done automatically in the same way that z-scores are done for randomisations. The randomisation system can detect if the component calculations have been run and do the categorisation based on the p-ranks.

Colouring in the GUI will be more interesting but can still be done. (And has been).

Remaining items:
@shawnlaffan shawnlaffan self-assigned this Sep 1, 2022
@shawnlaffan shawnlaffan added this to the Release_4.0 milestone Sep 8, 2022
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
Initial work to calculate CANAPE
aade66f 
Updates issue #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
Refactor CANAPE codes into a sub
adccff9 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
Add code to check validity of CANAPE calcs
0bd3412 
And minor refactor of the spatial code

Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
Implement calculate_canape for trees
a22ee64 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
Commented code for the future
b5f1684 
#819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
GUI spatial outputs: Colour grid using CANAPE codes
aef0ef2 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
GUI cluster outputs: Colour grid using CANAPE codes
92aec17 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
GUI cluster outputs: Colour dendrogram using CANAPE codes
8ab08ca 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
GUI cluster tab: hide legend when plotting CANAPE
4dfff11 
Includes code that might be useful later.

Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
GUI spatial: hide legend when plotting CANAPE
598a37a 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 9, 2022
@shawnlaffan
CANAPE: categorise using PE_WE not PE_WE_P
8c6f6cf 
The latter returns 0 when nothing is on the tree,
but we want to exclude such cells.

Updates #819
shawnlaffan added a commit that referenced this issue Sep 10, 2022
@shawnlaffan
CANAPE: ensure we clear any pre-existing values when non-sig
3a4c973 
It is possible that an element can switch from
significant to non-significant.  If so we need
to clear the existing CANAPE codes.

Updates #819
shawnlaffan added a commit that referenced this issue Sep 10, 2022
@shawnlaffan
CANAPE: ensure we clear any pre-existing values when non-sig
40ea63e 
It is possible that an element can switch from
significant to non-significant.  If so we need
to clear the existing CANAPE codes.

Updates #819
shawnlaffan added a commit that referenced this issue Sep 10, 2022
@shawnlaffan
Add tests for CANAPE protocol
b2ad4fa 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 11, 2022
@shawnlaffan
CANAPE: categorise using PE_WE not PE_WE_P
60404b6 
The latter returns 0 when nothing is on the tree,
but we want to exclude such cells.

Updates #819
shawnlaffan added a commit that referenced this issue Sep 11, 2022
@shawnlaffan
CANAPE: ensure we clear any pre-existing values when non-sig
7e93bb2 
It is possible that an element can switch from
significant to non-significant.  If so we need
to clear the existing CANAPE codes.

Updates #819
shawnlaffan added a commit that referenced this issue Sep 11, 2022
@shawnlaffan
Add tests for CANAPE protocol
6fe3479 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 11, 2022
@shawnlaffan
CANAPE: Update legend when plotted
5543a62 
And reset when it is turned off.

Updates #819
This was referenced Sep 11, 2022
Closed
Merged
shawnlaffan added a commit that referenced this issue Sep 11, 2022
@shawnlaffan
GUI: Simplify CANAPE legend flag
0989ab9 
Updates #819
@shawnlaffan
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reopen - there are still associated tasks

@shawnlaffan shawnlaffan reopened this Sep 11, 2022
shawnlaffan added a commit that referenced this issue Sep 16, 2022
@shawnlaffan
Add tests for the CANAPE calculations (and z-scores while we are at it)
f41d9e4 
Updates #819
shawnlaffan added a commit that referenced this issue Sep 16, 2022
@shawnlaffan
Include CANAPE when reintegrating randomisations
e854165 
Updates #819
@shawnlaffan shawnlaffan mentioned this issue Sep 20, 2022
Merged
@shawnlaffan
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All tasks complete, mark as fixed

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