Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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
Assignees
@shawnlaffan
Labels
enhancement
Milestone
Release_4.0

Comments

@shawnlaffan
Copy link
Owner

shawnlaffan commented Sep 1, 2022 •
edited

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
Open
Merged
shawnlaffan added a commit that referenced this issue Sep 11, 2022
@shawnlaffan
GUI: Simplify CANAPE legend flag
0989ab9 
Updates #819
@shawnlaffan
Copy link
Owner Author

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
Copy link
Owner Author

All tasks complete, mark as fixed

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@shawnlaffan shawnlaffan

Labels
enhancement
Projects
None yet
Milestone
Release_4.0
Development

No branches or pull requests
1 participant
@shawnlaffan