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D-optimal experimental designs #299

Merged
merged 118 commits into from
Jan 16, 2025
Merged

D-optimal experimental designs #299

merged 118 commits into from
Jan 16, 2025

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RuneChristensen-NN
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Gives user the option to create d-optimal designs with minimal effort.
Uses ProcessOptimiser's Space class

Introduces "patsy" as a dependency

RuneChristensen-NN and others added 30 commits September 23, 2024 14:50
@RuneChristensen-NN
notebook with some initial tests of DOE - lifting dexpy code
c5ea722 
"""
@RuneChristensen-NN
Minor cleaning of initial_testing notebook. Added some license and co…
7264623 
…pyright information related to use of dexpy functions.
@RuneChristensen-NN
Made some code wrapper
dca5b51
@RuneChristensen-NN
Cleaned and comments
fce9706
@RuneChristensen-NN
Beginning to modularize it
7298478
@RuneChristensen-NN
starting the init file
0edd32b
@RuneChristensen-NN
cleaned doe_to_real_space
1ea495b
@RuneChristensen-NN
Updated modularization efforts - nearly done for optimal
cbc5473
@RuneChristensen-NN
example amnd classical designs WIP
0199c56
@RuneChristensen-NN
Broke large function into smaller functions
82b9c14
@RuneChristensen-NN
formatted
1c94741
@RuneChristensen-NN
light cleaning before merging back
3df9004
@RuneChristensen-NN
updated version to fit develop
864d6f7
@RuneChristensen-NN
Merge pull request #286 from RuneChristensen-NN/first_doe_tests
6c2c3de 
updated version to fit develop
@RuneChristensen-NN
Merge pull request #285 from novonordisk-research/develop
d4ae98c 
Getting the DOE branch up to date
@RuneChristensen-NN
Include dexpy License notice
8644631
@RuneChristensen-NN
Merge pull request #287 from RuneChristensen-NN/first_doe_tests
86e4449 
Include dexpy License notice
@RuneChristensen-NN
Prepping for categorical
77b6809
@RuneChristensen-NN
Pulling full factorial function from pyDOE
3fe2005
@RuneChristensen-NN
More flexible model making - prep for using cat variables with two le…
2b1d427 
…vels
@RuneChristensen-NN
WIP: implementing categorical variables - Made function the smooth in…
575e2e5 
…itial guess to 1 or -1
@RuneChristensen-NN
Added a bit of code to ensure cat factors are always -1 or 1
bf7fbab
@RuneChristensen-NN
better comments
fa8e877
@RuneChristensen-NN
Fully implemented 2 level categorical
68cb0e1
@RuneChristensen-NN
removed old testing files
112ad92
@RuneChristensen-NN
example in docstring includes cat var
4c29555
@RuneChristensen-NN
Function split up and clean up
16a3951
@RuneChristensen-NN
Moved som more general functions to a utils file
6a5f728
@RuneChristensen-NN
Linting
9df15f6
@RuneChristensen-NN
fixed random_but_group_replicates to actually randomize
c230e07
@RuneChristensen-NN RuneChristensen-NN self-assigned this Dec 17, 2024
SRFU-NN
SRFU-NN approved these changes Jan 8, 2025
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Lots of comments, but nothing that points to anything being wrong. Mostly "help me understand", with a few "I would have done this differently, but it is just a suggestion".

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RuneChristensen-NN
RuneChristensen-NN commented Jan 15, 2025
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Running through @SRFU-NN review comments. Still a bit to go

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RuneChristensen-NN and others added 19 commits January 16, 2025 09:24
Minor review comments implemented
53de04f
Tiny changes and versioning to dexpy ref
c1f6c4d
@RuneChristensen-NN @SRFU-NN
Update ProcessOptimizer/samplers/doe/optimal_design.py
84a621b 
Co-authored-by: Søren Furbo <104423389+SRFU-NN@users.noreply.github.com>
Merge branch 'DOE_D_Optimal' of https://github.com/novonordisk-resear…
bbb42c7 
…ch/ProcessOptimizer into DOE_D_Optimal
checking that seed is int rather than true'ish
38f763e
using POs random generator
ba831f3
Cleaned up random state generator. Logic in PO utils
7a8eab8
@RuneChristensen-NN
Merge pull request #314 from novonordisk-research/develop
1ba800c 
Update D_optimal_branch
Merge branch 'DOE_D_Optimal' of https://github.com/novonordisk-resear…
bc48e0c 
…ch/ProcessOptimizer into DOE_D_Optimal
Using PO rng for shufling the data
18ca6d1
consistent docstrings
6e5c4b2
Consistency maintained push
dbe8b48
@RuneChristensen-NN @SRFU-NN
Update ProcessOptimizer/samplers/doe/optimal_design.py
78911c5 
Co-authored-by: Søren Furbo <104423389+SRFU-NN@users.noreply.github.com>
Cleaned up model_order_and_include_powers function
090eb32
seeding of exp randomisation during sort. Fixed such that you can ask…
6c2803c 
… for 0 experiments and get an error instead of model rank num experiments.
Updated the tests for random seed and more tests for checking
20f376f
Fixing some things in the tests
9a68f25
Checking type and size of "res"
84bbe9c
Fixed test errors
f0d8a9b
@RuneChristensen-NN RuneChristensen-NN merged commit e70b2b0 into develop Jan 16, 2025
6 checks passed
@RuneChristensen-NN RuneChristensen-NN deleted the DOE_D_Optimal branch January 16, 2025 15:28
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@SRFU-NN SRFU-NN SRFU-NN approved these changes

@sqbl sqbl Awaiting requested review from sqbl

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@RuneChristensen-NN RuneChristensen-NN

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@RuneChristensen-NN @SRFU-NN