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New DiseasyImmunity module and waning function #101

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New DiseasyImmunity module and waning function #101

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SofiaOtero
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@SofiaOtero SofiaOtero commented Apr 15, 2024 •
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Intent

This PR will add a files:

  • DiseasyImmunity module

References #100

Approach

Selecting the best approach to fit the waning immunity for our SEIR models

Known issues

Checklist

  • The PR passes all local unit tests
  • I have documented any new features introduced
  • If the PR adds a new feature, please add an entry in NEWS.md
  • A reviewer is assigned to this PR

@SofiaOtero SofiaOtero linked an issue Apr 15, 2024 that may be closed by this pull request
FEATURE: Create a module to describe waning immunity #100
Open
@RasmusSkytte RasmusSkytte marked this pull request as draft April 15, 2024 08:22
SofiaOtero and others added 24 commits April 15, 2024 16:17
@SofiaOtero
Edit analytic approach and add stochastic approach
a1dcea3
@SofiaOtero
Merge branch 'feature/DiseasyImmunity' of https://github.com/ssi-dk/d…
0405b04 
…iseasy into feature/DiseasyImmunity
@RasmusSkytte
feat(waning): Add probability of occupancy helper
f0a67d8
@RasmusSkytte
feat(waning): Improve validation of occupancy helper
f2fb2a2
@RasmusSkytte
chore(waning): Fix lints
8553a5d
@RasmusSkytte
chore(waning): Simplify phypo slightly
f9686e6
@RasmusSkytte
chore(waning): Move hypoexponential helpers to separate file
a14fc9e
@RasmusSkytte
feat(waning): Allow K < 3
2cfd539
@RasmusSkytte
chore: Update pak.lock
ded3475
@RasmusSkytte
chore: Update pak.lock
55b39a1
@RasmusSkytte
chore: Update pak.lock
526fcd9
@SofiaOtero
Fixed to be used with occupancy function and adds elbow method
70b2f0e
@SofiaOtero
chore: Update pak.lock
7a93a81
@SofiaOtero
Fixes obj function to run from K=1
28e2ade
@SofiaOtero
Merge branch 'feature/DiseasyImmunity' of https://github.com/ssi-dk/d…
8b20d58 
…iseasy into feature/DiseasyImmunity
@SofiaOtero
chore: Update pak.lock
636793c
@RasmusSkytte
chore: Update pak.lock
b42ab08
@SofiaOtero
Adds to DiseasyImmunity model and creating test file
03ca7de
@SofiaOtero
chore: Update pak.lock
60ccddc
@SofiaOtero
docs: update documentation
dc19cad
@SofiaOtero
add functionality to DiseasyImmunity and fixes to analytic_approach
19792b8
@SofiaOtero
chore: Update pak.lock
9c580e5
@SofiaOtero
docs: update documentation
4281522
@SofiaOtero
Adding custom waning and approximate_compartmental
871e908
SofiaOtero and others added 19 commits May 17, 2024 11:57
@SofiaOtero
docs: update documentation
effdde5
@SofiaOtero
chore: Update pak.lock
ff6f7d9
@SofiaOtero
now fully working approximate_compartmental function
072158b
@SofiaOtero
Add plot functionallity
89533ef
@RasmusSkytte
fix(DiseasyBaseModule): Correctly hash lists of functions
6eba85a
@SofiaOtero
Catching on app_compartmental and add file for vignette
303d55f
@SofiaOtero
Vignette for the immunity module and some env and other fixes
cd33edd
@RasmusSkytte
docs(DiseasyImmunity): Update Roxygen documentation
c1d08ae
@RasmusSkytte
feat(DiseasyImmunity): Invisibly return models
8d5a4c1 
I am not sure that "set_" functions should return the models.

For now, I return them invisibly until I determine if they need to be returned.
@RasmusSkytte
feat(DiseasyImmunity): Update checkmate input validation
c0321c6
@RasmusSkytte
chore(DiseasyImmunity): Fix spelling, lints, formatting
8c69e37
@RasmusSkytte
docs(hypoexponential): Update Roxygen docs
ff25d21
@RasmusSkytte
feat(DiseasyImmunity): Integrate occupancy_probability into module
42f2b3b
@RasmusSkytte
fix(DiseasyImmunity): Improve detection of available_waning_models
d08be67
@RasmusSkytte
docs(DiseasyImmunity): Adjust vignette wording
3bf60f2
@RasmusSkytte
docs(DiseasyImmunity): rename model_name to model in `$set_waning…
4bc293c 
…_model()`

Since `model` can also be a function, we should not call it `model_name`
@RasmusSkytte
docs(hypoexponential): Add examples
0700281
@RasmusSkytte
fix(hypoexponential): Correctly pass args to qhypo and return only root
c976169
@RasmusSkytte
chore(WORDLIST): Add entry for hypoexponential
aa858f5
@RasmusSkytte RasmusSkytte mentioned this pull request Jul 3, 2024
Merged
4 tasks
@RasmusSkytte RasmusSkytte mentioned this pull request Jul 5, 2024
Merged
8 tasks
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FEATURE: Create a module to describe waning immunity
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@SofiaOtero @RasmusSkytte