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Add vignette and plotting methods for DiseasyModelRegression #164

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Add vignette and plotting methods for DiseasyModelRegression #164

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RasmusSkytte
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@RasmusSkytte RasmusSkytte commented Feb 4, 2025 •
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Intent

Fixes #34

.. also implements the $plot() method for DiseasyModelRegression

Approach

Plot method from DiseasyModelOde adapted to DiseasyModelRegression.

A first draft for a vignette has been created

Known issues

Waiting on the following

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

RasmusSkytte and others added 30 commits January 27, 2025 15:18
@RasmusSkytte
fix(seir_example_data): Set seed using withr
3b64a2a
@RasmusSkytte
feat(SEIR-initialisation): Use synthetic features to compute incidence
49062f8
@RasmusSkytte
docs(SEIR-initialisation): Align the use of colours in vignette
cafd663
@RasmusSkytte
feat(initialise_state_vector): Add checkmate checks missing arguments
3b58c9a
@RasmusSkytte
feat(initialise_state_vector): Change default label for variant to "All"
a56604b
@RasmusSkytte
fix(initialise_state_vector): Convert from incidence data to required…
3245b97 
… metric
@RasmusSkytte
feat(DiseasyModelOde): Add incidence_feature_name parameter
f523613
@RasmusSkytte
docs: Align model parameters with mlr3 standard
e33b903
@RasmusSkytte
feat(DiseasyModelOde): Add function to initialise and solve ode
8463946
@RasmusSkytte
fix(DiseasyModel): Rename old references $get_training_data() -> `$…
49174b2 
…get_data()`
@RasmusSkytte
feat(DiseasyModelOde): Simplify detection of missing stratifications
d8278c0
@RasmusSkytte
feat(DiseasyModelOde): Fix the internal solver wrapper
1faf9a4
@RasmusSkytte
feat(DiseasyModelOde): Introduce maps from model rates to observables
fd319f2
@RasmusSkytte
feat(DiseasyBaseModule): Generalise the plotting method
1512a18
@RasmusSkytte
feat(DiseasyModelOde): Adjust the output of $solve_ode
f7c86b2
@RasmusSkytte
feat(DiseasyModelOde): Implement the $get_results() method
0d52363
@RasmusSkytte
feat(DiseasyModelOde): Implement a reduce system in $get_results()
4404c4f
@RasmusSkytte
feat(DiseasyObservables): Add override for last_queryable_date
634acb6
@RasmusSkytte
feat(DiseasyModelOde): Implement a plotting method
aa73784
@RasmusSkytte
fix(DiseasyModelOdeSeir): Inherit from DiseasyModelOde not `Diseasy…
7e23692 
…Model`
@RasmusSkytte
docs: Add first draft of vignette for DiseasyModelOdeSeir
22abfa2
@RasmusSkytte
feat(DiseasyModelOdeSeir): Validate incidence_max_order_derivatives…
1431a51 
… parameter
@RasmusSkytte
feat(DiseasyModelOde): Change model output to "n_infected"
f0eb473
@RasmusSkytte
feat(DiseasyModelOde): Add default map for "n_infected"
67a7e02
@RasmusSkytte
fix(DiseasyModelOde): Fix the default map for "incidence"
3ffd406
@RasmusSkytte
feat(DiseasyModelOde): Merge default and user mapings
d7be68f
@RasmusSkytte
feat(DiseasystoreSeirExample): Use cache for faster tests / vignette …
462fcfe 
…rendering
@RasmusSkytte
feat(DiseasyModelOde): Use different colors for each mapping
ae9a32a
@RasmusSkytte
feat(DiseasyModelOde): Adjust column order in $get_results()
828db2b
@RasmusSkytte
feat(DiseasyModelOde): Re-order the output of $get_results()
6829dcc
@RasmusSkytte RasmusSkytte force-pushed the feature/regression-model-vignette branch from b0d0c78 to 7c46c2a Compare February 4, 2025 13:26
RasmusSkytte and others added 18 commits February 4, 2025 14:37
@RasmusSkytte
docs(plot): Remove broken example
c80a69a
@RasmusSkytte
chore: Update diseasy-model-ode cache
4ebbfbc
@RasmusSkytte
chore: Update pak.lock
05e922a
@RasmusSkytte
feat(DiseasyModelOde): Simplify the plotting method
244968c
@RasmusSkytte
feat(DiseasyModelOde): Improve plot method
f108d61
@RasmusSkytte
docs(diseasy-model-ode): Use same colors as initialisation vignette
92576cc
@RasmusSkytte
feat(diseasy-model-ode): Disable caching for the vignette
29f5422
@RasmusSkytte
docs: Add vignette for regression model templates
1ed4432
@RasmusSkytte
feat(DiseasyModel): Add "plotting" period to $get_data()
bd4b90d
@RasmusSkytte
feat(DiseasyModelOdeSeir): Ensure only training data is used in `$ini…
6b0abc8 
…tialise_state_vector()`
@RasmusSkytte
feat(DiseasyModelRegression): Cast prediction_length as integer to in…
117f70d 
…crease cache hits
@RasmusSkytte
feat(DiseasyModelRegression): Add plotting method
2be0204
@RasmusSkytte
fix(DiseasyModel): Fix table name collisions
7524039
@RasmusSkytte
fix(DiseasyModelRegression): Only return results after training period
55d0c69
@RasmusSkytte
fix(DiseasyModelRegression): Correctly get R to format the plot as in…
9ae1890 
…structed
@RasmusSkytte
feat(DiseasyModelRegression): Improve plotting method
1237a17
@RasmusSkytte
docs(diseasy-model-regression): Improve the user vignette
20ec260
@RasmusSkytte
chore: Update pak.lock
17bfb3b
@RasmusSkytte RasmusSkytte force-pushed the feature/regression-model-vignette branch from 9c92c16 to 17bfb3b Compare February 4, 2025 13:43
@RasmusSkytte RasmusSkytte force-pushed the feature/regression-model-vignette branch from 14590bc to 9eb50d6 Compare February 7, 2025 09:26
@RasmusSkytte RasmusSkytte mentioned this pull request Feb 7, 2025
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DiseasyModelG_/B_: Add vignettes that showcases the reference models
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