From 479a47e3984711aea565512738773f06fdc696e3 Mon Sep 17 00:00:00 2001 From: Adam REMAKI Date: Wed, 9 Aug 2023 20:32:52 +0200 Subject: [PATCH] Clean compute params (#24) Clean compute params --- README.md | 2 +- changelog.md | 7 + docs/assets/charts/estimates_densities.json | 2 +- docs/assets/charts/fitted_visit.json | 2 +- .../charts/interactive_fitted_visit.html | 14 +- docs/assets/charts/interactive_visit.html | 14 +- docs/assets/charts/normalized_probe.json | 2 +- .../charts/normalized_probe_dashboard.html | 22 +- docs/assets/charts/visit.json | 2 +- docs/components/probe.md | 20 +- docs/index.md | 33 +-- edsteva/__init__.py | 2 +- .../algos/loss_minimization.py | 1 + .../rectangle_function/rectangle_function.py | 13 +- edsteva/models/step_function/step_function.py | 13 +- edsteva/probes/base/base.py | 23 +- edsteva/probes/biology/biology.py | 156 +++++++------ .../per_measurement.py | 20 +- .../completeness_predictors/per_visit.py | 20 +- .../viz_configs/n_measurement/defaults.py | 14 +- .../viz_configs/per_measurement/defaults.py | 14 +- .../biology/viz_configs/per_visit/defaults.py | 14 +- .../completeness_predictors/per_condition.py | 32 ++- .../completeness_predictors/per_visit.py | 32 ++- edsteva/probes/condition/condition.py | 108 +++++---- .../viz_configs/n_condition/defaults.py | 14 +- .../viz_configs/per_condition/defaults.py | 14 +- .../viz_configs/per_visit/defaults.py | 14 +- .../note/completeness_predictors/per_note.py | 20 +- .../note/completeness_predictors/per_visit.py | 20 +- edsteva/probes/note/note.py | 110 +++++---- .../note/viz_configs/n_note/defaults.py | 14 +- .../note/viz_configs/per_note/defaults.py | 14 +- .../note/viz_configs/per_visit/defaults.py | 14 +- edsteva/probes/utils/filter_df.py | 91 ++++---- edsteva/probes/utils/prepare_df.py | 215 +++++++++--------- edsteva/probes/utils/utils.py | 23 +- .../completeness_predictors/per_visit.py | 18 +- edsteva/probes/visit/visit.py | 80 ++++--- .../visit/viz_configs/n_visit/defaults.py | 14 +- .../visit/viz_configs/per_visit/defaults.py | 14 +- edsteva/utils/checks.py | 21 -- .../normalized_probe/normalized_probe.py | 7 +- edsteva/viz/dashboards/probe/wrapper.py | 10 +- .../estimates_densities.py | 46 ++-- .../normalized_probe/normalized_probe.py | 25 +- edsteva/viz/plots/probe/wrapper.py | 20 +- edsteva/viz/utils.py | 52 +---- notebooks/generate_plots_for_doc.ipynb | 12 +- pyproject.toml | 2 +- tests/test_custom_probe.py | 113 +++------ tests/test_probes.py | 69 +++--- tests/test_viz.py | 6 +- 53 files changed, 822 insertions(+), 832 deletions(-) diff --git a/README.md b/README.md index 7b16b54a..5f3b24df 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,7 @@ pip install edsteva We recommend pinning the library version in your projects, or use a strict package manager like [Poetry](https://python-poetry.org/). ``` -pip install edsteva==0.2.4 +pip install edsteva==0.2.5 ``` ## Example diff --git a/changelog.md b/changelog.md index 3a2e1b56..1b5fda96 100644 --- a/changelog.md +++ b/changelog.md @@ -1,4 +1,11 @@ # Changelog +## v0.2.5 - 10-08-2023 + +- New Probe parameters: + - Age range: Age of patient at visit + - Provenance source: Where the patient came from before the visit (emergency, consultation, etc.) + - stay source: Type of care (MCO, PSY, SSY) +- Refacto the params type to make it more uniform. ## v0.2.4 - 28-07-2023 - Viz: Simplify normalized probe plot diff --git a/docs/assets/charts/estimates_densities.json b/docs/assets/charts/estimates_densities.json index 3d700a84..9c33052a 100644 --- a/docs/assets/charts/estimates_densities.json +++ b/docs/assets/charts/estimates_densities.json @@ -1 +1 @@ -{"config": {"view": {"continuousWidth": 300, "continuousHeight": 300}, "axis": {"labelFontSize": 12, "labelLimit": 500, "titleFontSize": 13}, "legend": {"labelFontSize": 12, "labelLimit": 500, "titleFontSize": 13}}, "vconcat": [{"vconcat": [{"layer": [{"mark": {"type": "bar", "size": 10}, "encoding": {"x": {"axis": {"format": "%Y, %b", 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a/docs/assets/charts/interactive_fitted_visit.html b/docs/assets/charts/interactive_fitted_visit.html index ca2669fb..eb526d5f 100644 --- a/docs/assets/charts/interactive_fitted_visit.html +++ b/docs/assets/charts/interactive_fitted_visit.html @@ -11,11 +11,11 @@
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Interactive filters