bella-companion 0.0.6__py3-none-any.whl → 0.0.8__py3-none-any.whl
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- bella_companion/cli.py +21 -9
- bella_companion/fbd_empirical/__init__.py +4 -0
- bella_companion/fbd_empirical/notbooks.ipynb +85 -274
- bella_companion/fbd_empirical/run_beast.py +46 -32
- bella_companion/fbd_empirical/summarize_logs.py +15 -32
- bella_companion/simulations/__init__.py +8 -1
- bella_companion/simulations/figures/epi_skyline_results.py +2 -2
- bella_companion/simulations/figures/explain/pdp.py +21 -27
- bella_companion/simulations/figures/explain/shap.py +1 -1
- bella_companion/simulations/figures/fbd_2traits_results.py +1 -1
- bella_companion/simulations/figures/fbd_no_traits_results.py +2 -2
- bella_companion/simulations/figures/scenarios.py +2 -2
- bella_companion/simulations/generate_data.py +4 -2
- bella_companion/simulations/metrics.py +62 -0
- bella_companion/simulations/scenarios/epi_multitype.py +1 -1
- bella_companion/simulations/scenarios/fbd_2traits.py +1 -4
- bella_companion/simulations/summarize_logs.py +3 -4
- bella_companion/utils/__init__.py +7 -11
- bella_companion/utils/beast.py +2 -2
- {bella_companion-0.0.6.dist-info → bella_companion-0.0.8.dist-info}/METADATA +2 -2
- bella_companion-0.0.8.dist-info/RECORD +42 -0
- bella_companion/fbd_empirical/figure.py +0 -37
- bella_companion/fbd_empirical/params.json +0 -11
- bella_companion-0.0.6.dist-info/RECORD +0 -42
- /bella_companion/{utils/plots.py → simulations/figures/utils.py} +0 -0
- {bella_companion-0.0.6.dist-info → bella_companion-0.0.8.dist-info}/WHEEL +0 -0
- {bella_companion-0.0.6.dist-info → bella_companion-0.0.8.dist-info}/entry_points.txt +0 -0
bella_companion/cli.py
CHANGED
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@@ -4,12 +4,11 @@ from pathlib import Path
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from dotenv import load_dotenv
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from bella_companion.
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from bella_companion.fbd_empirical import run_beast as run_fbd_empirical
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from bella_companion.fbd_empirical import summarize_logs as summarize_fbd_empirical
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from bella_companion.simulations import generate_data, generate_figures, print_metrics
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from bella_companion.simulations import run_beast as run_simulations
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from bella_companion.simulations import summarize_logs as summarize_simulations
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def main():
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@@ -28,15 +27,28 @@ def main():
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subparsers.add_parser(
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"sim-run", help="Run BEAST2 analyses on simulation datasets."
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).set_defaults(func=
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).set_defaults(func=run_simulations)
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subparsers.add_parser(
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"sim-
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).set_defaults(func=
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"sim-summarize", help="Summarize BEAST2 log outputs for simulations."
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).set_defaults(func=summarize_simulations)
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subparsers.add_parser(
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"sim-metrics", help="Compute and print metrics from simulation results."
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).set_defaults(func=print_metrics)
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subparsers.add_parser(
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"sim-figures", help="Generate plots and figures from simulation results."
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).set_defaults(func=generate_figures)
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subparsers.add_parser(
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"fbd-empirical-run", help="Run BEAST2 analyses on empirical FBD datasets."
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).set_defaults(func=run_fbd_empirical)
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subparsers.add_parser(
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"fbd-empirical-summarize",
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help="Summarize BEAST2 log outputs for empirical FBD datasets.",
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).set_defaults(func=summarize_fbd_empirical)
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args = parser.parse_args()
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args.func()
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