bella-companion 0.0.6__py3-none-any.whl → 0.0.8__py3-none-any.whl

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Files changed (27) hide show
  1. bella_companion/cli.py +21 -9
  2. bella_companion/fbd_empirical/__init__.py +4 -0
  3. bella_companion/fbd_empirical/notbooks.ipynb +85 -274
  4. bella_companion/fbd_empirical/run_beast.py +46 -32
  5. bella_companion/fbd_empirical/summarize_logs.py +15 -32
  6. bella_companion/simulations/__init__.py +8 -1
  7. bella_companion/simulations/figures/epi_skyline_results.py +2 -2
  8. bella_companion/simulations/figures/explain/pdp.py +21 -27
  9. bella_companion/simulations/figures/explain/shap.py +1 -1
  10. bella_companion/simulations/figures/fbd_2traits_results.py +1 -1
  11. bella_companion/simulations/figures/fbd_no_traits_results.py +2 -2
  12. bella_companion/simulations/figures/scenarios.py +2 -2
  13. bella_companion/simulations/generate_data.py +4 -2
  14. bella_companion/simulations/metrics.py +62 -0
  15. bella_companion/simulations/scenarios/epi_multitype.py +1 -1
  16. bella_companion/simulations/scenarios/fbd_2traits.py +1 -4
  17. bella_companion/simulations/summarize_logs.py +3 -4
  18. bella_companion/utils/__init__.py +7 -11
  19. bella_companion/utils/beast.py +2 -2
  20. {bella_companion-0.0.6.dist-info → bella_companion-0.0.8.dist-info}/METADATA +2 -2
  21. bella_companion-0.0.8.dist-info/RECORD +42 -0
  22. bella_companion/fbd_empirical/figure.py +0 -37
  23. bella_companion/fbd_empirical/params.json +0 -11
  24. bella_companion-0.0.6.dist-info/RECORD +0 -42
  25. /bella_companion/{utils/plots.py → simulations/figures/utils.py} +0 -0
  26. {bella_companion-0.0.6.dist-info → bella_companion-0.0.8.dist-info}/WHEEL +0 -0
  27. {bella_companion-0.0.6.dist-info → bella_companion-0.0.8.dist-info}/entry_points.txt +0 -0
bella_companion-0.0.6.dist-info/RECORD DELETED
@@ -1,42 +0,0 @@
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- bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- bella_companion/cli.py,sha256=5GbOREOkW0C1Dt43i7Y-Xy1jTr8Tx779is-uQ1nlnUc,1162
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- bella_companion/fbd_empirical/data/body_mass.csv,sha256=-UkKNtm9m3g4PjY3BcfdP6z5nL_I6p9cq6cgZ-bWKI8,30360
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- bella_companion/fbd_empirical/data/change_times.csv,sha256=zmc9_z91-XMwKyIoP9v9dVlLcf4MeIHkQiHLjoMriOo,120
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- bella_companion/fbd_empirical/data/sampling_change_times.csv,sha256=Gwi9RcMFy89RyvfxKVZ_MoKVRHOZLuwB_3LEaq8asMQ,32
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- bella_companion/fbd_empirical/data/trees.nwk,sha256=zhvLvPLZelhMThVmvOENkmi3p2aPAARb8KMdHTm6mss,4645318
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- bella_companion/fbd_empirical/figure.py,sha256=4paOXCB1EcxuHzLPxDSleQU2AQ_ndTedtzS1ugiKICs,1018
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- bella_companion/fbd_empirical/notbooks.ipynb,sha256=O45kmz0lZENRDFbKXEWPsIKATfF5GVeS5tCYmrGLnqk,83326
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- bella_companion/fbd_empirical/params.json,sha256=hU23LniClZL_GSBAxIEJUJgMa93AM8zdtFOq6mt3vkI,311
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- bella_companion/fbd_empirical/run_beast.py,sha256=pUX4f77kQ_F_tJwRY7Sfz8NUql0sY4VKE1i8pZGte6Y,1952
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- bella_companion/fbd_empirical/summarize_logs.py,sha256=O6rhE606Wa98a8b1KKlLPjUOro1pfyqVTLdQksQMG0g,1439
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- bella_companion/simulations/__init__.py,sha256=EBZAcI8skNPKjrA7CjrqH9ea7DTntmydAD0RqsxNUMM,352
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- bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
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- bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
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- bella_companion/simulations/figures/epi_multitype_results.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
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- bella_companion/simulations/figures/epi_skyline_results.py,sha256=Ej1iGHLnLkUohx7oC9gRTLe8T--5WS-JtyViLbxraLA,1647
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- bella_companion/simulations/figures/explain/__init__.py,sha256=DnmVIWO65nTT5VsWnbS7NyYgKEY_eo4oMCtCY_ML2Vk,260
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- bella_companion/simulations/figures/explain/pdp.py,sha256=bSrH-TZcT2mVZIBXTUeoRvShsX2bIUyhUvgmbzXLIbg,3925
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- bella_companion/simulations/figures/explain/shap.py,sha256=tjYX5H3C-IiygG9scXhLgtlCRxEBlsQ2OW5gVWL15kY,1936
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- bella_companion/simulations/figures/fbd_2traits_results.py,sha256=YP_ksmh5Sj2WnoxqRuSLt-gd-W7k2lUHs4idAbvbdhw,2708
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- bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=O6hx_OZVSHmW0xq9T4q4oz6eskC_xcFZGMEdX8ZilrU,1942
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- bella_companion/simulations/figures/scenarios.py,sha256=OKh9_-ZvzNgWsO3-Vd0Aw3ndjVf76i_OuCvsKI-5r2s,2795
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- bella_companion/simulations/generate_data.py,sha256=H8OV4ZlTGZB-jXaROTPmOsK3UxRiU-GrX40l-shliw8,728
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- bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
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- bella_companion/simulations/run_beast.py,sha256=Sw9wKNe1VlGNvYr-yiYv3LqUYVlcjcMAz_9Pzr-xyL0,3214
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- bella_companion/simulations/scenarios/__init__.py,sha256=3Kl1lKcFpfb3vLX64DmSW4XCF5kXU1ZoHtstFH-ZIzU,876
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- bella_companion/simulations/scenarios/common.py,sha256=_ddaSuTvEVdttGkXB4HPc2B7IB1F_GBOCW3cVOPZ-ZM,807
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- bella_companion/simulations/scenarios/epi_multitype.py,sha256=GWGIiqvYwX_FrT_3RXkZKYGDht9nZ7ceHRBKUvXDPnA,2432
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- bella_companion/simulations/scenarios/epi_skyline.py,sha256=JqnOVATECxBUqEbkR5lBlMI2O8k4hO6ipR8k9cHUsm0,2365
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- bella_companion/simulations/scenarios/fbd_2traits.py,sha256=G24WCAHrWPwvQeElsy4UMl1I9ALFnVQp6wXuc25Ie-g,3552
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- bella_companion/simulations/scenarios/fbd_no_traits.py,sha256=R6CH0fVeQg-Iesl39pq2uY8ICVEO4VZbvUVUCGwauJU,2520
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- bella_companion/simulations/scenarios/scenario.py,sha256=_FRWAyOFbw94lAzd3zCD-1ek4TrssoiXfXRQPShLiIA,620
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- bella_companion/simulations/summarize_logs.py,sha256=5IdzR9IwjeF2LgZmzpuK0rPfYMct2OUgEp0QyUbUS7g,1263
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- bella_companion/utils/__init__.py,sha256=bb0-pCjQNwGaUgG2v9htgOLlOMiB1-kdZnSQ_QY2QAo,647
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- bella_companion/utils/beast.py,sha256=5Vsv98VTE9HrY56WzUSMECjD_rIPxHTMRMD1ZzmA6wY,2181
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- bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
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- bella_companion/utils/plots.py,sha256=dB_GiJ1HGrZ93cqODz6kB-HeDRPwlm2MkMe9rJZGnfs,3117
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- bella_companion/utils/slurm.py,sha256=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
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- bella_companion-0.0.6.dist-info/METADATA,sha256=3smSTa-FBJ-RUBiIt7fiK3VGp4EBlw4nAaScxOkDUG8,576
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- bella_companion-0.0.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- bella_companion-0.0.6.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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- bella_companion-0.0.6.dist-info/RECORD,,