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Experiment: Test Combining #46

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dc8875e
Update parameters.json to add blood test parameters
korourke5 Sep 8, 2025
80177d8
Edit parameters.json and prepare.py to include
korourke5 Sep 8, 2025
e04997e
Added the scenarios created and updated readme
korourke5 Sep 8, 2025
69d2ec0
Merge remote-tracking branch 'origin/experiment-
korourke5 Sep 12, 2025
4192820
Updated prepare.py and parameters.json to include
korourke5 Sep 12, 2025
4af3868
Added results in summary, updated the S3 bin
korourke5 Oct 23, 2025
bda348f
Update README.md with results.
korourke5 Oct 23, 2025
6135dda
Delete crcsim/experiment/summary/~$summarized.xlsx
korourke5 Oct 23, 2025
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181 changes: 179 additions & 2 deletions crcsim/experiment/parameters.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -100,9 +100,185 @@
"cost_perforation": 6487,
"compliance_rate_given_prev_compliant": [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 ],
"compliance_rate_given_not_prev_compliant": [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ]
},
"Blood": {
"proportion": 0.0,
"routine_start": 45,
"routine_end": 75,
"routine_freq": 3,
"specificity": 0.90,
"sensitivity_polyp1": 0,
"sensitivity_polyp2": 0,
"sensitivity_polyp3": 0.13,
"sensitivity_cancer": 0.83,
"cost": 895,
"proportion_perforation": 0,
"cost_perforation": 0,
"compliance_rate_given_prev_compliant": [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 ],
"compliance_rate_given_not_prev_compliant": [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ]
},
"FIT_Blood_TestCombiningMethod.PARALLEL": {
"sensitivity_polyp1": 0.07000000000000006,
"sensitivity_polyp2": 0.07000000000000006,
"sensitivity_polyp3": 0.3214,
"sensitivity_cancer": 0.9558,
"specificity": 0.873,
"cost": 922,
"proportion": 1.0,
"routine_start": 45,
"routine_end": 75,
"routine_freq": 1,
"proportion_perforation": 0,
"cost_perforation": 0,
"compliance_rate_given_prev_compliant": [
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],
"compliance_rate_given_not_prev_compliant": [
0.0,
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0.0,
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]
},
"FIT_Blood_TestCombiningMethod.SERIAL": {
"sensitivity_polyp1": 0.0,
"sensitivity_polyp2": 0.0,
"sensitivity_polyp3": 0.0286,
"sensitivity_cancer": 0.6142,
"specificity": 0.997,
"cost": 922,
"proportion": 1.0,
"routine_start": 45,
"routine_end": 75,
"routine_freq": 1,
"proportion_perforation": 0,
"cost_perforation": 0,
"compliance_rate_given_prev_compliant": [
1.0,
1.0,
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1.0,
1.0,
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],
"compliance_rate_given_not_prev_compliant": [
0.0,
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0.0,
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]
}
},
"routine_tests": [ "FIT", "Colonoscopy" ],
"routine_tests": [ "FIT", "Colonoscopy", "Blood", "FIT_Blood_TestCombiningMethod.PARALLEL", "FIT_Blood_TestCombiningMethod.SERIAL" ],
"diagnostic_test": "Colonoscopy",
"surveillance_test": "Colonoscopy",
"polypectomy_proportion_lethal": 0.00002,
Expand All @@ -122,4 +298,5 @@
"death_rate_white_male_rates": [ 0.005273, 0.000389, 0.000273, 0.000199, 0.000147, 0.000143, 0.000126, 0.000112, 0.000100, 0.000091, 0.000090, 0.000105, 0.000145, 0.000215, 0.000309, 0.000412, 0.000520, 0.000642, 0.000778, 0.000921, 0.001068, 0.001209, 0.001330, 0.001424, 0.001497, 0.001561, 0.001624, 0.001682, 0.001737, 0.001792, 0.001847, 0.001900, 0.001952, 0.002003, 0.002053, 0.002111, 0.002174, 0.002233, 0.002285, 0.002340, 0.002413, 0.002516, 0.002649, 0.002811, 0.002999, 0.003203, 0.003433, 0.003709, 0.004047, 0.004445, 0.004874, 0.005331, 0.005844, 0.006408, 0.007003, 0.007607, 0.008219, 0.008857, 0.009542, 0.010285, 0.011098, 0.011952, 0.012814, 0.013657, 0.014502, 0.015384, 0.016444, 0.017624, 0.018968, 0.020586, 0.022109, 0.024359, 0.026347, 0.028810, 0.031309, 0.034486, 0.038026, 0.042286, 0.046547, 0.051534, 0.057008, 0.062923, 0.069911, 0.078099, 0.086754, 0.096549, 0.106472, 0.119677, 0.134128, 0.149846, 0.166829, 0.185047, 0.204441, 0.224919, 0.246354, 0.268590, 0.291442, 0.314700, 0.338142, 0.361537, 1.000000 ],

"us_age_distribution_rates": [ 0.01237, 0.01236, 0.01234, 0.01231, 0.01208, 0.01214, 0.01213, 0.01209, 0.01211, 0.01225, 0.01225, 0.01225, 0.01264, 0.01270, 0.01260, 0.01257, 0.01262, 0.01257, 0.01257, 0.01293, 0.01318, 0.01304, 0.01310, 0.01319, 0.01332, 0.01362, 0.01389, 0.01409, 0.01443, 0.01466, 0.01460, 0.01401, 0.01366, 0.01340, 0.01342, 0.01348, 0.01304, 0.01320, 0.01317, 0.01301, 0.01323, 0.01241, 0.01214, 0.01200, 0.01164, 0.01197, 0.01159, 0.01174, 0.01224, 0.01290, 0.01303, 0.01232, 0.01204, 0.01203, 0.01223, 0.01294, 0.01315, 0.01311, 0.01306, 0.01319, 0.01326, 0.01278, 0.01266, 0.01248, 0.01198, 0.01183, 0.01129, 0.01081, 0.01033, 0.00995, 0.00965, 0.00930, 0.00912, 0.00941, 0.00689, 0.00671, 0.00645, 0.00649, 0.00557, 0.00499, 0.00462, 0.00424, 0.00395, 0.00352, 0.00324, 0.00298, 0.00255, 0.00234, 0.00211, 0.00188, 0.00168, 0.00140, 0.00120, 0.00099, 0.00079, 0.00064, 0.00049, 0.00036, 0.00027, 0.00019, 0.00028 ]
}

}
21 changes: 21 additions & 0 deletions crcsim/experiment/prepare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,9 @@ def create_scenarios() -> List:
# transform test proportions for the FIT scenarios.
.transform(transform_routine_test_proportion("Colonoscopy", 1.0))
.transform(transform_routine_test_proportion("FIT", 0.0))
.transform(transform_routine_test_proportion("Blood", 0.0))
.transform(transform_routine_test_proportion("FIT_Blood_TestCombiningMethod.PARALLEL", 0.0))
.transform(transform_routine_test_proportion("FIT_Blood_TestCombiningMethod.SERIAL", 0.0))
.transform(transform_lesion_risk_alpha(1.19))
)

Expand All @@ -137,6 +140,24 @@ def create_scenarios() -> List:
.transform(transform_lesion_risk_alpha(1.19))
)

scenarios.append(
Scenario(name=f"Blood_{scenario}", params=get_default_params())
.transform(transform_initial_compliance(screening_rate))
.transform(transform_lesion_risk_alpha(1.19))
)

scenarios.append(
Scenario(name=f"FIT_Blood_TestCombiningMethod.PARALLEL_{scenario}", params=get_default_params())
.transform(transform_initial_compliance(screening_rate))
.transform(transform_lesion_risk_alpha(1.19))
)

scenarios.append(
Scenario(name=f"FIT_Blood_TestCombiningMethod.SERIAL_{scenario}", params=get_default_params())
.transform(transform_initial_compliance(screening_rate))
.transform(transform_lesion_risk_alpha(1.19))
)
Comment on lines +148 to +179
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@sandypreiss sandypreiss Sep 10, 2025

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After we modify the test combining script to set the proportion for combined tests to 0, the base params will assign FIT to all agents. So these tests also need to use transform_routine_test_proportion to set the proportion for the relevant test to 1 and all others to 0 (same pattern as Colonoscopy).


return scenarios


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