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Merged
morganle-48 merged 2 commits into from
Dec 19, 2025
Merged

Add calibration coefficients #147

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18b5a30
added multipliers to the config and the load scenario
Dec 16, 2025
aa6a864
updated national prob death from dialysis
Dec 18, 2025
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1 change: 1 addition & 0 deletions renal_capacity_model/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,7 @@ def __init__(
"pre_emptive_transplant_cadaver_donor_dist"
]
self.death_post_transplant_glm = config_dict["death_post_transplant_glm"]
self.multipliers = config_dict["multipliers"]
# time to event distribution parameters (these are the same regardless of geography)
self.ttd_con_care = ttd_con_care_values
self.tw_before_dialysis = tw_before_dialysis_values
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156 changes: 87 additions & 69 deletions renal_capacity_model/config_values.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,112 +185,112 @@
"death_post_dialysis_modality": { # prevalent patients
"ichd": {
"early": {
1: 0.18,
2: 0.28,
3: 0.36,
4: 0.48,
5: 0.54,
6: 0.60,
1: 0.30,
2: 0.47,
3: 0.64,
4: 0.81,
5: 0.93,
6: 0.98,
},
"late": {
1: 0.14,
2: 0.28,
3: 0.36,
4: 0.49,
5: 0.53,
6: 0.62,
1: 0.26,
2: 0.46,
3: 0.68,
4: 0.77,
5: 0.94,
6: 0.98,
},
},
"hhd": {
"early": {
1: 0.11,
2: 0.18,
3: 0.27,
1: 0.12,
2: 0.21,
3: 0.33,
4: 0.37,
5: 0.51,
6: 0.51,
5: 0.47,
6: 0.30,
},
"late": {
1: 0.11,
2: 0.18,
3: 0.27,
4: 0.37,
5: 0.51,
6: 0.51,
1: 0.0,
2: 0.25,
3: 0.24,
4: 0.46,
5: 0.42,
6: 0.00,
},
},
"pd": {
"early": {
1: 0.04,
2: 0.09,
3: 0.15,
4: 0.22,
5: 0.28,
6: 0.42,
1: 0.05,
2: 0.13,
3: 0.22,
4: 0.37,
5: 0.42,
6: 0.55,
},
"late": {
1: 0.04,
2: 0.02,
3: 0.14,
4: 0.24,
5: 0.33,
6: 0.33,
1: 0.07,
2: 0.21,
3: 0.33,
4: 0.28,
5: 0.37,
6: 0.46,
},
},
},
"death_post_dialysis_modality_incident": { # incident patients
"ichd": {
"early": {
1: 0.07,
2: 0.12,
3: 0.16,
4: 0.22,
5: 0.27,
6: 0.33,
1: 0.12,
2: 0.23,
3: 0.37,
4: 0.53,
5: 0.69,
6: 0.82,
},
"late": {
1: 0.06,
2: 0.13,
3: 0.18,
4: 0.22,
5: 0.27,
6: 0.33,
1: 0.14,
2: 0.29,
3: 0.43,
4: 0.56,
5: 0.70,
6: 0.82,
},
},
"hhd": {
"early": {
1: 0.05,
2: 0.14,
3: 0.19,
4: 0.24,
5: 0.20,
6: 0.30,
1: 0.00,
2: 0.00,
3: 0.01,
4: 0.01,
5: 0.02,
6: 0.06,
},
"late": {
1: 0.09,
2: 0.17,
3: 0.15,
4: 0.21,
5: 0.15,
6: 0.29,
1: 0.00,
2: 0.00,
3: 0.01,
4: 0.00,
5: 0.03,
6: 0.00,
},
},
"pd": {
"early": {
1: 0.04,
1: 0.02,
2: 0.06,
3: 0.11,
4: 0.21,
5: 0.29,
3: 0.10,
4: 0.20,
5: 0.27,
6: 0.36,
},
"late": {
1: 0.04,
2: 0.1,
3: 0.11,
4: 0.22,
5: 0.32,
6: 0.40,
1: 0.01,
2: 0.04,
3: 0.07,
4: 0.12,
5: 0.19,
6: 0.26,
},
},
},
Expand All @@ -314,6 +314,24 @@
"ref_stat": -0.127, # early = 0 , late =1
},
},
"multipliers": {
"ttd": {
"ichd": 1.0,
"hhd": 1.0,
"pd": 1.0,
"live": 1.0,
"cadaver": 1.0,
},
"ttma": {
"ichd": 1.0,
"hhd": 1.0,
"pd": 1.0,
},
"ttgf": {
"live": 1.0,
"cadaver": 1.0,
},
},
}

# Time to death: conservative care
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19 changes: 18 additions & 1 deletion renal_capacity_model/load_scenario.py
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Original file line number Diff line number Diff line change
Expand Up @@ -957,7 +957,24 @@ def load_scenario_from_excel(
"pd": input_scenario.iat[38, 1],
"living_with_transplant": input_scenario.iat[39, 1],
}

config_from_excel["multipliers"] = {
"ttd": {
"ichd": input_scenario.iat[232, 1],
"hhd": input_scenario.iat[233, 1],
"pd": input_scenario.iat[234, 1],
"live": input_scenario.iat[241, 1],
"cadaver": input_scenario.iat[242, 1],
},
"ttma": {
"ichd": input_scenario.iat[236, 1],
"hhd": input_scenario.iat[237, 1],
"pd": input_scenario.iat[238, 1],
},
"ttgf": {
"live": input_scenario.iat[244, 1],
"cadaver": input_scenario.iat[245, 1],
},
}
config_from_excel["death_post_transplant_glm"] = {
"live": {
"intercept": input_scenario.iat[120, 7],
Expand Down
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