Skip to content

Refactor time until death calculations #160

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
yiwen-h merged 5 commits into from
Jan 19, 2026
Merged

Refactor time until death calculations #160

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
d99ddcb
be explicit in config_values about shape and scale
yiwen-h Jan 16, 2026
bccc970
use calculate_time_to_event function to keep things DRY in model
yiwen-h Jan 18, 2026
fe6599b
fix bug in getting transplant type from prevalent patient location
yiwen-h Jan 19, 2026
2050815
update saving worksheets so we only save data for years of sim duration
yiwen-h Jan 19, 2026
201e46b
Merge branch 'main' into 151_153_refactor-time-until-death-calculations
yiwen-h Jan 19, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
192 changes: 96 additions & 96 deletions renal_capacity_model/config_values.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -264,151 +264,151 @@
"initialisation": {
"not_listed": {
"early": {
1: [0.926963321, 2127.231053],
2: [1.102888443, 2360.960064],
3: [1.042024424, 1757.881403],
4: [1.102673686, 1641.614239],
5: [1.149855608, 1561.636782],
6: [1.151814597, 1190.40286],
1: {"shape": 0.926963321, "scale": 2127.231053},
2: {"shape": 1.102888443, "scale": 2360.960064},
3: {"shape": 1.042024424, "scale": 1757.881403},
4: {"shape": 1.102673686, "scale": 1641.614239},
5: {"shape": 1.149855608, "scale": 1561.636782},
6: {"shape": 1.151814597, "scale": 1190.40286},
},
"late": {
1: [1.099732869, 4314.8445],
2: [1.239811029, 2204.356655],
3: [1.025879638, 1940.947327],
4: [1.17279732, 1700.235305],
5: [1.168619527, 1512.312581],
6: [1.156286321, 1253.912137],
1: {"shape": 1.099732869, "scale": 4314.8445},
2: {"shape": 1.239811029, "scale": 2204.356655},
3: {"shape": 1.025879638, "scale": 1940.947327},
4: {"shape": 1.17279732, "scale": 1700.235305},
5: {"shape": 1.168619527, "scale": 1512.312581},
6: {"shape": 1.156286321, "scale": 1253.912137},
},
},
"listed": {
"early": {
1: [1.426589565, 13064.21921],
2: [1.501319694, 8229.734667],
3: [1.475457685, 6126.819295],
4: [1.388640715, 4221.17834],
5: [1.381583619, 2805.868318],
6: [1.262968437, 1862.925138],
1: {"shape": 1.426589565, "scale": 13064.21921},
2: {"shape": 1.501319694, "scale": 8229.734667},
3: {"shape": 1.475457685, "scale": 6126.819295},
4: {"shape": 1.388640715, "scale": 4221.17834},
5: {"shape": 1.381583619, "scale": 2805.868318},
6: {"shape": 1.262968437, "scale": 1862.925138},
},
"late": {
1: [1.403897083, 13250.96392],
2: [1.359190822, 8393.578341],
3: [1.435707658, 5981.108405],
4: [1.326446673, 4096.723314],
5: [1.469351223, 2905.94038],
6: [1.244780918, 1800.673553],
1: {"shape": 1.403897083, "scale": 13250.96392},
2: {"shape": 1.359190822, "scale": 8393.578341},
3: {"shape": 1.435707658, "scale": 5981.108405},
4: {"shape": 1.326446673, "scale": 4096.723314},
5: {"shape": 1.469351223, "scale": 2905.94038},
6: {"shape": 1.244780918, "scale": 1800.673553},
},
},
"received_Tx": {
"early": {
1: [1.945083614, 11291.09043],
2: [1.765333669, 8449.099418],
3: [1.750669869, 6535.672038],
4: [1.61142907, 4693.44361],
5: [1.51886545, 3189.62546],
6: [1.315655704, 2078.132622],
1: {"shape": 1.945083614, "scale": 11291.09043},
2: {"shape": 1.765333669, "scale": 8449.099418},
3: {"shape": 1.750669869, "scale": 6535.672038},
4: {"shape": 1.61142907, "scale": 4693.44361},
5: {"shape": 1.51886545, "scale": 3189.62546},
6: {"shape": 1.315655704, "scale": 2078.132622},
},
"late": {
1: [1.982364823, 10573.47681],
2: [1.658109448, 8611.590105],
3: [1.699130074, 6499.195977],
4: [1.491659213, 4669.1818],
5: [1.678178577, 3296.367133],
6: [1.306592647, 1990.733317],
1: {"shape": 1.982364823, "scale": 10573.47681},
2: {"shape": 1.658109448, "scale": 8611.590105},
3: {"shape": 1.699130074, "scale": 6499.195977},
4: {"shape": 1.491659213, "scale": 4669.1818},
5: {"shape": 1.678178577, "scale": 3296.367133},
6: {"shape": 1.306592647, "scale": 1990.733317},
},
},
},
"incidence": {
"not_listed": {
"early": {
1: [1.021124756, 1630.450226],
2: [1.033558934, 1601.726618],
3: [1.175150289, 1788.324784],
4: [1.171027698, 1671.61871],
5: [1.182843607, 1604.030346],
6: [1.111932566, 1324.708399],
1: {"shape": 1.021124756, "scale": 1630.450226},
2: {"shape": 1.033558934, "scale": 1601.726618},
3: {"shape": 1.175150289, "scale": 1788.324784},
4: {"shape": 1.171027698, "scale": 1671.61871},
5: {"shape": 1.182843607, "scale": 1604.030346},
6: {"shape": 1.111932566, "scale": 1324.708399},
},
"late": {
1: [1.025446743, 2098.5119],
2: [0.86558945, 2071.301577],
3: [0.787953011, 1428.187242],
4: [1.093861294, 1533.652413],
5: [0.817406992, 1170.501979],
6: [0.829891, 841.5931435],
1: {"shape": 1.025446743, "scale": 2098.5119},
2: {"shape": 0.86558945, "scale": 2071.301577},
3: {"shape": 0.787953011, "scale": 1428.187242},
4: {"shape": 1.093861294, "scale": 1533.652413},
5: {"shape": 0.817406992, "scale": 1170.501979},
6: {"shape": 0.829891, "scale": 841.5931435},
},
},
"listed": {
"early": {
1: [1.76722409, 7565.454427],
2: [2.071602421, 5267.578147],
3: [1.842843082, 5294.787645],
4: [2.276835063, 3862.063689],
5: [1.990617668, 3148.737229],
6: [2.435166079, 2479.412332],
1: {"shape": 1.76722409, "scale": 7565.454427},
2: {"shape": 2.071602421, "scale": 5267.578147},
3: {"shape": 1.842843082, "scale": 5294.787645},
4: {"shape": 2.276835063, "scale": 3862.063689},
5: {"shape": 1.990617668, "scale": 3148.737229},
6: {"shape": 2.435166079, "scale": 2479.412332},
},
"late": {
1: [2.732803839, 5100.306997],
2: [1.7523112, 6999.685955],
3: [2.667855187, 3817.522327],
4: [2.39938038, 3728.91519],
5: [2.195794462, 2550.374846],
6: [2.435166079, 2479.412332],
1: {"shape": 2.732803839, "scale": 5100.306997},
2: {"shape": 1.7523112, "scale": 6999.685955},
3: {"shape": 2.667855187, "scale": 3817.522327},
4: {"shape": 2.39938038, "scale": 3728.91519},
5: {"shape": 2.195794462, "scale": 2550.374846},
6: {"shape": 2.435166079, "scale": 2479.412332},
},
},
"received_Tx": {
"early": {
1: [2.51486622, 6903.239543],
2: [3.159509376, 5391.985192],
3: [2.70710626, 5381.509481],
4: [2.893707823, 4282.49379],
5: [2.35276178, 3550.906294],
6: [4.316362639, 3118.52084],
1: {"shape": 2.51486622, "scale": 6903.239543},
2: {"shape": 3.159509376, "scale": 5391.985192},
3: {"shape": 2.70710626, "scale": 5381.509481},
4: {"shape": 2.893707823, "scale": 4282.49379},
5: {"shape": 2.35276178, "scale": 3550.906294},
6: {"shape": 4.316362639, "scale": 3118.52084},
},
"late": {
1: [3.160772244, 5169.606112],
2: [2.323615011, 7944.757158],
3: [3.8964386, 4637.1169],
4: [5.45663996, 3913.875032],
5: [3.071596253, 3120.115725],
6: [4.316362639, 3118.52084],
1: {"shape": 3.160772244, "scale": 5169.606112},
2: {"shape": 2.323615011, "scale": 7944.757158},
3: {"shape": 3.8964386, "scale": 4637.1169},
4: {"shape": 5.45663996, "scale": 3913.875032},
5: {"shape": 3.071596253, "scale": 3120.115725},
6: {"shape": 4.316362639, "scale": 3118.52084},
},
},
},
}

tw_cadTx_values = {
1: [1.12, 719],
2: [1.23, 734],
3: [1.31, 794],
4: [1.31, 762],
5: [1.23, 619],
6: [1.02, 385],
1: {"shape": 1.12, "scale": 719},
2: {"shape": 1.23, "scale": 734},
3: {"shape": 1.31, "scale": 794},
4: {"shape": 1.31, "scale": 762},
5: {"shape": 1.23, "scale": 619},
6: {"shape": 1.02, "scale": 385},
}

tw_liveTx_values = {
1: [1.03, 399],
2: [1.06, 464],
3: [1.08, 417],
4: [1.09, 420],
5: [1.22, 391],
6: [1.01, 342],
1: {"shape": 1.03, "scale": 399},
2: {"shape": 1.06, "scale": 464},
3: {"shape": 1.08, "scale": 417},
4: {"shape": 1.09, "scale": 420},
5: {"shape": 1.22, "scale": 391},
6: {"shape": 1.01, "scale": 342},
}

tw_cadTx_initialisation_values = {
1: [1.12, 1336],
2: [1.13, 1163],
3: [1.22, 1194],
4: [1.26, 1023],
5: [1.28, 839],
6: [1.28, 409],
1: {"shape": 1.12, "scale": 1336},
2: {"shape": 1.13, "scale": 1163},
3: {"shape": 1.22, "scale": 1194},
4: {"shape": 1.26, "scale": 1023},
5: {"shape": 1.28, "scale": 839},
6: {"shape": 1.28, "scale": 409},
}

tw_liveTx_initialisation_values = {
1: [0.96, 752],
2: [1.05, 1006],
3: [0.96, 903],
4: [1.01, 665],
5: [1.27, 765],
6: [1.27, 765],
1: {"shape": 0.96, "scale": 752},
2: {"shape": 1.05, "scale": 1006},
3: {"shape": 0.96, "scale": 903},
4: {"shape": 1.01, "scale": 665},
5: {"shape": 1.27, "scale": 765},
6: {"shape": 1.27, "scale": 765},
}

# Time waiting before dialysis
Expand Down
2 changes: 1 addition & 1 deletion renal_capacity_model/entity.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,6 @@ def __init__(
self.time_living_with_live_transplant: float | None = None
self.time_living_with_cadaver_transplant: float | None = None
self.transplant_count = 0
self.time_on_waiting_list = 0
self.time_on_waiting_list: float = 0
self.time_enters_waiting_list: float | None = None
self.time_of_transplant: float | None = None
18 changes: 18 additions & 0 deletions renal_capacity_model/helpers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -315,3 +315,21 @@ def check_time_to_event_curve_dfs(tte_df_name: str, tte_df: pd.DataFrame):
assert list(tte_df.columns) == cols
except AssertionError:
raise ValueError(f"Check {tte_df_name} csv - incorrect indices/columns")


def calculate_time_to_event(
rng: np.random.Generator, scale: float, shape: float, multiplier: float = 1
) -> float:
"""Calculate time to event, sampling from a Weibull distribution and multiplying
it with a scale and optional multiplier

Args:
rng (np.random.Generator): Random Number Generator
scale (float): Scale to be used for the calculation
shape (float): Shape parameter for Weibull distribution
multiplier (float, optional): Optional multiplier. Defaults to 1.

Returns:
float: Sampled time to event
"""
return (scale * rng.weibull(shape)) * multiplier
7 changes: 6 additions & 1 deletion renal_capacity_model/main.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,12 @@ def main(
)
for excel_file in [path_to_inputs_file, path_to_outputs_file]:
filepaths.append(copy_excel_files(excel_file, run_start_time))
write_results_to_excel(filepaths[1], combined_results, trial.costs_dfs)
write_results_to_excel(
filepaths[1],
combined_results,
trial.costs_dfs,
sim_years=int(config.sim_duration / 365),
)


if __name__ == "__main__":
Expand Down
Loading