pop_size=D.POP_SIZE,
parameters=P.ParametersFixed(diagnostic=P.Diagnostic.NSB))
# simulate the cohort over the specified time steps
myCohort_NSB.simulate(sim_length=D.SIM_LENGTH)
# print the outcomes of this simulated cohort
Support.print_outcomes(sim_outcomes=myCohort_NSB.cohortOutcomes,
diagnostic_name=P.Diagnostic.NSB)
# histograms of the simulated cohort
Support.print_histograms(sim_outcomes=myCohort_NSB.cohortOutcomes,
diagnostic_name=P.Diagnostic.NSB)
PathCls.graph_sample_path(sample_path=myCohort.cohortOutcomes.nLivingPatients,
title='Survival Curve (Standard of Care Diagnostic)',
x_label='Time-Step (Week)',
y_label='Number Survived')
PathCls.graph_sample_path(
sample_path=myCohort_NSB.cohortOutcomes.nLivingPatients,
title='Survival Curve (SOC + Urine LAM)',
x_label='Time-Step (Week)',
y_label='Number Survived')
survival_curves = [
myCohort.cohortOutcomes.nLivingPatients,
myCohort_NSB.cohortOutcomes.nLivingPatients
]
# graph survival curve
# graph survival curve
# record the observations
path2.record(0.5, 4)
path2.record(1.8, -2)
path2.record(5.5, 1)
# third sample path with initial size = 1
path3 = Path.PrevalencePathBatchUpdate('Path 3',
0,
times_of_changes=[1.5, 2, 5],
increments=[2, -1, 0],
sim_rep=1)
# plot path 1 only
Path.graph_sample_path(sample_path=path1,
title='Plotting a single sample path',
x_label='time',
y_label='observed value',
legend='Path 1',
color_code='r')
# plot path 3 only
Path.graph_sample_path(
sample_path=path3,
title='Plotting a single sample path that is updated in batch',
x_label='time',
y_label='observed value',
legend='Path 3',
color_code='r')
# plot both paths
Path.graph_sample_paths(sample_paths=[path1, path2],
title='Plot two sample paths with different color',
def print_histograms(sim_outcomes, diagnostic_name):
# plot the sample path (survival curve)
PathCls.graph_sample_path(sample_path=sim_outcomes.nLivingPatients,
title=f'Survival Curve {diagnostic_name}',
x_label='Time-Step (Week)',
y_label='Number Survived')
# plot the histogram of survival times
Figs.graph_histogram(
data=sim_outcomes.survivalTimes,
title=f'Histogram of Patient Survival Time {diagnostic_name}',
x_label='Survival Time (Week)',
y_label='Count',
bin_width=1)
# Figs.graph_histogram(
# data=sim_outcomes.timesINFECTEDtoHOSP_TBD,
# title=f'Histogram of INFECTED to HOSP_TBD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesINFECTEDtoHOSP_TBM,
# title=f'Histogram of INFECTED to HOSP_TBM {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesINFECTEDtoDX_TBD,
# title=f'Histogram of INFECTED to DX_TBD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesINFECTEDtoCLEARED,
# title=f'Histogram of INFECTED to CLEARED {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesCLEAREDtoDEAD,
# title=f'Histogram of CLEARED to DEAD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesHOSP_TBDtoDEAD,
# title=f'Histogram of HOSP_TBD to DEAD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesHOSP_TBDtoDX_TBD,
# title=f'Histogram of HOSP_TBD to DX_TBD {diagnostic_name}',
# x_label='Survival Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesHOSP_TBMtoDEAD,
# title=f'Histogram of HOSP_TBM to DEAD {diagnostic_name}',
# x_label='Survival Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesHOSP_TBMtoDX_TBM,
# title=f'Histogram of HOSP_TBM to DX_TBM {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesDX_TBDtoDEAD,
# title=f'Histogram of DX_TBD to DEAD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesDX_TBDtoCLEARED,
# title=f'Histogram of DX_TBD to CLEARED {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesDX_TBMtoDEAD,
# title=f'Histogram of DX_TBM to DEAD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesDX_TBMtoCLEARED,
# title=f'Histogram of DX_TBM to CLEARED {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesINFECTED,
# title=f'Histogram of INFECTED {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesHOSP_TBM,
# title=f'Histogram of HOSP_TBM {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesHOSP_TBD,
# title=f'Histogram of HOSP_TBD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesDX_TBD,
# title=f'Histogram of DX_TBD {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesDX_TBM,
# title=f'Histogram of DX_TBM {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
#
# Figs.graph_histogram(
# data=sim_outcomes.timesCLEARED,
# title=f'Histogram of CLEARED {diagnostic_name}',
# x_label='Time (Week)',
# y_label='Count',
# bin_width=1)
# Figs.graph_histogram(
# data=sim_outcomes.costs,
# title=f'Histogram of Cost {diagnostic_name}',
# x_label='Cost (Dollars)',
# y_label='Count',
# bin_width=1)
Figs.graph_histogram(
data=sim_outcomes.costsPresenting,
title=f'Histogram of Cost (Patients Presenting) {diagnostic_name}',
x_label='Cost (Dollars)',
y_label='Count',
bin_width=1)
# selected therapy
therapy_none = P.Therapies.NO
# create a cohort
myCohort_0 = Cls.Cohort(id=0,
pop_size=D.POP_SIZE,
parameters=P.ParametersFixed(therapy=therapy_none))
# simulate the cohort over the specified time steps
myCohort_0.simulate(sim_length=D.SIM_LENGTH)
# plot the sample path (survival curve)
Path.graph_sample_path(
sample_path=myCohort_0.cohortOutcomes.nLivingPatients,
title='Survival Curvel for No Therapy',
x_label='Time-Step (Year)',
y_label='Number Survived')
# plot the histogram of survival times
Fig.graph_histogram(
data=myCohort_0.cohortOutcomes.survivalTimes,
title='Histogram of Patient Survival Times for No Therapy',
x_label='Survival Time (Year)',
y_label='Count',
bin_width=1)
# print the outcomes of this simulated cohort
Support.print_outcomes(sim_outcomes=myCohort_0.cohortOutcomes,therapy_name=therapy_none)