def print_comparative_outcomes(sim_output_no_drug, sim_output_with_drug):
""" prints expected and percentage increase in survival time when drug is available
:param sim_output_no_drug: output of a fair game
:param sim_output_with_drug: output of an unfair game
"""
# increase in survival time
increase = Stat.DifferenceStatIndp(name='Increase in casino rewards',
x=sim_output_with_drug.get_rewards(),
y_ref=sim_output_no_drug.get_rewards())
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=increase.get_mean(),
interval=increase.get_t_CI(alpha=P.ALPHA),
deci=1)
print(
"Average increase in casino rewards and {:.{prec}%} confidence interval:"
.format(1 - P.ALPHA, prec=0), estimate_CI)
# % increase in survival time
relative_diff = Stat.RelativeDifferenceIndp(
name='Average % increase in casino rewards',
x=sim_output_with_drug.get_rewards(),
y_ref=sim_output_no_drug.get_rewards())
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=relative_diff.get_mean(),
interval=relative_diff.get_bootstrap_CI(alpha=P.ALPHA,
num_samples=1000),
deci=1,
form=Format.FormatNumber.PERCENTAGE)
print(
"Average percentage increase in casino rewards and {:.{prec}%} confidence interval:"
.format(1 - P.ALPHA, prec=0), estimate_CI)
def print_outcomes(simOutput, therapy_name, Problem7):
""" prints the outcomes of a simulated cohort
:param simOutput: output of a simulated cohort
:param therapy_name: the name of the selected therapy
:param Problem7: is this for problem 7?
"""
# mean and confidence interval text of patient survival time
survival_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_survival_times().get_mean(),
interval=simOutput.get_sumStat_survival_times().get_t_CI(alpha=ALPHA),
deci=2)
# mean and confidence interval text of time to STROKE
time_to_STROKE_death_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_time_to_STROKE().get_mean(),
interval=simOutput.get_sumStat_time_to_STROKE().get_t_CI(alpha=ALPHA),
deci=2)
# print outcomes
print(therapy_name)
if Problem7 == "No":
print(" Estimate of mean survival time and {:.{prec}%} confidence interval:".format(1 - ALPHA, prec=0),
survival_mean_CI_text)
elif Problem7 == "Yes":
print(" Estimate of mean number of strokes and {:.{prec}%} confidence interval:".format(1 - ALPHA, prec=0),
time_to_STROKE_death_CI_text)
def print_outcomes(simOutput, treatment):
# mean and CI text for patient survival time
survival_mean_CI_text = Format.format_estimate_interval(
estimate=simOutput.get_sumStat_survival_times().get_mean(),
interval=simOutput.get_sumStat_survival_times().get_t_CI(alpha=Data.ALPHA),
deci=2
)
# mean and CI text of discounted total cost
cost_mean_CI_text = Format.format_estimate_interval(
estimate=simOutput.get_sumStat_costs().get_mean(),
interval=simOutput.get_sumStat_costs().get_t_CI(alpha=Data.ALPHA),
deci=2
)
# mean and CI text of discounted utility
utility_mean_CI_text = Format.format_estimate_interval(
estimate=simOutput.get_sumStat_utilities().get_mean(),
interval=simOutput.get_sumStat_utilities().get_t_CI(alpha=Data.ALPHA),
deci=2
)
# print outcomes
print(treatment)
print(" Estimate of mean survival time and {:.{prec}%} confidence interval:".format(1 - Data.ALPHA, prec=0),
survival_mean_CI_text)
print(" Estimate of discounted cost and {:.{prec}%} confidence interval:".format(1 - Data.ALPHA, prec=0),
cost_mean_CI_text)
print(" Estimate of discounted utility and {:.{prec}%} confidence interval:".format(1 - Data.ALPHA, prec=0),
utility_mean_CI_text)
def print_outcomes(simOutput, therapy_name):
""" prints the outcomes of a simulated cohort
:param simOutput: output of a simulated cohort
:param therapy_name: the name of the selected therapy
"""
# mean and confidence interval text of patient survival time
survival_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_survival_times().get_mean(),
interval=simOutput.get_sumStat_survival_times().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
# mean and confidence interval text of time to stroke
strokes_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_count_strokes().get_mean(),
interval=simOutput.get_sumStat_count_strokes().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
# print outcomes
print(therapy_name)
print(
" Estimate of mean and {:.{prec}%} confidence interval of survival time:"
.format(1 - Settings.ALPHA, prec=0), survival_mean_CI_text)
print(
" Estimate of mean and {:.{prec}%} confidence interval of time to stroke:"
.format(1 - Settings.ALPHA, prec=0), strokes_mean_CI_text)
print("")
def print_outcomes(simOutput, therapy_name):
""" prints the outcomes of a simulated cohort
:param simOutput: output of a simulated cohort
:param therapy_name: the name of the selected therapy
"""
# mean and confidence interval text of patient survival time
# ect_mean_CI_text = F.format_estimate_interval(
# estimate=simOutput.get_sumStat_eclampsia_times.get_mean(),
# interval=simOutput.get_sumStat_eclampsia_times().get_t_CI(alpha=Settings.ALPHA),
# deci=2)
cost_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_cost().get_mean(),
interval=simOutput.get_sumStat_discounted_cost().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
utility_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_utility().get_mean(),
interval=simOutput.get_sumStat_discounted_utility().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
# print outcomes
print(therapy_name)
#print(" Estimate of mean and {:.{prec}%} CI of time to seizure:".format(1 - Settings.ALPHA, prec=0),
# ect_mean_CI_text)
print(
" Estimate of discounted cost and {:.{prec}%} CI:".format(
1 - Settings.ALPHA, prec=0), cost_mean_CI_text)
print(
" Estimate of discounted utility and {:.{prec}%} CI:".format(
1 - Settings.ALPHA, prec=0), utility_mean_CI_text)
print("")
def print_comparative_outcomes(sim_output_high, sim_output_low):
# increase in survival time
increase = Stat.DifferenceStatIndp(name='Increase in game score',
x=sim_output_high,
y_ref=sim_output_low)
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=increase.get_mean(),
interval=increase.get_t_CI(alpha=0.05),
deci=1)
print(
"Average increase in game score and {:.{prec}%} confidence interval:".
format(1 - 0.05, prec=0), estimate_CI)
# % increase in survival time
relative_diff = Stat.RelativeDifferenceIndp(
name='Average % increase in game score',
x=sim_output_high,
y_ref=sim_output_low)
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=relative_diff.get_mean(),
interval=relative_diff.get_bootstrap_CI(alpha=0.05, num_samples=1000),
deci=1,
form=Format.FormatNumber.PERCENTAGE)
print(
"Average percentage increase in game score and {:.{prec}%} confidence interval:"
.format(1 - 0.05, prec=0), estimate_CI)
def print_outcomes(simOutput, therapy_name):
""" prints the outcomes of a simulated cohort
:param simOutput: output of a simulated cohort
:param therapy_name: the name of the selected therapy
"""
# mean and confidence interval text of patient survival time
survival_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_survival_times().get_mean(),
interval=simOutput.get_sumStat_survival_times().get_t_CI(alpha=Settings.ALPHA),
deci=2)
# mean and confidence interval text of discounted total cost
cost_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_cost().get_mean(),
interval=simOutput.get_sumStat_discounted_cost().get_t_CI(alpha=Settings.ALPHA),
deci=0,
form=F.FormatNumber.CURRENCY)
# mean and confidence interval text of discounted total utility
utility_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_utility().get_mean(),
interval=simOutput.get_sumStat_discounted_utility().get_t_CI(alpha=Settings.ALPHA),
deci=2)
# print outcomes
print(therapy_name)
print(" Estimate of mean survival time and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA, prec=0),
survival_mean_CI_text)
print(" Estimate of discounted cost and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA, prec=0),
cost_mean_CI_text)
print(" Estimate of discounted utility and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA, prec=0),
utility_mean_CI_text)
print("")
def print_comparative_outcomes(simOutputs_mono, simOutputs_combo):
""" prints average increase in survival time, discounted cost, and discounted utility
under combination therapy compared to mono therapy
:param simOutputs_mono: output of a cohort simulated under mono therapy
:param simOutputs_combo: output of a cohort simulated under combination therapy
"""
# Antibiotics exposure time
increase_exposure_time = simOutputs_combo.get_sumStat_survival_times().get_total() \
- simOutputs_mono.get_sumStat_survival_times().get_total()
print("Increase in total antibiotics exposure time (day):",
increase_exposure_time)
#### Survival time ####
increase_survival_time = Stat.DifferenceStatIndp(
name='Increase in survival time',
x=simOutputs_combo.get_survival_times(),
y_ref=simOutputs_mono.get_survival_times())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_survival_time.get_mean(),
interval=increase_survival_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average change in antibiotic exposure time (day) "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA,
prec=0), estimate_CI)
#### Discounted total cost ####
increase_discounted_cost = Stat.DifferenceStatIndp(
name='Increase in discounted total cost',
x=simOutputs_combo.get_costs(),
y_ref=simOutputs_mono.get_costs())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_cost.get_mean(),
interval=increase_discounted_cost.get_t_CI(alpha=Settings.ALPHA),
deci=0,
form=F.FormatNumber.CURRENCY)
print(
"Average increase in discounted total cost "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA,
prec=0), estimate_CI)
#### Discounted total utility ####
increase_discounted_utility = Stat.DifferenceStatIndp(
name='Increase in discounted total utility',
x=simOutputs_combo.get_utilities(),
y_ref=simOutputs_mono.get_utilities())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_utility.get_mean(),
interval=increase_discounted_utility.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in discounted total utility "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA,
prec=0), estimate_CI)
def print_outcomes(simOutput, screening):
# mean and CI text of discounted total cost
cost_mean_CI_text = Format.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_cost().get_mean(),
interval=simOutput.get_sumStat_discounted_cost().get_t_CI(
alpha=Data.ALPHA),
deci=2)
# mean and CI text of discounted utility
utility_mean_CI_text = Format.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_utility().get_mean(),
interval=simOutput.get_sumStat_discounted_utility().get_t_CI(
alpha=Data.ALPHA),
deci=2)
# print outcomes
print(screening)
print(
" Estimate of discounted cost and {:.{prec}%} confidence interval:".
format(1 - Data.ALPHA, prec=0), cost_mean_CI_text)
print(
" Estimate of discounted utility and {:.{prec}%} confidence interval:".
format(1 - Data.ALPHA, prec=0), utility_mean_CI_text)
def print_comparative_outcomes(sim_output_fair_coins, sim_output_unfair_coins):
""" prints expected and percentage increase in survival time when drug is available
:param sim_output_no_drug: output of a cohort simulated when drug is not available
:param sim_output_with_drug: output of a cohort simulated when drug is available
"""
# increase in rewards
increase = Stat.DifferenceStatIndp(
name='Increase in survival time',
x=sim_output_unfair_coins.get_rewards(),
y_ref=sim_output_fair_coins.get_rewards())
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=increase.get_mean(),
interval=increase.get_t_CI(alpha=P.ALPHA),
deci=1)
print(
"Average increase in rewards for casino owners and {:.{prec}%} confidence interval"
" when using unfair coins:".format(1 - P.ALPHA, prec=0), estimate_CI)
# % increase in rewards
relative_diff = Stat.RelativeDifferenceIndp(
name='Average % increase in survival time',
x=sim_output_unfair_coins.get_rewards(),
y_ref=sim_output_fair_coins.get_rewards())
# estimate and CI
estimate_CI2 = Format.format_estimate_interval(
estimate=-relative_diff.get_mean(),
interval=-relative_diff.get_bootstrap_CI(alpha=P.ALPHA,
num_samples=1000),
deci=1,
form=Format.FormatNumber.PERCENTAGE)
print(
"Average percentage of increase rewards for casino owners and {:.{prec}%} confidence interval"
" when using unfair coins:".format(1 - P.ALPHA, prec=0), estimate_CI2)
def print_comparative_outcomes(sim_output_unfair, sim_output_fair):
increase = Stat.DifferenceStatIndp(name='Increase in rewards',
x=sim_output_unfair.get_rewards(),
y_ref=sim_output_fair.get_rewards())
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=increase.get_mean(),
interval=increase.get_t_CI(alpha=P.ALPHA),
deci=1)
print(
"Average increase in reward and {:.{prec}%} confidence interval:".
format(1 - P.ALPHA, prec=0), estimate_CI)
# % increase in survival time
relative_diff = Stat.RelativeDifferenceIndp(
name='Average % increase in rewards',
x=sim_output_unfair.get_rewards(),
y_ref=sim_output_fair.get_rewards())
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=relative_diff.get_mean(),
interval=relative_diff.get_bootstrap_CI(alpha=P.ALPHA,
num_samples=1000),
deci=1,
form=Format.FormatNumber.PERCENTAGE)
print(
"Average percentage increase in reward and {:.{prec}%} confidence interval:"
.format(1 - P.ALPHA, prec=0), estimate_CI)
def print_comparative_outcomes(simOutputs_mono, simOutputs_combo):
""" prints average increase in survival time, discounted cost, and discounted utility
under combination therapy compared to mono therapy
:param simOutputs_mono: output of a cohort simulated under mono therapy
:param simOutputs_combo: output of a cohort simulated under combination therapy
"""
# increase in survival time under combination therapy with respect to mono therapy
increase_survival_time = Stat.DifferenceStatIndp(
name='Increase in survival time',
x=simOutputs_combo.get_survival_times(),
y_ref=simOutputs_mono.get_survival_times())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_survival_time.get_mean(),
interval=increase_survival_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in survival time "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA,
prec=0), estimate_CI)
# increase in discounted total cost under combination therapy with respect to mono therapy
increase_discounted_cost = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_combo.get_costs(),
y_ref=simOutputs_mono.get_costs())
# estimate and CI
estimate_CI_cost = F.format_estimate_interval(
estimate=increase_discounted_cost.get_mean(),
interval=increase_discounted_cost.get_t_CI(alpha=Settings.ALPHA),
deci=0,
form=F.FormatNumber.CURRENCY)
print(
"Average increase in discounted cost "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA,
prec=0),
estimate_CI_cost)
# increase in discounted total utility under combination therapy with respect to mono therapy
increase_discounted_utility = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_combo.get_utilities(),
y_ref=simOutputs_mono.get_utilities())
# estimate and CI
estimate_CI_utility = F.format_estimate_interval(
estimate=increase_discounted_utility.get_mean(),
interval=increase_discounted_utility.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in discounted utility "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA,
prec=0),
estimate_CI_utility)
def print_comparative_outcomes(simOutputs_ANNUAL, simOutputs_SEMI):
""" prints average increase in infection time, discounted cost, and discounted utility
under combination therapy compared to mono therapy
:param simOutputs_mono: output of a cohort simulated under mono therapy
:param simOutputs_combo: output of a cohort simulated under combination therapy
"""
decrease_infection_time = Stat.DifferenceStatIndp(
name="decrease in infection time",
x=simOutputs_SEMI.get_infection_durations(),
y_ref=simOutputs_ANNUAL.get_infection_durations())
estimate_CI = F.format_estimate_interval(
estimate=decrease_infection_time.get_mean(),
interval=decrease_infection_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
estimate_CI = F.format_estimate_interval(
estimate=decrease_infection_time.get_mean(),
interval=decrease_infection_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average decrease in infection duration "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
# increase in discounted total cost under combination therapy with respect to mono therapy
increase_discounted_cost = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_SEMI.get_costs(),
y_ref=simOutputs_ANNUAL.get_costs())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_cost.get_mean(),
interval=increase_discounted_cost.get_t_CI(alpha=Settings.ALPHA),
deci=0,
form=F.FormatNumber.CURRENCY)
print(
"Average increase in discounted cost "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
# increase in discounted total utility under combination therapy with respect to mono therapy
increase_discounted_utility = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_SEMI.get_utilities(),
y_ref=simOutputs_ANNUAL.get_utilities())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_utility.get_mean(),
interval=increase_discounted_utility.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in discounted utility "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
def print_comparative_outcomes(simOutputs_warfarin, simOutputs_Dabigitran150):
""" prints average increase in survival time, discounted cost, and discounted utility
under dab therapy compared to warf therapy
:param simOutputs_warfarin: output of a cohort simulated under warfarin therapy
:param simOutputs_Dabigitran150: output of a cohort simulated under dab therapy
"""
# increase in survival time under dab therapy with respect to warf therapy
increase_survival_time = Stat.DifferenceStatIndp(
name="Increase in survival time",
x=simOutputs_Dabigitran150.get_survival_times(),
y_ref=simOutputs_warfarin.get_survival_times())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_survival_time.get_mean(),
interval=increase_survival_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in survival time "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
# increase in discounted total cost under dab therapy with respect to warfarin therapy
increase_discounted_cost = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_Dabigitran150.get_costs(),
y_ref=simOutputs_warfarin.get_costs())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_cost.get_mean(),
interval=increase_discounted_cost.get_t_CI(alpha=Settings.ALPHA),
deci=0,
form=F.FormatNumber.CURRENCY)
print(
"Average increase in discounted cost "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
# increase in discounted total utility under dab therapy with respect to warfarin therapy
increase_discounted_utility = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_Dabigitran150.get_utilities(),
y_ref=simOutputs_warfarin.get_utilities())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_utility.get_mean(),
interval=increase_discounted_utility.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in discounted utility "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
def print_outcomes(simOutput, therapy_name):
""" prints the outcomes of a simulated cohort
:param simOutput: output of a simulated cohort
:param therapy_name: the name of the selected therapy
"""
# mean and confidence interval text of patient survival time
survival_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_survival_times().get_mean(),
interval=simOutput.get_sumStat_survival_times().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
# mean of number of stroke
stroke_mean = F.format_estimate_interval(
estimate=simOutput.get_sumStat_stroke().get_mean(),
interval=simOutput.get_sumStat_stroke().get_t_CI(alpha=Settings.ALPHA),
deci=2)
# mean and confidence interval text of time to AIDS
#time_to_HIV_death_CI_text = F.format_estimate_interval(
#estimate=simOutput.get_sumStat_time_to_AIDS().get_mean(),
#interval=simOutput.get_sumStat_time_to_AIDS().get_t_CI(alpha=Settings.ALPHA),
#deci=2)
# mean and confidence interval text of discounted total cost
#cost_mean_CI_text = F.format_estimate_interval(
#estimate=simOutput.get_sumStat_discounted_cost().get_mean(),
#interval=simOutput.get_sumStat_discounted_cost().get_t_CI(alpha=Settings.ALPHA),
#deci=0,
#form=F.FormatNumber.CURRENCY)
# mean and confidence interval text of discounted total utility
#utility_mean_CI_text = F.format_estimate_interval(
#estimate=simOutput.get_sumStat_discounted_utility().get_mean(),
#interval=simOutput.get_sumStat_discounted_utility().get_t_CI(alpha=Settings.ALPHA),
#deci=2)
# print outcomes
print(therapy_name)
print(
" Estimate of mean survival time and {:.{prec}%} confidence interval:"
.format(1 - Settings.ALPHA, prec=0), survival_mean_CI_text)
print(
" Estimate of mean number of stroke {:.{prec}%} confidence interval:".
format(1 - Settings.ALPHA, prec=0), stroke_mean)
#print(" Estimate of mean time to AIDS and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA, prec=0),
#time_to_HIV_death_CI_text)
#print(" Estimate of discounted cost and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA, prec=0),
#cost_mean_CI_text)
#print(" Estimate of discounted utility and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA, prec=0),
#utility_mean_CI_text)
print("")
def print_comparative_outcomes(simOutputs_A, simOutputs_B):
# prints average increase in survival time, discounted cost, and discounted utility
# increase in survival time comparing two therapies
increase_survival_time = Stat.DifferenceStatIndp(
name="Increase in survival time",
x=simOutputs_B.get_survival_times(),
y_ref=simOutputs_A.get_survival_times())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_survival_time.get_mean(),
interval=increase_survival_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in survival time "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
# increase in discounted total cost comparing two therapies
increase_discounted_cost = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_B.get_costs(),
y_ref=simOutputs_A.get_costs())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_cost.get_mean(),
interval=increase_discounted_cost.get_t_CI(alpha=Settings.ALPHA),
deci=0,
form=F.FormatNumber.CURRENCY)
print(
"Average increase in discounted cost "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
# increase in discounted total utility comparing two therapies
increase_discounted_utility = Stat.DifferenceStatIndp(
name='Increase in discounted cost',
x=simOutputs_B.get_utilities(),
y_ref=simOutputs_A.get_utilities())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_discounted_utility.get_mean(),
interval=increase_discounted_utility.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in discounted utility "
"and {:.{prec}%} CI:".format(1 - Settings.ALPHA, prec=0), estimate_CI)
def print_comparative_outcomes(simOutputs_no_therapy, simOutputs_anticoagulation):
"""
:param simOutputs_no_therapy:
:param simOutputs_anticoagulation:
:return:
"""
# increase in survival time under anticoagulation therapy with respect to no therapy
if Settings.PSA_ON:
increase_survival_time = Stat.DifferenceStatPaired(
name='Increase in survival time',
x=simOutputs_anticoagulation.get_survival_times(),
y_ref=simOutputs_no_therapy.get_survival_times())
else:
increase_survival_time = Stat.DifferenceStatIndp(
name='Increase in survival time',
x=simOutputs_anticoagulation.get_survival_times(),
y_ref=simOutputs_no_therapy.get_survival_times())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_survival_time.get_mean(),
interval=increase_survival_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print("Average increase in survival time "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA, prec=0),
estimate_CI)
def print_comparative_outcomes(simOutputs_mono, simOutputs_combo):
""" prints average increase in survival time, discounted cost, and discounted utility
under combination therapy compared to mono therapy
:param simOutputs_mono: output of a cohort simulated under mono therapy
:param simOutputs_combo: output of a cohort simulated under combination therapy
"""
# increase in survival time under combination therapy with respect to mono therapy
if Settings.PSA_ON:
increase_survival_time = Stat.DifferenceStatPaired(
name='Increase in survival time',
x=simOutputs_combo.get_survival_times(),
y_ref=simOutputs_mono.get_survival_times())
else:
increase_survival_time = Stat.DifferenceStatIndp(
name='Increase in survival time',
x=simOutputs_combo.get_survival_times(),
y_ref=simOutputs_mono.get_survival_times())
# estimate and CI
estimate_CI = F.format_estimate_interval(
estimate=increase_survival_time.get_mean(),
interval=increase_survival_time.get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(
"Average increase in survival time "
"and {:.{prec}%} confidence interval:".format(1 - Settings.ALPHA,
prec=0), estimate_CI)
def get_mean_survival_proj_interval(self, alpha, deci):
mean = self._multiCohorts.get_overall_mean_survival()
proj_interval = self._multiCohorts.get_PI_mean_surviavl(alpha)
return FormatSupport.format_estimate_interval(mean, proj_interval,
deci)
def get_survival_estimate_credible_interval(self, alpha, deci):
sum_stat = StatSupport.SummaryStat('Posterior Samples',
self._survivalResamples)
estimate = sum_stat.get_mean()
credible_interval = sum_stat.get_PI(alpha)
return FormatSupport.format_estimate_interval(estimate,
credible_interval, deci)
def print_mean_stroke_outcomes(simOutput, therapyName):
mean_strokes_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_strokes().get_mean(),
interval=simOutput.get_sumStat_strokes().get_t_CI(alpha=Settings.ALPHA),
deci=2)
print(" Estimate of mean number of strokes and {:.{prec}%} confidence interval:".format(1 - Data.ALPHA, prec=0),
mean_strokes_CI_text)
def print_outcomes(multi_cohort, strategy_name):
reward_mean_PI_text = Format.format_estimate_interval(
estimate=multi_cohort.get_mean_total_reward(),
interval=multi_cohort.get_PI_total_reward(alpha=P.ALPHA),
deci=1)
print(strategy_name)
print(
"Estimate of mean game reward and {:.{prec}%} prediction interval:".
format(1 - P.ALPHA, prec=0), reward_mean_PI_text)
def print_outcomes(sim_output, coin_type):
reward_mean_CI_text = Format.format_estimate_interval(
estimate=sim_output.get_ave_reward(),
interval=sim_output.get_CI_reward(alpha=P.ALPHA),
deci=1)
print(coin_type)
print("Estimate of game reward and {:.{prec}%} confidence interval:".format(1 - P.ALPHA, prec=0),
reward_mean_CI_text)
def print_outcomes(simOutput, therapy_name):
""" prints the outcomes of a simulated cohort
:param simOutput: output of a simulated cohort
:param therapy_name: the name of the selected therapy
"""
# total of patient exposure time to antibiotics
survival_total_text = simOutput.get_sumStat_survival_times().get_total()
# mean and confidence interval text of patient survival time
survival_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_survival_times().get_mean(),
interval=simOutput.get_sumStat_survival_times().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
# mean and confidence interval text of discounted total cost
cost_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_cost().get_mean(),
interval=simOutput.get_sumStat_discounted_cost().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
# mean and confidence interval text of discounted total cost
utility_mean_CI_text = F.format_estimate_interval(
estimate=simOutput.get_sumStat_discounted_utility().get_mean(),
interval=simOutput.get_sumStat_discounted_utility().get_t_CI(
alpha=Settings.ALPHA),
deci=2)
# print outcomes
print(therapy_name)
print(" Estimate of total patient exposure time to antibiotics (days):",
survival_total_text)
print(
" Estimate of mean and {:.{prec}%} confidence interval of survival time:"
.format(1 - Settings.ALPHA, prec=0), survival_mean_CI_text)
print(
" Estimate of mean and {:.{prec}%} confidence interval of discounted total cost:"
.format(1 - Settings.ALPHA, prec=0), cost_mean_CI_text)
print(
" Estimate of mean and {:.{prec}%} confidence interval of discounted total utility:"
.format(1 - Settings.ALPHA, prec=0), utility_mean_CI_text)
print("")
def print_outcomes(sim_output, strategy_name):
rewards_mean_CI_text = Format.format_estimate_interval(
estimate=sim_output.get_ave_reward(),
interval=sim_output.get_CI_reward(alpha=P.ALPHA),
deci=1)
print(strategy_name)
print(
"Estimate of mean game rewards and {:.{prec}%} confidence interval:".
format(1 - P.ALPHA, prec=1), rewards_mean_CI_text)
def print_outcomes(multi_gameset, coin_type):
reward_mean_PI_text = Format.format_estimate_interval(
estimate=multi_gameset.get_overall_mean_reward(),
interval=multi_gameset.get_PI_mean_reward(alpha=P.ALPHA),
deci=1)
print(coin_type)
print(
" Estimate of mean game reward and {:.{prec}%} prediction interval:".
format(1 - P.ALPHA, prec=0), reward_mean_PI_text)
def get_mean_survival_time_proj_interval(self, alpha, deci):
"""
:param alpha: the significance level
:param deci: decimal places
:returns text in the form of 'mean (lower, upper)' of projection interval
"""
mean = self._multiCohorts.get_overall_mean_survival()
proj_interval = self._multiCohorts.get_PI_mean_survival(alpha)
return FormatSupport.format_estimate_interval(mean, proj_interval, deci)
def outcomes(simulation_output, strategy):
# mean and CI of game reward
rewardCImean = Format.format_estimate_interval(
estimate=simulation_output.get_ave_reward(),
interval=simulation_output.get_CI_reward(alpha=P.alpha),
deci=1)
# print game reward statistics
print(strategy)
print(
" Estimate of the gambler's mean game reward and {:.{prec}%} confidence interval:"
.format(1 - P.alpha, prec=0), rewardCImean)
def get_compare(sim_output_fair, sim_output_unfair):
increase = Stat.DifferenceStatIndp(name='Increase in Reward',
x=sim_output_fair.get_rewards(),
y_ref=sim_output_unfair.get_rewards())
# estimate and CI
estimate_CI = Format.format_estimate_interval(
estimate=increase.get_mean(),
interval=increase.get_t_CI(alpha=alpha),
deci=1)
print(
"Average increase in reward ($) and {:.{prec}%} confidence interval:".
format(1 - alpha, prec=0), estimate_CI)
def outcomes(simulation_output, strategy):
# mean and prediction interval text of game reward
rewardPImean = Format.format_estimate_interval(
estimate=simulation_output.get_mean_total_reward(),
interval=simulation_output.get_PI_total_reward(alpha=P.alpha),
deci=1)
# print game reward statistics
print(strategy)
print(
" Estimate of the gambler's total reward from 10 games and {:.{prec}%} prediction interval:"
.format(1 - P.alpha, prec=0), rewardPImean)
