def report_CEA_CBA(sim_outcomes_none, sim_outcomes_anticoag):
""" performs cost-effectiveness and cost-benefit analyses
:param sim_outcomes_none: outcomes of a cohort simulated under no therapy
:param sim_outcomes_anticoag: outcomes of a cohort simulated under anticoagultation therapy
"""
# define two strategies
no_therapy_strategy = Econ.Strategy(
name='No Therapy',
cost_obs=sim_outcomes_none.costs,
effect_obs=sim_outcomes_none.utilities,
color='red'
)
anticoag_therapy_strategy = Econ.Strategy(
name='Anticoagulation Therapy',
cost_obs=sim_outcomes_anticoag.costs,
effect_obs=sim_outcomes_anticoag.utilities,
color='blue'
)
# do cost-effectiveness analysis
# (the first strategy in the list of strategies is assumed to be the 'Base' strategy)
CEA = Econ.CEA(
strategies=[no_therapy_strategy, anticoag_therapy_strategy],
if_paired=False
)
# plot cost-effectiveness figure
CEA.plot_CE_plane(
title='Cost-Effectiveness Analysis',
x_label='Additional QALYs',
y_label='Additional Cost',
x_range=(-0.6, 1.5),
y_range=(-5000, 50000),
interval_type='c'
)
# report the CE table
CEA.build_CE_table(
interval_type='c',
alpha=D.ALPHA,
cost_digits=0,
effect_digits=2,
icer_digits=2)
# cost-benefit analysis
CBA = Econ.CBA(
strategies=[no_therapy_strategy, anticoag_therapy_strategy],
wtp_range=[0, 100000],
if_paired=False
)
# show the net monetary benefit figure
CBA.plot_incremental_nmbs(
title='Cost-Benefit Analysis',
x_label='Willingness-to-pay per QALY ($)',
y_label='Incremental Net Monetary Benefit ($)',
interval_type='c',
show_legend=True,
figure_size=(6, 5)
)
def report_CEA_CBA(multi_cohort_outcomes_mono, multi_cohort_outcomes_combo):
""" performs cost-effectiveness and cost-benefit analyses
:param multi_cohort_outcomes_mono: outcomes of a multi-cohort simulated under mono therapy
:param multi_cohort_outcomes_combo: outcomes of a multi-cohort simulated under combination therapy
"""
# define two strategies
mono_therapy_strategy = Econ.Strategy(
name='Mono Therapy',
cost_obs=multi_cohort_outcomes_mono.meanCosts,
effect_obs=multi_cohort_outcomes_mono.meanQALYs,
color='green')
combo_therapy_strategy = Econ.Strategy(
name='Combination Therapy',
cost_obs=multi_cohort_outcomes_combo.meanCosts,
effect_obs=multi_cohort_outcomes_combo.meanQALYs,
color='blue')
# do CEA
CEA = Econ.CEA(strategies=[mono_therapy_strategy, combo_therapy_strategy],
if_paired=True)
# show the cost-effectiveness plane
CEA.plot_CE_plane(title='Cost-Effectiveness Analysis',
x_label='Additional Discounted QALY',
y_label='Additional Discounted Cost',
fig_size=(6, 5),
add_clouds=True,
transparency=0.2)
# report the CE table
CEA.build_CE_table(
interval_type='p', # uncertainty (projection) interval
alpha=D.ALPHA,
cost_digits=0,
effect_digits=2,
icer_digits=2,
file_name='CETable.csv')
# CBA
NBA = Econ.CBA(strategies=[mono_therapy_strategy, combo_therapy_strategy],
wtp_range=(0, 50000),
if_paired=True)
# show the net monetary benefit figure
NBA.plot_incremental_nmbs(
title='Cost-Benefit Analysis',
x_label='Willingness-To-Pay for One Additional QALY ($)',
y_label='Incremental Net Monetary Benefit ($)',
interval_type='p',
show_legend=True,
figure_size=(6, 5),
)
def report_CEA_CBA(sim_outcomes_none, sim_outcomes_anti):
""" performs cost-effectiveness and cost-benefit analyses
:param sim_outcomes_mono: outcomes of a cohort simulated under mono therapy
:param sim_outcomes_combo: outcomes of a cohort simulated under combination therapy
"""
# define two strategies
no_therapy_strategy = Econ.Strategy(name='No Anticoagulation ',
cost_obs=sim_outcomes_none.costs,
effect_obs=sim_outcomes_none.utilities,
color='green')
anti_therapy_strategy = Econ.Strategy(
name='With Anticoagulation',
cost_obs=sim_outcomes_anti.costs,
effect_obs=sim_outcomes_anti.utilities,
color='blue')
# do CEA
CEA = Econ.CEA(strategies=[no_therapy_strategy, anti_therapy_strategy],
if_paired=False)
# plot cost-effectiveness figure
CEA.plot_CE_plane(title='Cost-Effectiveness Analysis',
x_label='Additional QALYs',
y_label='Additional Cost',
interval_type='c',
x_range=(-0.5, 1),
y_range=(-1000, 10000))
# report the CE table
CEA.build_CE_table(interval_type='c',
alpha=D.ALPHA,
cost_digits=0,
effect_digits=2,
icer_digits=2,
file_name='CETable.csv')
# CBA
NBA = Econ.CBA(strategies=[no_therapy_strategy, anti_therapy_strategy],
wtp_range=[0, 50000],
if_paired=False)
# show the net monetary benefit figure
NBA.plot_incremental_nmbs(title='Cost-Benefit Analysis',
x_label='Willingness-to-pay per QALY ($)',
y_label='Incremental Net Monetary Benefit ($)',
interval_type='c',
show_legend=True,
figure_size=(6, 5))
from SimPy import EconEval as EV
S0 = EV.Strategy(name='Base', cost_obs=[100], effect_obs=[1])
S1 = EV.Strategy(name='A1', cost_obs=[800], effect_obs=[0.5])
S2 = EV.Strategy(name='A2', cost_obs=[2000], effect_obs=[10])
S3 = EV.Strategy(name='A3', cost_obs=[500], effect_obs=[7])
S4 = EV.Strategy(name='A4', cost_obs=[-100], effect_obs=[2])
S5 = EV.Strategy(name='A5', cost_obs=[200], effect_obs=[2])
S6 = EV.Strategy(name='A6', cost_obs=[1000], effect_obs=[7.2])
S7 = EV.Strategy(name='A7', cost_obs=[1100], effect_obs=[7.3])
cea = EV.CEA(strategies=[S0, S1, S2, S3, S4, S5, S6, S7],
if_paired=False,
health_measure='u')
# show the ce plane:
cea.plot_CE_plane()
# build table
cea.build_CE_table(interval_type='n')
print('On frontier')
frontier_strategies = cea.get_strategies_on_frontier()
for i, s in enumerate(frontier_strategies):
print(s.name)
if i > 0:
print('incCost:', s.incCost.get_mean())
print('incEffect:', s.incEffect.get_mean())
print('ICER:', s.icer.get_ICER())
import numpy as np
from SimPy import EconEval as EV
np.random.seed(seed=1)
S0 = EV.Strategy(name='Base',
cost_obs=np.random.normal(loc=100, scale=10, size=100),
effect_obs=np.random.normal(loc=1, scale=.2, size=100),
color='red')
S1 = EV.Strategy(name='A1',
cost_obs=np.random.normal(loc=800, scale=50, size=100),
effect_obs=np.random.normal(loc=0.5, scale=0.1, size=100),
color='blue')
S2 = EV.Strategy(name='A2',
cost_obs=np.random.normal(loc=2000, scale=200, size=100),
effect_obs=np.random.normal(loc=10, scale=1, size=100),
color='green')
S3 = EV.Strategy(name='A3',
cost_obs=np.random.normal(loc=500, scale=50, size=100),
effect_obs=np.random.normal(loc=7, scale=1, size=100),
color='orange')
S4 = EV.Strategy(name='A4',
cost_obs=np.random.normal(loc=-100, scale=10, size=100),
effect_obs=np.random.normal(loc=2, scale=0.1, size=100),
color='purple')
cea = EV.CEA(strategies=[S0, S1, S2, S3, S4], if_paired=False, health_measure='u')
print('On frontier')
for s in cea.get_strategies_on_frontier():
def populate_sets_of_scenarios(list_of_scenario_sets,
save_cea_results=False,
colors_of_scenarios=None,
interval_type='n',
effect_multiplier=1,
cost_multiplier=1,
switch_cost_effect_on_figure=False,
wtp_range=None):
"""
:param list_of_scenario_sets: (list) of sets of scenarios
:param save_cea_results: set it to True if the CE table should be generated
:param colors_of_scenarios: (dictionary) of colors for scenarios
:param interval_type: select from Econ.Interval (no interval, CI, or PI)
:param effect_multiplier:
:param cost_multiplier:
:param switch_cost_effect_on_figure: displays cost on the x-axis and effect on the y-axis
:param wtp_range: for net monetary benefit analysis
"""
# populate series to display on the cost-effectiveness plane
for i, scenario_set in enumerate(list_of_scenario_sets):
if scenario_set.ifPopulated:
continue
# create the base strategy
scn = scenario_set.scenarioDF.scenarios['Base']
base_strategy = Econ.Strategy(
name='Base',
label='Base',
cost_obs=scn.outcomes[COST_MEASURE],
effect_obs=scn.outcomes[HEALTH_MEASURE],
color=None
if colors_of_scenarios is None else colors_of_scenarios[0])
# add base
scenario_set.strategies = [base_strategy]
# add other scenarios
i = 0
for key, scenario in scenario_set.scenarioDF.scenarios.items():
# add only non-Base strategies that can be on this series
if scenario.name != 'Base' and scenario_set.if_acceptable(
scenario):
# find labels of each strategy
label_list = []
for varCon in scenario_set.varConditions:
if varCon.ifIncludedInLabel:
# value of this variable
value = scenario.variables[varCon.varName]
# if there is not label rules
if varCon.labelRules is None:
if varCon.labelFormat == '':
label_list.append(str(value) + ',')
else:
label_list.append(
varCon.labelFormat.format(value) +
', ')
else:
label = varCon.get_label(value)
if label == '':
pass
else:
label_list.append(label + ', ')
for outcomeCon in scenario_set.outcomeConditions:
if outcomeCon.ifIncludedInLabel:
# value of this variable
value = Stat.SummaryStat(
name=outcomeCon.outcomeName,
data=scenario.outcomes[
outcomeCon.outcomeName]).get_mean()
# if there is not label rules
if outcomeCon.labelRules is None:
if outcomeCon.labelFormat == '':
label_list.append(str(value) + ',')
else:
label_list.append(
outcomeCon.labelFormat.format(value) +
', ')
else:
label = outcomeCon.get_label(value)
if label == '':
pass
else:
label_list.append(label + ', ')
label = ''.join(str(x) for x in label_list)
if len(label) > 0:
if label[-1] == ' ' or label[-1] == ',':
label = label[:-1]
if label[-1] == ' ' or label[-1] == ',':
label = label[:-1]
# legends
scenario_set.legend.append(label)
# color of this strategy
color = None
if colors_of_scenarios is not None:
color = colors_of_scenarios[i + 1]
if scenario_set.xyLabelsProvided:
label = scenario_set.xyLabels[i]
scenario_set.strategies.append(
Econ.Strategy(
name=scenario.name,
label=label,
cost_obs=scenario.outcomes[COST_MEASURE],
effect_obs=scenario.outcomes[HEALTH_MEASURE],
color=color))
i += 1
# do CEA on this series
scenario_set.build_CE_curve(
save_cea_results=save_cea_results,
interval_type=interval_type,
effect_multiplier=effect_multiplier,
cost_multiplier=cost_multiplier,
switch_cost_effect_on_figure=switch_cost_effect_on_figure,
wtp_range=wtp_range)
scenario_set.ifPopulated = True
import numpy as np
from SimPy import EconEval as ce
N = 100
np.random.seed(573)
s_center = np.array([[10000, 0.2], [20000, 0.7], [50000, 1.2]])
s0 = ce.Strategy("s0",
s_center[0, 0] + np.random.normal(0, 1000, N),
s_center[0, 1] + np.random.normal(0, 0.01, N),
color='red')
s1 = ce.Strategy("s1",
s_center[1, 0] + np.random.normal(0, 1000, N),
s_center[1, 1] + np.random.normal(0, 0.01, N),
color='blue')
s2 = ce.Strategy("s2",
s_center[2, 0] + np.random.normal(0, 1000, N),
s_center[2, 1] + np.random.normal(0, 0.05, N),
color='green')
cea = ce.CEA([s0, s1, s2], if_paired=True)
cea.plot_CE_plane()
nmb_paired = ce.CBA([s0, s1, s2], wtp_range=[0, 100000], if_paired=True)
nmb_indp = ce.CBA([s0, s1, s2], wtp_range=[0, 100000],
if_paired=False) # list of frontier strategies as input
# Try NMB_Lines figure - paired CI
nmb_paired.plot_incremental_nmbs(title="deltaNMB lines for paired CI",
import numpy as np
from SimPy import EconEval as EV
np.random.seed(seed=1)
S0 = EV.Strategy(name='Base',
cost_obs=np.random.normal(loc=100, scale=10, size=100),
effect_obs=np.random.normal(loc=1, scale=.2, size=100))
S1 = EV.Strategy(name='A1',
cost_obs=np.random.normal(loc=800, scale=50, size=100),
effect_obs=np.random.normal(loc=0.5, scale=0.1, size=100))
S2 = EV.Strategy(name='A2',
cost_obs=np.random.normal(loc=2000, scale=200, size=100),
effect_obs=np.random.normal(loc=10, scale=1, size=100))
S3 = EV.Strategy(name='A3',
cost_obs=np.random.normal(loc=500, scale=50, size=100),
effect_obs=np.random.normal(loc=7, scale=1, size=100))
S4 = EV.Strategy(name='A4',
cost_obs=np.random.normal(loc=-100, scale=10, size=100),
effect_obs=np.random.normal(loc=2, scale=0.1, size=100))
cea = EV.CEA(strategies=[S0, S1, S2, S3, S4],
if_paired=False,
health_measure='u')
print('On frontier')
for s in cea.get_strategies_on_frontier():
print(s.name)
print('Not on frontier')
from SimPy import EconEval as EV
S0 = EV.Strategy(name='Base', cost_obs=[100], effect_obs=[1])
S1 = EV.Strategy(name='A1', cost_obs=[800], effect_obs=[0.5])
S2 = EV.Strategy(name='A2', cost_obs=[2000], effect_obs=[10])
S3 = EV.Strategy(name='A3', cost_obs=[500], effect_obs=[7])
S4 = EV.Strategy(name='A4', cost_obs=[-100], effect_obs=[2])
cea = EV.CEA(strategies=[S0, S1, S2, S3, S4], if_paired=False, health_measure='u')
print('On frontier')
for s in cea.get_strategies_on_frontier():
print(s.name)
print('Not on frontier')
for s in cea.get_strategies_not_on_frontier():
print(s.name)
cea.plot_CE_plane(add_clouds=False)
cea.build_CE_table(cost_digits=0, interval_type='n')
import numpy as np
from SimPy import EconEval as ce
np.random.seed(573)
# create the centers of strategies
s_center = np.random.normal(0, 5000, (10, 2))
s0 = ce.Strategy("s1", s_center[0, 0] + np.random.normal(0, 200, 10),
s_center[0, 1] + np.random.normal(0, 200, 10))
s1 = ce.Strategy("s2", s_center[1, 0] + np.random.normal(0, 200, 10),
s_center[1, 1] + np.random.normal(0, 100, 10))
s2 = ce.Strategy("s3", s_center[2, 0] + np.random.normal(0, 200, 10),
s_center[2, 1] + np.random.normal(0, 200, 10))
s3 = ce.Strategy("s4", s_center[3, 0] + np.random.normal(0, 200, 10),
s_center[3, 1] + np.random.normal(0, 200, 10))
s4 = ce.Strategy("s5", s_center[4, 0] + np.random.normal(0, 200, 10),
s_center[4, 1] + np.random.normal(0, 200, 10))
s5 = ce.Strategy("s6", s_center[5, 0] + np.random.normal(0, 200, 10),
s_center[5, 1] + np.random.normal(0, 200, 10))
s6 = ce.Strategy("s7", s_center[6, 0] + np.random.normal(0, 200, 10),
s_center[6, 1] + np.random.normal(0, 200, 10))
s7 = ce.Strategy("s8", s_center[7, 0] + np.random.normal(0, 200, 10),
s_center[7, 1] + np.random.normal(0, 200, 10))
s8 = ce.Strategy("s9", s_center[8, 0] + np.random.normal(0, 200, 10),
s_center[8, 1] + np.random.normal(0, 200, 10))
s9 = ce.Strategy("s10", s_center[9, 0] + np.random.normal(0, 200, 10),
s_center[9, 1] + np.random.normal(0, 200, 10))
# create a CEA object -- unpaired
myCEA = ce.CEA([s0, s1, s2, s3, s4, s5, s6, s7, s8, s9], if_paired=False)