def draw_survival_curves_and_histograms(simOutputs_mono, simOutputs_combo):
""" draws the survival curves and the histograms of time until HIV deaths
:param simOutputs_mono: output of a cohort simulated under mono therapy
:param simOutputs_combo: output of a cohort simulated under combination therapy
"""
# get survival curves of both treatments
survival_curves = [
simOutputs_mono.get_survival_curve(),
simOutputs_combo.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step (year)',
y_label='Number of alive patients',
legends=['Mono Therapy', 'Combination Therapy'])
# histograms of survival times
set_of_survival_times = [
simOutputs_mono.get_survival_times(),
simOutputs_combo.get_survival_times()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=1,
legend=['Mono Therapy', 'Combination Therapy'],
transparency=0.6)
def draw_survival_curves_and_histograms(sim_output_no_drug,
sim_output_with_drug):
""" draws the survival curves and the histograms of survival time
: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
"""
# get survival curves of both treatments
survival_curves = [
sim_output_no_drug.get_survival_curve(),
sim_output_with_drug.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step',
y_label='Number of alive patients',
legends=['No Drug', 'With Drug'])
# histograms of survival times
set_of_survival_times = [
sim_output_no_drug.get_survival_times(),
sim_output_with_drug.get_survival_times()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time',
y_label='Counts',
bin_width=1,
legend=['No Drug', 'With Drug'],
transparency=0.6)
def draw_survival_curves_and_histograms(simOutputs_standard,
simOutputs_population):
""" draws the survival curves and the histograms of time until cancer
:param simOutputs_standard: output of a cohort simulated under standard testing
:param simOutputs_population: output of a cohort simulated under population testing
"""
# get survival curves of both treatments
survival_curves = [
simOutputs_standard.get_survival_curve(),
simOutputs_population.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(
sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step (year)',
y_label='Number of alive patients',
legends=['Standard Testing', 'Population Testing'])
# histograms of survival times
set_of_survival_times = [
simOutputs_standard.get_survival_times(),
simOutputs_population.get_survival_times()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=1,
legend=['Mono Therapy', 'Combination Therapy'],
transparency=0.6)
def draw_survival_curves_and_histograms(simOutputs_warfarin,
simOutputs_Dabigitran150):
""" draws the survival curves and the histograms of time until stoke deaths
:param simOutputs_warfarin: output of a cohort simulated under warfarin therapy
:param simOutputs_Dabigitran150: output of a cohort simulated under dab150 therapy
"""
# get survival curves of both treatments
survival_curves = [
simOutputs_warfarin.get_survival_curve(),
simOutputs_Dabigitran150.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step (year)',
y_label='Number of alive patients',
legends=['Warfarin', 'Dabigitran150 Therapy'])
# histograms of survival times
set_of_survival_times = [
simOutputs_warfarin.get_survival_times(),
simOutputs_Dabigitran150.get_survival_times()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=1,
legend=['Warfarin Therapy', 'Dabigitran150 Therapy'],
transparency=0.6)
def draw_infection_curves_and_histograms(simOutputs_ANNUAL, simOutputs_SEMI):
""" draws the infection curves and the histograms of time until HIV deaths
:param simOutputs_mono: output of a cohort simulated under mono therapy
:param simOutputs_combo: output of a cohort simulated under combination therapy
"""
# histograms of infection times
set_of_infection_times = [
simOutputs_ANNUAL.get_infection_durations(),
simOutputs_SEMI.get_infection_durations()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_infection_times,
title='Histogram of Infection Duration',
x_label='Infection Duration (Year)',
y_label='Counts',
bin_width=1,
legend=['Annual Treatment', 'Semi-Annual Treatment'],
transparency=0.6)
#get infection curves of both treatments
infection_curves = [
simOutputs_ANNUAL.get_infection_curve(),
simOutputs_SEMI.get_infection_curve()
]
# graph infection curve
PathCls.graph_sample_paths(sample_paths=infection_curves,
title='infection curve',
x_label='Simulation time step (year)',
y_label='Number of infected patients',
legends=['ANNUAL', '6-month'])
def draw_survival_curves_and_histograms(simOutputs_mono, simOutputs_combo):
""" draws the survival curves and the histograms of time until HIV deaths
:param simOutputs_mono: output of a cohort simulated under mono therapy
:param simOutputs_combo: output of a cohort simulated under combination therapy
"""
# get survival curves of both treatments
survival_curves = [
simOutputs_mono.get_survival_curve(),
simOutputs_combo.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(sample_paths=survival_curves,
title='Exposure of antibiotics',
x_label='Simulation time step (day)',
y_label='Number of patients using antibiotics',
legends=['Standard treatment', 'PCT-guided'])
# histograms of survival times
set_of_survival_times = [
simOutputs_mono.get_survival_times(),
simOutputs_combo.get_survival_times()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_survival_times,
title='Histogram of exposure time to antibiotics',
x_label='Exposure time to antibiotics (day)',
y_label='Counts',
bin_width=1,
legend=['Standard care', 'PCT-guided'],
transparency=0.5)
def draw_survival_curves_and_histograms(simOutputs_none, simOutputs_anticoag):
""" draws the survival curves and the histograms of time until HIV deaths
:param simOutputs_none: output of a cohort simulated under the natural history of disease
:param simOutputs_anticoag: output of a cohort simulated under angicoagulation therapy recepit
"""
# get survival curves of both treatments
survival_curves = [
simOutputs_none.get_survival_curve(),
simOutputs_anticoag.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(
sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step (year)',
y_label='Number of alive patients',
legends=['No Therapy', 'Anticoagulation Therapy'])
# histograms of survival times
set_of_survival_times = [
simOutputs_none.get_survival_times(),
simOutputs_anticoag.get_survival_times()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=1,
legend=['No Therapy', 'Anticoagulation Therapy'],
transparency=0.6)
# histograms of the number of strokes
set_of_stroke_counts = [
simOutputs_none.get_if_developed_stroke(),
simOutputs_anticoag.get_if_developed_stroke()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_stroke_counts,
title='Histogram of patient stroke counts',
x_label='Number of strokes',
y_label='Counts',
bin_width=1,
legend=['No Therapy', 'Anticoagulation Therapy'],
transparency=0.6)
def draw_stroke_histograms(simOutputs_none, simOutputs_anticoag):
set_of_strokes = [
simOutputs_none.get_numbers_of_strokes(),
simOutputs_anticoag.get_numbers_of_strokes()
]
Figs.graph_histograms(
data_sets=set_of_strokes,
title='Histogram of number of strokes',
x_label='Number of Strokes',
y_label='Counts',
bin_width=1,
legend=['No Therapy', 'Anticoagulation Therapy'],
transparency=0.6
)
def draw_reward_histograms(sim_output_fair_coin, sim_output_unfair_coin):
set_of_game_rewards = [
sim_output_fair_coin.get_rewards(),
sim_output_unfair_coin.get_rewards()
]
Fig.graph_histograms(
data_sets=set_of_game_rewards,
title='Histogram of game reward',
x_label='Game rewards',
y_label='Counts',
bin_width=50,
legend=['Fair Coin', 'Unfair Coin'],
transparency=0.6
)
def draw_histogram(sim_output_fair, sim_output_unfair):
# histograms of payouts
set_of_payouts = [
sim_output_fair.get_payouts(),
sim_output_unfair.get_payouts()
]
# graph histograms
Fig.graph_histograms(data_sets=set_of_payouts,
title='Histogram of payouts',
x_label='Payouts',
y_label='Counts',
bin_width=50,
legend=['Fair Coin', 'Unfair Coin'],
transparency=0.6)
def make_plots(output_fair_coin, output_biased_coin):
# makes histogram of the game rewards
# histograms of game rewards
set_of_game_rewards = [
output_fair_coin.get_rewards(),
output_biased_coin.get_rewards()
]
Figs.graph_histograms(data_sets=set_of_game_rewards,
title='Histogram of Game Rewards',
x_label='Game rewards',
y_label='Counts',
bin_width=20,
legend=['Fair coin', 'Unfair coin'],
transparency=0.6)
def draw_histograms(multiGames1, multiGames2):
# histograms of average rewards
set_of_rewards = [
multiGames1.get_all_total_rewards(),
multiGames2.get_all_total_rewards()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_rewards,
title='Histogram of total rewards (in 10 games)',
x_label='Rewards',
y_label='Counts',
bin_width=15,
legend=['50%', '45%'],
transparency=0.5,
x_range=[-1500, 1000])
def draw_histograms(multi_cohort_fair_coin, multi_cohort_unfair_coin):
set_of_game_rewards = [
multi_cohort_fair_coin.get_all_mean_reward(),
multi_cohort_unfair_coin.get_all_mean_reward()
]
# graph histograms
Fig.graph_histograms(
data_sets=set_of_game_rewards,
title='Histogram of average game reward',
x_label='Game reward',
y_label='Counts',
bin_width=50,
legend=['Fair Coin', 'Unfair Coin'],
transparency=0.5,
# x_range=[-50, 0]
)
def make_plots(games_fair_coin, games_biased_coin):
# histograms of total game rewards
set_of_game_rewards = [
games_fair_coin.get_all_total_rewards(),
games_biased_coin.get_all_total_rewards()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_game_rewards,
title="Histogram of the Gambler's Total Rewards from 10 Games",
x_label='Total Rewards',
y_label='Count',
bin_width=40,
legend=['Fair coin', 'Unfair coin'],
transparency=0.6,
)
def draw_histograms(multi_cohort_fair, multi_cohort_unfair):
""" draws the histograms of average survival time
:param multi_cohort_fair: multiple cohorts simulated when using fair coins
:param multi_cohort_unfair: multiple cohorts simulated when using unfair coins
"""
# histograms of average survival times
set_of_game_rewards = [
multi_cohort_fair.get_all_total_rewards(),
multi_cohort_unfair.get_all_total_rewards()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_game_rewards,
title='Histogram of average game rewards',
x_label='Game rewards',
y_label='Counts',
legend=['Fair coin', 'Unfair coin'],
transparency=0.5,
x_range=[0, 20])
def draw_survival_curves_and_histograms(sim_output_fair_coin,
sim_output_unfair_coin):
""" draws the histograms of game rewards
:param sim_output_fair_coin: output of a set of games simulated when the coin is fair
:param sim_output_unfair_coin: output of a set of games simulated when the coin is unfair
"""
# histograms of game rewards
set_of_game_rewards = [
sim_output_fair_coin.get_rewards(),
sim_output_unfair_coin.get_rewards()
]
# graph histograms
Figs.graph_histograms(data_sets=set_of_game_rewards,
title='Histogram of Game Rewards',
x_label='Game rewards',
y_label='Counts',
bin_width=20,
legend=['Fair coin', 'Unfair coin'],
transparency=0.6)
def draw_histograms(multi_games_fair_coin, multi_games_unfair_coin):
""" draws the histograms of average game rewards
:param multi_games_fair_coin: multiple sets of games simulated when the coin is fair
:param multi_games_unfair_coin: multiple sets of games simulated when the coin is unfair
"""
# histograms of average game rewards
set_of_game_rewards = [
multi_games_fair_coin.get_all_total_rewards(),
multi_games_unfair_coin.get_all_total_rewards()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_game_rewards,
title="Histogram of the Gambler's Average Total Game Rewards",
x_label='Mean Game Rewards',
y_label='Count',
bin_width=40,
legend=['Fair coin', 'Unfair coin'],
transparency=0.6,
)
def draw_survival_curves_and_histograms(sim_output_1, sim_output_2):
""" draws the survival curves and the histograms of survival time
: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
"""
# histograms of rewards
set_of_rewards = [
sim_output_1.get_rewards(),
sim_output_2.get_rewards()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_rewards,
title='Histogram of rewards',
x_label='Rewards',
y_label='Counts',
bin_width=15,
legend=['50%', '45%'],
transparency=0.6
)
def draw_histograms(multigamesetsfair, multigamesetsunfair):
""" draws the histograms of average survival time
:param multi_cohort_no_drug: multiple cohorts simulated when drug is not available
:param multi_cohort_with_drug: multiple cohorts simulated when drug is available
"""
# histograms of average survival times
totalreward = [
multigamesetsfair.get_all_total_rewards(),
multigamesetsunfair.get_all_total_rewards()
]
# graph histograms
Figs.graph_histograms(
data_sets= totalreward,
title='Histogram of total reward',
x_label='Reward',
y_label='Counts',
bin_width=50,
legend=['Fair coin', 'Unfair coin'],
transparency=0.5,
)
def draw_reward_histograms(sim_output_fair_coin, sim_output_unfair_coin):
""" draws the histograms of game rewards
:param sim_output_fair_coin: output of a cohort simulated game-set with a fair coin
:param sim_output_unfair_coin: output of a cohort simulated game-set with an unfair coin
"""
# histograms of game rewards
set_of_game_rewards = [
sim_output_fair_coin.get_rewards(),
sim_output_unfair_coin.get_rewards()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_game_rewards,
title='Histogram of game reward',
x_label='Game rewards',
y_label='Counts',
bin_width=50,
legend=['Fair Coin', 'Unfair Coin'],
transparency=0.6
)
def draw_survival_curves_and_histograms(simOutputs_no_therapy, simOutputs_anticoagulation):
"""
:param simOutputs_no_therapy: no therapy
:param simOutputs_anticoagulation: anticoagulation
:return:
"""
# get survival curves of both treatments
survival_curves = [
simOutputs_no_therapy.get_survival_curve(),
simOutputs_anticoagulation.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(
sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step (year)',
y_label='Number of alive patients',
legends=['No Therapy', 'Anticoagulation Therapy']
)
# histograms of survival times
set_of_survival_times = [
simOutputs_no_therapy.get_survival_times(),
simOutputs_anticoagulation.get_survival_times()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=1,
legend=['No Therapy', 'Anticoagualtion Therapy'],
transparency=0.6
)
def draw_histograms(multi_cohort_fair_coin, multi_cohort_unfair_coin):
""" draws the histograms of average survival time
:param multi_cohort_fair_coin: multiple gamesets simulated when the coin is fair
:param multi_cohort_unfair_coin: multiple gamesets simulated when the coin is unfair
"""
# histograms of game rewards
set_of_game_rewards = [
multi_cohort_fair_coin.get_all_mean_reward(),
multi_cohort_unfair_coin.get_all_mean_reward()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_game_rewards,
title='Histogram of average game reward',
x_label='Game reward',
y_label='Counts',
bin_width=50,
legend=['Fair Coin', 'Unfair Coin'],
transparency=0.5,
# x_range=[-50, 0]
)
def draw_histograms(multi_cohort_UnfairCoin, multi_cohort_FairCoin):
""" draws the histograms of average survival time
:param multi_cohort_no_drug: multiple cohorts simulated when drug is not available
:param multi_cohort_with_drug: multiple cohorts simulated when drug is available
"""
# histograms of average survival times
set_of_survival_times = [
multi_cohort_UnfairCoin.get_mean_total_reward(),
multi_cohort_FairCoin.get_mean_total_reward()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_survival_times,
title='Histogram of average patient survival time',
x_label='Survival time',
y_label='Counts',
bin_width=1,
legend=['No Drug', 'With Drug'],
transparency=0.5,
x_range=[6, 20]
)
def histograms(sim_output_fair_coin, sim_output_unfair_coin):
""" draws the histograms of rewards
:param sim_output_fair_coin: output of a set of games simulated with a fair coin
:param sim_output_unfair_coin: output of a set of games simulated with an unfair coin
"""
# histograms of survival times
set_of_rewards = [
sim_output_fair_coin.get_rewards(),
sim_output_unfair_coin.get_rewards()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_rewards,
title="Histogram of Rewards from 1000 Games obtained from the steady-state simulation model",
x_label="Game Rewards",
y_label="Frequency",
bin_width=25,
legend=['Fair Coin', 'Unfair Coin'],
transparency=0.5
)
def draw_survival_curves_and_histograms(simOutputs_anti, simOutputs_none):
""" draws the survival curves and the histograms of time until STROKE deaths
:param simOutputs_anti: output of a cohort simulated under ANTI therapy
:param simOutputs_none: output of a cohort simulated under NONE therapy
"""
# get survival curves of both treatments
survival_curves = [
simOutputs_anti.get_survival_curve(),
simOutputs_none.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(
sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step (year)',
y_label='Number of alive patients',
legends=['Anticoagulant Therapy', 'None Therapy']
)
# histograms of survival times
set_of_survival_times = [
simOutputs_anti.get_survival_times(),
simOutputs_none.get_survival_times()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=1,
legend=['Anticoagulant Therapy', 'None Therapy'],
transparency=0.6
)
def draw_survival_curves_and_histograms(simOutputs_warfarin,
simOutputs_dabigatran_110,
simOutputs_dabigatran_150):
# draws the survival curves and the histograms of time until death
# get survival curves of all treatments
survival_curves = [
simOutputs_warfarin.get_survival_curve(),
simOutputs_dabigatran_110.get_survival_curve(),
simOutputs_dabigatran_150.get_survival_curve()
]
# graph survival curve
PathCls.graph_sample_paths(
sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step (year)',
y_label='Number of alive patients',
legends=['Warfarin', 'Dabigatran 110', 'Dabigatran 150'])
# histograms of survival times
set_of_survival_times = [
simOutputs_warfarin.get_survival_times(),
simOutputs_dabigatran_110.get_survival_times(),
simOutputs_dabigatran_150.get_survival_times()
]
# graph histograms
Figs.graph_histograms(
data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=0.5,
legend=['Warfarin', 'Dabigatran 110', 'Dabigatran 150'],
transparency=0.6)
##PLOT:
cohortOUT_1 = CohortOutputs(cohort_1)
cohortOUT_2 = CohortOutputs(cohort_2)
survival_curves = [
cohortOUT_1.get_survival_curve(),
cohortOUT_2.get_survival_curve()
]
survival_curves = [
cohortOUT_1.get_survival_curve(),
cohortOUT_2.get_survival_curve()
]
PathCls.graph_sample_paths(sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step',
y_label='Number of alive patients',
legends=['No Drug', 'With Drug'])
set_STROKE_times = [
cohort_1.get_time_to_STROKE(),
cohort_2.get_time_to_STROKE()
]
Figs.graph_histograms(data_sets=set_STROKE_times,
title='Histogram of patient STROKE time',
x_label='Survival time',
y_label='Counts',
bin_width=1,
legend=['WELL', 'POST DRUG'],
transparency=0.6)
print(meansurvival, CI_of_Expected)
print(meansurvival_TWO, CI_of_Expected_TWO)
cohortOUT_ONE = CohortOutcomes(cohort_ONE)
cohortOUT_TWO = CohortOutcomes(cohort_TWO)
survival_curves = [
cohortOUT_ONE.get_survival_curve(),
cohortOUT_TWO.get_survival_curve()
]
PathCls.graph_sample_paths(sample_paths=survival_curves,
title='Survival curve',
x_label='Simulation time step',
y_label='Number of alive patients',
legends=['No Drug', 'With Drug'])
set_of_STROKE_times = [
cohort_ONE.get_STROKE_time(),
cohort_TWO.get_STROKE_time()
]
Figs.graph_histograms(data_sets=set_of_STROKE_times,
title='Histogram of patient STROKE time',
x_label='Survival time',
y_label='Counts',
bin_width=1,
legend=['No Drug', 'With Drug'],
transparency=0.6)
import Q3 as NoAnticoag
import Q5 as Anticoag
import scr.FigureSupport as Fig
NoAnticoag = NoAnticoag.CohortSim.get_number_strokes()
Anticoag = Anticoag.CohortAnticoagSim.get_number_strokes()
# generate histograms
Fig.graph_histograms(data_sets=[NoAnticoag, Anticoag],
title='Number of strokes',
x_label='Number of strokes',
y_label='Number of patients',
legend=['No Anticoagulation', 'Anticoagulation'])
