def plot_survival_curves_and_histograms(sim_outcomes_mono, sim_outcomes_combo):
""" draws the survival curves and the histograms of time until HIV deaths
:param sim_outcomes_mono: outcomes of a cohort simulated under mono therapy
:param sim_outcomes_combo: outcomes of a cohort simulated under combination therapy
"""
# get survival curves of both treatments
survival_curves = [
sim_outcomes_mono.nLivingPatients, sim_outcomes_combo.nLivingPatients
]
# graph survival curve
Path.plot_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'],
color_codes=['green', 'blue'])
# histograms of survival times
set_of_survival_times = [
sim_outcomes_mono.survivalTimes, sim_outcomes_combo.survivalTimes
]
# graph histograms
Hist.plot_histograms(data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time (year)',
y_label='Counts',
bin_width=1,
legends=['Mono Therapy', 'Combination Therapy'],
color_codes=['green', 'blue'],
transparency=0.6)
def plot_survival_curves_and_histograms(sim_outcomes_none, sim_outcomes_anticoag):
""" draws the survival curves and the histograms of time until HIV deaths
:param sim_outcomes_none: outcomes of a cohort simulated under no therapy
:param sim_outcomes_anticoag: outcomes of a cohort simulated under anticoagulation
"""
# get survival curves of both treatments
survival_curves = [
sim_outcomes_none.nLivingPatients,
sim_outcomes_anticoag.nLivingPatients
]
# graph survival curve
Path.plot_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'],
color_codes=['red', 'blue']
)
# histograms of survival times
set_of_strokes = [
sim_outcomes_none.nStrokes,
sim_outcomes_anticoag.nStrokes
]
# graph histograms
Hist.plot_histograms(
data_sets=set_of_strokes,
title='Histogram of number of strokes',
x_label='Number of Strokes',
y_label='Counts',
bin_width=1,
legends=['No Therapy', 'Anticoagulation'],
color_codes=['red', 'blue'],
transparency=0.5
)
def draw_survival_curves_and_histograms(cohort_no_drug, cohort_with_drug):
""" draws the survival curves and the histograms of survival time
:param cohort_no_drug: a cohort simulated when drug is not available
:param cohort_with_drug: a cohort simulated when drug is available
"""
# get survival curves of both treatments
survival_curves = [
cohort_no_drug.cohortOutcomes.nLivingPatients,
cohort_with_drug.cohortOutcomes.nLivingPatients
]
# graph survival curve
Path.plot_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'],
color_codes=['blue', 'orange'],
transparency=0.5)
# histograms of survival times
set_of_survival_times = [
cohort_no_drug.cohortOutcomes.survivalTimes,
cohort_with_drug.cohortOutcomes.survivalTimes
]
# graph histograms
Hist.plot_histograms(data_sets=set_of_survival_times,
title='Histogram of patient survival time',
x_label='Survival time',
y_label='Counts',
bin_width=2,
legends=['No Drug', 'With Drug'],
color_codes=['blue', 'orange'],
transparency=0.5)
size=Sets.PRIOR_N)
# create multiple cohorts
multiCohort = Cls.MultiCohort(
ids=range(Sets.PRIOR_N),
pop_sizes=[Sets.SIM_POP_SIZE] * Sets.PRIOR_N,
mortality_probs=mortality_samples # [p1, p2, ....]
)
# simulate all cohorts
multiCohort.simulate(Sets.TIME_STEPS)
# plot the sample paths
Path.plot_sample_paths(
sample_paths=multiCohort.multiCohortOutcomes.survivalCurves,
title='Survival Curves',
x_label='Time-Step (Year)',
y_label='Number Survived',
transparency=0.5)
# plot the histogram of average survival time
Hist.plot_histogram(
data=multiCohort.multiCohortOutcomes.meanSurvivalTimes,
title='Histogram of Mean Survival Time',
x_label='Mean Survival Time (Year)',
y_label='Count',
x_range=[2.5, 21.5],
bin_width=0.5)
# create the histogram of the mortality probabilities
Hist.plot_histogram(
data=mortality_samples,
color_code='r',
connect='step')
# plot path 3 only
Path.plot_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.plot_sample_paths(sample_paths=[path1, path2],
title='Plot two sample paths with different color',
x_label='time',
y_label='observed value',
legends=['Path 1', 'Path 2'],
transparency=0.75)
Path.plot_sample_paths(sample_paths=[path1, path2],
title='Plot 2 sample paths with the same color',
x_label='time',
y_label='observed value',
legends='Path',
transparency=0.5,
common_color_code='g')
Path.plot_sets_of_sample_paths(sets_of_sample_paths=[[path1, path2],
[path3, path4]],
title='Plot 2 sets of sample paths',
x_label='time',