except ValueError:
sys.exit("amount of runs is not a number.")
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batchruntests1.xml")
simulation.runConfig.setParameter("output_prefix", "BatchRunsTesting")
# Create forks with different values for RNG
RNG_values = []
for i in range(amount_of_runs):
RNG_values.append(random.randint(0, 4294967294))
for rng in RNG_values:
# Create fork
fork = simulation.fork("rng_" + str(rng))
fork.runConfig.setParameter("rng_seed", rng)
# Run all forks
simulation.runForks()
# Get attack rates
for rng in RNG_values:
summary_file = os.path.join(pystride.workspace, "BatchRunsTesting",
"rng_" + str(rng), "summary.csv")
with open(summary_file) as csvfile:
reader = csv.DictReader(csvfile)
print("RNG = " + str(rng) + ": Num cases = " +
str(next(reader)['num_cases']))
t_end = time.perf_counter()
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batch_measles.xml")
simulation.runConfig.setParameter("output_prefix", "BatchRngTypeTesting")
# Initialize the random values
rng_values = []
for i in range(amount_of_runs)):
rng_values.append(random.randint(0, 4294967294))
## Create Forks
for rng_type in RNG_TYPES:
for rng_value in rng_values:
# measles_16
fork16 = simulation.fork("measles_16_" + rng_type + "_" + str(rng_value))
fork16.runConfig.setParameter("r0", 16)
fork16.runConfig.setParameter("rng_type", rng_type)
fork16.runConfig.setParameter("rng_seed", rng_value)
# measles_60
fork60 = simulation.fork("measles_60_" + rng_type + "_" + str(rng_value))
fork60.runConfig.setParameter("r0", 60)
fork60.runConfig.setParameter("rng_type", rng_type)
fork60.runConfig.setParameter("rng_seed", rng_value)
# Run all forks
simulation.runForks()
# Print related data
def print_test(name, test_type):
results_file = os.path.join(pystride.workspace, "totalResults.txt")
with open(results_file, "a+") as results:
import itertools
import pystride
from pystride.Simulation import Simulation
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
simulation.runConfig.setParameter("num_days", 10)
# Create forks with varying parameters
for b0, ir in list(itertools.product([14, 10, 5], [0.2, 0.4, 0.6])):
# Create fork
fork = simulation.fork("b0_" + str(b0) + "-ir_" + str(ir))
fork.diseaseConfig.setParameter("transmission/b0", b0)
fork.runConfig.setParameter("immunity_rate", ir)
fork.runConfig.setParameter("r0", 15)
# Run all forks
simulation.runForks()
amount_of_runs = int(sys.argv[1])
except ValueError:
sys.exit("amount of runs is not a number.")
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batch_measles.xml")
simulation.runConfig.setParameter("output_prefix", "BatchThreadTesting")
## Create Forks
# measles_16
for i in range(0, amount_of_runs):
fork = simulation.fork("measles_16_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
fork.runConfig.setParameter("r0", 16)
# measles_60
for i in range(0, amount_of_runs):
fork = simulation.fork("measles_60_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
fork.runConfig.setParameter("r0", 60)
# Run all forks
simulation.runForks()
# Get attack rates
def print_test(name, test_type):
results_file = os.path.join(pystride.workspace, "totalResults.txt")
sim = Simulation()
sim.loadRunConfig("config/common.xml")
# Set parameters that are the same for all simulations
sim.runConfig.setParameter("output_prefix", "Imitation")
sim.runConfig.setParameter("seeding_rate", 0)
# TODO natural immunity?
sim.runConfig.setParameter("immunity_rate", 0)
sim.runConfig.setParameter("vaccine_rate", 0)
sim.runConfig.setParameter("local_information_policy", "LocalDiscussion")
sim.runConfig.setParameter("global_information_policy", "NoLocalInformation")
sim.runConfig.setParameter("belief_policy/name", "Imitation")
sim.runConfig.setParameter("belief_policy/accept_threshold", 0.95)
sim.runConfig.setParameter("belief_policy/no_accept_threshold", -0.95)
sim.runConfig.setParameter("behaviour_policy", "Vaccination")
seeds = list(range(10))
# TODO belief and behaviour related parameters
# Create forks with varying seeds and behaviour parameters
for seed in list(itertools.product(seeds)):
# Create fork
fork = sim.fork(str(seed))
fork.runConfig.setParameter("rng_seed", seed)
# Run all forks
sim.runForks()
import pystride
from pystride.Simulation import Simulation
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
simulation.runConfig.setParameter("num_days", 10)
# Create 5 identical forks except for the seed
for index in range(5):
fork = simulation.fork("instance" + str(index))
fork.runConfig.setParameter("rng_seed", index)
# Run all forks
simulation.runForks()
amount_of_runs = int(sys.argv[1])
except ValueError:
sys.exit("amount of runs is not a number.")
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batch_default.xml")
simulation.runConfig.setParameter("output_prefix", "BatchThreadTesting")
## Create Forks
# Influenza_a
for i in range(0, amount_of_runs):
fork = simulation.fork("influenza_a_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
# influenza_b
for i in range(0, amount_of_runs):
fork = simulation.fork("influenza_b_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
fork.runConfig.setParameter("seeding_rate", 0)
# influenza_c
for i in range(0, amount_of_runs):
fork = simulation.fork("influenza_c_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
fork.runConfig.setParameter("seeding_rate", (1 - 0.9991) / 100)
fork.runConfig.setParameter("immunity_rate", 0.9991)
# Run all forks
simulation.runForks()
import pystride
from pystride.Simulation import Simulation
t_start = time.perf_counter()
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
simulation.runConfig.setParameter("output_prefix", "R0Runs")
# Create forks with different values for R0
r0_values = [0, 4, 8, 12, 16]
for r0 in r0_values:
# Create fork
fork = simulation.fork("r0_" + str(r0))
fork.runConfig.setParameter("r0", r0)
# Run all forks
simulation.runForks()
# Get attack rates
for r0 in r0_values:
summary_file = os.path.join(pystride.workspace, "R0Runs", "r0_" + str(r0),
"summary.csv")
with open(summary_file) as csvfile:
reader = csv.DictReader(csvfile)
print("R0 = " + str(r0) + ": Num cases = " +
str(next(reader)['num_cases']))
t_end = time.perf_counter()
