def read_time_file(filename):
global seed_file_cache
if filename not in seed_file_cache:
with open(filename, "r") as FILE:
time_seeds = [[num for num in line.split(',')] for line in FILE]
Console.debug("Times of seeding:", variables=[time_seeds])
# convert to dates and counts
time_seeds = np.array(time_seeds)
time_seeds_trust = time_seeds[:, 1].astype(int)
time_seeds_count = time_seeds[:, 2].astype(int)
time_seeds_date = [[i.split('-')] for i in time_seeds[:, 0]]
time_seeds_date = [[int(i[0][0]),
int(i[0][1]),
int(i[0][2])] for i in time_seeds_date]
time_seeds_date = [
datetime(i[0], i[1], i[2]).date() for i in time_seeds_date
]
# store outputs
seed_file_cache[filename] = "STORED"
seed_file_cache["time_seeds_date"] = time_seeds_date
seed_file_cache["time_seeds_trust"] = time_seeds_trust
seed_file_cache["time_seeds_count"] = time_seeds_count
return seed_file_cache["time_seeds_date"], seed_file_cache[
"time_seeds_trust"], seed_file_cache["time_seeds_count"]
def iterate_lockdown(network, population, **kwargs):
from metawards.iterators import iterate_default
advance_funcs = iterate_default(network=network,
population=population,
**kwargs)
# read parameters from custom user parameters
params = network.params
nstages = int(params.user_params["nstages"])
start_day = int(params.user_params["start_day"])
R0 = params.user_params["R0"]
duration = params.user_params["duration"]
scale_uv = params.user_params["scale_uv"]
cutoff = params.user_params["cutoff"]
day = population.day
if day >= start_day:
# in lockdown
# which stage are we in?
stage = 0
scl = scale_uv[0] / R0
cut = cutoff[0]
end_day = start_day + int(duration[0])
if day <= end_day:
stage = 0
else:
for i in range(1, nstages):
end_day += int(duration[i])
scl = scale_uv[i] / R0
cut = cutoff[i]
if day <= end_day:
stage = i
break
if day > end_day:
print("Lockdown ended")
scl = 1.0
cut = 1000 # 1000 km
population.scale_uv = scl
params.dyn_dist_cutoff = cut
Console.debug("LOCKDOWN", variables=[stage, scl, cut])
return advance_funcs
def read_file(filename, nage):
global file_cache
if filename not in file_cache:
with open(filename, "r") as FILE:
contact_matrix = [[num for num in line.split(',')]
for line in FILE]
# set up interaction matrix
matrix = [[0.0 for i in range(nage)] for j in range(nage)]
for i in range(nage):
for j in range(nage):
matrix[i][j] = float(contact_matrix[i][j])
Console.debug("Interaction matrix", variables=[matrix])
file_cache[filename] = matrix
return file_cache[filename]
def read_age_file(filename):
global seed_file_cache
if filename not in seed_file_cache:
with open(filename, "r") as FILE:
age_probs = [[num for num in line.split(',')] for line in FILE]
Console.debug("Age-level seeding probabilities:",
variables=[age_probs])
# convert to correct format
age_probs = np.array(age_probs)
age_probs_ind = age_probs[:, 0].astype(int)
age_probs = age_probs[:, 1].astype(float)
# save in cache
seed_file_cache[filename] = "STORED"
seed_file_cache["age_probs_ind"] = age_probs_ind
seed_file_cache["age_probs"] = age_probs
return seed_file_cache["age_probs_ind"], seed_file_cache["age_probs"]
def read_seed_file(filename):
global seed_file_cache
if filename not in seed_file_cache:
with open(filename, "r") as FILE:
ward_probs = [[num for num in line.split(',')] for line in FILE]
Console.debug("Ward-level seeding probabilities:",
variables=[ward_probs])
# convert to correct format
ward_probs = np.array(ward_probs)
ward_probs_ind = ward_probs[:, 0].astype(int)
ward_probs_trust = ward_probs[:, 1].astype(int)
ward_probs = ward_probs[:, 2].astype(float)
# save in cache
seed_file_cache[filename] = "STORED"
seed_file_cache["ward_probs_ind"] = ward_probs_ind
seed_file_cache["ward_probs_trust"] = ward_probs_trust
seed_file_cache["ward_probs"] = ward_probs
return seed_file_cache["ward_probs_ind"], seed_file_cache[
"ward_probs_trust"], seed_file_cache["ward_probs"]
def iterate_debug(**kwargs):
Console.debug("Something")
return []