def mkcfg(sample):
cfg = config_load(args.yaml, sample)
for meta in ("model", "tmax", "steps", "samples", "output"):
arg = getattr(args, meta)
if arg is not None:
cfg["meta"][meta] = arg
for init in ("N", "IU"):
arg = getattr(args, init)
if arg is not None:
cfg["initial"][init] = arg
for v in args.var:
k, v = v.split("=", 1)
v = float(v)
cfg["parameters"][k] = v
if isinstance(cfg["meta"]["model"], str):
model = models.get(cfg["meta"]["model"])
if model is None:
log.error("Unknown model: {}".format(cfg["meta"]["model"]))
sys.exit(255)
cfg["meta"]["model"] = model
log.debug("Config: {}".format(cfg))
return cfg
plt.setp(ax.get_xticklabels(), rotation=30, horizontalalignment='right')
# ax.set_xlim([70, ax.get_xlim()[1]])
ax.set_xlabel('Date')
return
st.title("UK COVID-19 Policy Simulator")
st.markdown("""
Compare COVID-19 control policies in the UK using the [PTTI](https://github.com/ptti/ptti) model.
""")
st.sidebar.title("COVID-19 Policy Choices")
HTML_WRAPPER = """<div style="overflow-x: auto; border: 1px solid #e6e9ef; border-radius: 0.25rem; padding: 1rem; margin-bottom: 2.5rem">{}</div>"""
cfg = config_load(
os.path.join("..", "examples", "structured",
"ptti-past.yaml")) # To pull basics - actual load below.
start = date(int(cfg['meta']['start'][0:4]), int(cfg['meta']['start'][5:7]),
int(cfg['meta']['start'][8:10]))
cfg_1 = os.path.join(
"..", "examples", "bowie",
"cal2809test8dur5eta9chi9.yaml") # Need High / Low Compliance.
cfg_2 = os.path.join("..", "examples", "bowie",
"recal5_dur7_lock10beta23c167pow16mob1.yaml")
cfg_3 = os.path.join("..", "examples", "bowie",
"recal2809dur7beta23c167pow16hols155.yaml")
Scenario = st.sidebar.radio("Scenario to use",
['Scenario 1', 'Scenario 2', 'Scenario 3'],
index=0)
plt.setp(ax.get_xticklabels(), rotation=30, horizontalalignment='right')
# ax.set_xlim([70, ax.get_xlim()[1]])
ax.set_xlabel('Date')
return
st.title("UK COVID-19 Policy Simulator")
st.markdown("""
Compare COVID-19 control policies in the UK using the [PTTI](https://github.com/ptti/ptti) model.
""")
st.sidebar.title("COVID-19 Policy Choices")
HTML_WRAPPER = """<div style="overflow-x: auto; border: 1px solid #e6e9ef; border-radius: 0.25rem; padding: 1rem; margin-bottom: 2.5rem">{}</div>"""
cfg = config_load(
os.path.join("..", "examples", "structured",
"ptti-past.yaml")) # To pull basics - actual load below.
start = date(int(cfg['meta']['start'][0:4]), int(cfg['meta']['start'][5:7]),
int(cfg['meta']['start'][8:10]))
cfg_mask = os.path.join("..", "examples", "structured",
"ptti-masks.yaml") # Need High / Low Compliance.
cfg_relax = os.path.join("..", "examples", "structured", "ptti-relax.yaml")
cfg_reopen = os.path.join("..", "examples", "structured", "ptti-reopen.yaml")
cfg_flu = os.path.join("..", "examples", "structured", "ptti-fluseason.yaml")
# Add flu season to TTI...
cfg_ti = os.path.join("..", "examples", "structured", "ptti-all_ti.yaml")
#cfg_tti = os.path.join("..", "examples", "structured", "ptti-tti.yaml")
#cfg_uti = os.path.join("..", "examples", "structured", "ptti-uti.yaml")
#cfg_combo_tti = os.path.join("..", "examples", "structured", "ptti-combo-tti.yaml")
def command():
logging.basicConfig(
stream=sys.stdout,
level=logging.INFO,
format='%(asctime)s - %(name)s:%(levelname)s - %(message)s')
parser = argparse.ArgumentParser("fit")
parser.add_argument("-y", "--yaml", default=None, help="Config file")
parser.add_argument("-m",
"--mask",
nargs="*",
default=[],
help="Variables to mask")
parser.add_argument("-e",
"--end",
default=None,
help="Truncate the data at end date")
parser.add_argument("-t",
"--time",
default=0,
type=float,
help="Shift dataset time by given amount")
parser.add_argument(
"--dgu",
default=None,
help=
"coronavirus.data.gov.uk format for the dead\n\t\thttps://coronavirus.data.gov.uk/downloads/csv/coronavirus-deaths_latest.csv"
)
parser.add_argument("--data",
default=None,
help="generic YYYY-MM-DD,dead format for data")
args = parser.parse_args()
if args.yaml is None:
log.error("--yaml is a required argument")
dead = None
if args.data:
dead = data(args.data)
elif args.dgu:
dead = dgu(args.dgu)
if dead is None:
log.error("There are no dead. Need a data file of some sort")
if args.end:
end = time.strptime(args.end, "%Y-%m-%d")
idx = np.sum(dead[:, 0] <= end.tm_yday)
dead = dead[:idx]
cfg = config_load(args.yaml)
model = SEIRCTODEMem
cfg["meta"]["model"] = model
def getm(traj):
return traj[:, model.colindex("M")]
getp, setp = paramArray(cfg, args.mask)
## the times of the dead
dead_t = dead[:, 0] + args.time
## these are the actual counts of the dead
dead_d = dead[:, 1]
## this is the last day of data
tmax = max(dead_t)
## one output point per day
steps = int(tmax)
## we want a time-series of
times = np.linspace(0, tmax, steps)
## interpolate the dead onto this time support
dead_i = interp1d(dead_t,
dead_d,
kind="previous",
bounds_error=False,
fill_value=np.nan)(times)
## set to run for the specific required time at the specific step
cfg["meta"]["tmax"] = tmax
cfg["meta"]["steps"] = steps + 1
interventions = cfg.get("interventions", [])
## perform a stochastic gradient descent
t0, params = optimise(cfg, getm, setp, getp(cfg), times, dead_i,
interventions)
cfg["meta"]["t0"] = t0
setp(cfg, params)
save_human(cfg, "{}-fit.yaml".format(cfg["meta"]["output"]))
t, traj, _, _ = runModel(**cfg["meta"], **cfg)
M = getm(traj)
fig, (ax1, ax2) = plt.subplots(2, 1)
ax1.set_xlabel("Days since outbreak start")
ax1.set_ylabel("Cumulative infections")
ax1.set_xlim(0, tmax)
ax1.plot(t, M, label="Simulated")
ax1.plot(times, dead_i, label="Data")
for e in interventions:
ax1.axvline(e["time"], c=(0, 0, 0), lw=0.5, ls='--')
ax1.legend()
ax2.set_xlabel("Days since outbreak start")
ax2.set_ylabel("Cumulative infections")
ax2.set_xlim(0, tmax)
ax2.set_yscale("log")
ax2.plot(t, M, label="Simulated")
ax2.plot(times, dead_i, label="Data")
for e in interventions:
ax2.axvline(e["time"], c=(0, 0, 0), lw=0.5, ls='--')
ax2.legend()
plt.savefig("{}-fit.png".format(cfg["meta"]["output"]))
def basic_config():
configfile = os.path.join(
pkg_resources.get_distribution("ptti").location, "examples",
"ptti-methods.yaml")
return config_load(configfile)
parser.add_argument('seeds', type=str, nargs='+')
# Time resolution for events
parser.add_argument('-tres', type=float, default=1.0)
# Gnuplot linestyle for interventions
parser.add_argument('-ls-int', type=str, default='dt 1 lc 0')
# Gnuplot linestyle for triggers
parser.add_argument('-ls-trig', type=str, default='dt 1 lc rgb "#ff0000"')
args = parser.parse_args()
for seed in args.seeds:
# Open the original parameter file
param_history = []
with open(seed + '.yaml') as f:
data = config_load(seed + '.yaml')
params = data['parameters']
t0 = datetime.strptime(data["meta"]["start"], '%Y/%m/%d')
tmax = t0 + timedelta(days=data['meta']['tmax'])
param_history.append((0, params))
with open(seed + '-out-0-events.yaml') as f:
events = yaml.safe_load(f)
# Merge non-unique events
event_times = np.array([e['time'] for e in events])
event_times = np.round(event_times/args.tres)*args.tres
event_times, inds = np.unique(event_times, True)
for t, e_i in zip(event_times, inds):
e = events[e_i]
params = dict(param_history[-1][1])
params.update(e['parameters'])