def test_initialization_options(self):
br = mundi.region("BR")
it = mundi.region("IT")
# Initialize with no region
m = SIR()
assert m.population == 1_000_000
assert m.region is None
assert m.age_distribution is None
assert m.age_pyramid is None
# Use a region
m = SIR(region="BR")
assert m.population == br.population
assert_series_equal(m.age_distribution, br.age_distribution, check_names=False)
assert_frame_equal(m.age_pyramid, br.age_pyramid)
# Mix parameters a region
tol = 1e-6
m = SIR(region="BR", population=1000)
assert m.population == 1000
assert abs(m.age_distribution.sum() - 1000) < tol
assert abs(m.age_pyramid.sum().sum() - 1000) < tol
ratio = br.age_distribution / m.age_distribution
assert ((ratio - br.population / 1000).dropna().abs() < tol).all()
# Mixed values: brazilian population with the age_distribution proportions
# from Italy
m = SIR(region="BR", age_distribution="IT")
assert m.population == br.population
assert m.age_distribution.sum() == approx(br.population)
assert list(m.age_distribution / m.population) == approx(
it.age_distribution / it.population
)
def from_children(
cls,
region: Union[Region, str],
model_cls: Type[Model],
options=MappingProxyType({}),
**kwargs,
) -> "ModelGroup":
"""
Create a group from children of the given Region.
"""
region: Region = mundi.region(region)
children = region.children(
**extract_keys(("deep", "type", "subtype", "which"), kwargs))
name = kwargs.pop("name", "{region.name}")
group = []
if options:
options = {mundi.region(k): v for k, v in options.items()}
for child in children:
opts = options.get(child, {})
if isinstance(name, str):
opts["name"] = name.format(region=child, **kwargs, **opts)
group.append(model_cls(region=child, **kwargs, **opts))
return ModelGroup(group)
def region_input(default: str,
*,
advanced=False,
text=False,
where=st,
**kwargs) -> Region:
"""
Select region or sub-region based on mundi code.
"""
st = where
kwargs["where"] = where
default = mundi.code(default)
if text or advanced and st.checkbox(_("Advanced selection"), value=False):
try:
code = st.text_input(_("Select mundi region"), value=default)
return mundi.region(code)
except LookupError:
st.error(_("Region not found!"))
return mundi.region(default)
region = mundi.region(default)
if region.id == "BR":
return _br_region_input(**kwargs)
elif len(default) == 2:
return _from_sub_regions(region, _("Location"), where=where)
else:
raise NotImplementedError(f"Cannot select {default!r}")
def test_arbitrary_composite_region(self):
bsb = region("BR-5300108")
sp = region("BR-3550308")
reg = CompositeRegion([bsb, sp])
assert reg.population == bsb.population + sp.population
assert_series_equal(reg.age_distribution, bsb.age_distribution + sp.age_distribution)
def ibge_city(code):
if code.isdigit():
if len(code) == 7:
code = code[:-1]
elif len(code) != 6:
raise ValueError(_("invalid city code: {code}").format(code=code))
return mundi.region(country_code="BR", type="city", short_code=code)
return mundi.region(code)
def _from_template(code, template, where=st) -> Region:
"""
Select a Brazilian region from country up to municipality.
"""
code = mundi.region(code)
for label, type_, subtype in template:
kwargs = {"type": type_}
if subtype:
kwargs["subtype"] = subtype
new_code = _from_sub_regions(code, label, where=where, **kwargs)
if new_code == code:
return mundi.region(code)
code = new_code
return mundi.region(code)
def ask(self):
"""
Ask for user input and save values as properties in the app.
"""
self.where.header(("Options"))
self.region = self.where.text_input(_("Mundi region code"), value="BR")
try:
self.region = mundi.region(self.region)
except LookupError:
self.where.error("Invalid mundi region code.")
return
options = {
"model": _("A Pydemic Model"),
"region": _("A Mundi Region"),
"components": _("Input components"),
}
message = _("What do you want to explore?")
option = self.where.radio(message,
list(options),
format_func=options.get)
self.option = option
self.object = self.handle_explore_option(option)
def get_confirmed_daily_cases_for_region(region, disease=covid19) -> int:
"""
Return the number of newly confirmed cases per day.
"""
region = mundi.region(region)
df = region.pydemic.epidemic_curve(disease)
return safe_int(df["cases"].diff().iloc[-7:].mean())
def test_epidemiological_params_advanced(self, en):
br = mundi.region("BR")
st = Driver([
out.header("Epidemiology"),
ask.selectbox["custom"](...),
out.subheader(...),
ask.slider[2.0](...), # R0
ask.slider[3.0](...), # incubation period
ask.slider[3.0](...), # infectious period
ask.slider[50](...), # symptomatic cases
out.subheader(...),
ask.slider[5](...), # prob_severe
ask.slider[25](...), # prob_critical
ask.slider[10](...), # hospitalization_period
ask.slider[7](...), # icu_period
])
assert input.epidemiological_params(br, where=st) == {
"R0": 2.0,
"severe_period": 10,
"critical_period": 7,
"incubation_period": 3.0,
"infectious_period": 3.0,
"prob_critical": 0.0125,
"prob_severe": 0.05,
"prob_symptoms": 0.5,
}
assert st.is_empty()
def __init(self, region=None, population=None, age_distribution=None, age_pyramid=None):
if age_distribution is not None and age_pyramid is not None:
msg = "cannot set age_pyramid and age_distribution simultaneously"
raise ValueError(msg)
# Set region
if region is not None:
self.region = mundi.region(region)
population = population or self.region.population
elif not hasattr(self, "region"):
self.region = None
# Set age_pyramid
if age_pyramid is not None:
self.age_pyramid = fallback_to_region(age_pyramid, "age_pyramid")
elif hasattr(self, "age_pyramid"):
pass
elif self.region is not None:
self.age_pyramid = fallback_to_region(self.region, "age_pyramid")
else:
self.age_pyramid = None
# Set age_distribution
if age_distribution is not None:
value = fallback_to_region(age_distribution, "age_distribution")
self.age_distribution = value
elif hasattr(self, "age_distribution"):
pass
elif self.age_pyramid is not None:
self.age_distribution = self.age_pyramid.sum(1)
self.age_distribution.name = "age_distribution"
self.age_distribution.index.names = ["age"]
elif self.region is not None:
self.age_distribution = fallback_to_region(self.region, "age_distribution")
else:
self.age_distribution = None
# Set population and fix age_distribution and age_pyramid, if necessary
if hasattr(self, "population"):
pass
elif population is not None:
population = fallback_to_region(population, "population")
self.population = population
if self.age_distribution is not None:
ratio = population / self.age_distribution.sum()
if ratio != 1:
self.age_distribution *= ratio
if self.age_pyramid is not None:
ratio = population / self.age_pyramid.sum().sum()
if ratio != 1:
self.age_pyramid *= ratio
elif self.age_distribution is not None:
self.population = self.age_distribution.sum()
elif self.region is not None:
self.population = self.region.population
else:
self.population = 1_000_000
def get_regions(self, **query):
"""
Get all children in region that have the same values of the parameters passed
as keyword arguments.
"""
return [mundi.region(id_) for id_ in mundi.regions(**query).index]
def show_results(
parent_region,
regions,
columns,
targets,
days,
scenario,
disease=covid19,
transpose=False,
):
"""
Show results from user input.
"""
parent_region = mundi.region(parent_region)
parent_region.ui.cases_and_deaths(disease=disease, grid=True, logy=True)
if days and targets and columns:
info = scenario["info"]
info_cols = tuple(info)
df = get_dataframe(
regions, tuple(days), tuple(targets), tuple(columns), info_cols=info_cols
)
get = {**COL_NAMES, **info}.get
df.columns = pd.MultiIndex.from_tuples(
[tuple(_(get(x, x) for x in t)) for t in df.columns.to_list()]
)
if transpose:
df = df.T
st.subheader(_("Download results"))
st.dataframe_download(df, name="report-brazil.{ext}")
def show(self):
"""
Show results from user input.
"""
parent_region = self.user_inputs["parent_region"]
regions = self.user_inputs["regions"]
columns = self.user_inputs["columns"]
targets = self.user_inputs["targets"]
days = self.user_inputs["days"]
scenario = self.user_inputs["scenario"]
transpose = self.user_inputs["transpose"]
disease = self.user_inputs["disease"]
parent_region = mundi.region(parent_region)
parent_region.ui.cases_and_deaths(disease=disease, grid=True, logy=True)
if days and targets and columns:
info = scenario["info"]
info_cols = tuple(info)
df = self.get_dataframe(
regions, tuple(days), tuple(targets), tuple(columns), info_cols=info_cols
)
get = {**COL_NAMES, **info}.get
df.columns = pd.MultiIndex.from_tuples(
[tuple(_(get(x, x) for x in t)) for t in df.columns.to_list()]
)
if transpose:
df = df.T
st.subheader(_("Download results"))
st.dataframe_download(df, name="report-brazil.{ext}")
def region_name(code):
"""Region name from Mundi code."""
if code.startswith("*"):
return _("{name} (everything)").format(name=region_name(code[1:]))
reg = mundi.region(code)
return _(reg["name"])
def _from_sub_regions(code,
label,
fastrack=False,
where=st,
**kwargs) -> Region:
"""
Select a region from a list that starts with the parent region and its
children.
"""
region = mundi.region(code)
regions = sub_regions(region.id, **kwargs)
if len(regions) == 1 and fastrack:
return regions[0]
regions = ("*" + region.id, *regions)
return mundi.region(
where.selectbox(str(label), regions,
format_func=region_name).lstrip("*"))
def sari_br_state_content(region: str) -> bytes:
region = mundi.region(region)
ref = region.short_code.lower()
url = f"https://s3-sa-east-1.amazonaws.com/ckan.saude.gov.br/dados-{ref}.csv"
log.info(f"[sari-br] Downloading data for {region}")
response = requests.get(url)
log.info(f"[sari-br] Download complete!")
return response.content
def test_select_region(self, en):
st = Driver([
out.header("Location"),
ask.selectbox["BR-1"](...),
ask.selectbox["*BR-1"](...),
])
assert input.region_input("BR", where=st) == mundi.region("BR-1")
assert st.is_empty()
def _test_regional_model_to_json(self):
m = SIR(region="BR")
br = mundi.region("BR")
assert m.info.to_dict() == {
"demography.population": br.population,
"demography.age_distribution": br.age_distribution,
"demography.age_pyramid": br.age_pyramid,
}
assert m.info.to_dict(flat=True) == flatten_dict(m.info.to_dict())
def from_region(cls, transform, region, params=None, disease=None, **kwargs):
"""
Initialize data extracting curve from region.
"""
region = mundi.region(region)
disease = diseases.disease(disease)
data = disease.epidemic_curve(region)
kwargs.setdefault("population", region.population)
return cls(transform(data), params, **kwargs)
def from_region(cls, region, *, model_cls=None, init_cases=True, **kwargs):
"""
Initialize report from cases reported in region.
"""
region = mundi.region(region)
init_kwargs = extract_keys(INIT_KEYS, kwargs)
model = (model_cls or cls.model_cls)(region=region, **kwargs)
if init_cases:
model.set_cases()
return cls(model, **init_kwargs)
def _fatality_ratio(self, col, age_distribution=None, source=None, region=None):
table = self.mortality_table(source=source)
if age_distribution is None and region:
ages = mundi.region(region).age_distribution
elif age_distribution is None:
ages = world_age_distribution()
else:
ages = age_distribution
return age_adjusted_average(ages, table[col])
def get_model(region):
region = mundi.region(region)
data = region.pydemic.epidemic_curve()
empirical_CFR = (data["deaths"] / data["cases"]).mean()
notification_rate = min(0.5, covid19.CFR(region=region) / empirical_CFR)
m = SEAIR(region=region, R0=R0[region.id])
real_data = data.copy()
real_data["cases"] /= notification_rate
m.set_cases(real_data, save_observed=True)
m.run(60)
return m.clinical.overflow_model()
def test_info(self):
approx = lambda x: _approx(x, rel=0.005)
disease = get_disease("covid-19")
m = SIR(disease="covid-19", region="BR")
m.set_ic(cases=1e6)
m.run(60)
# Disease
infectious_period = disease.infectious_period(region="BR")
assert m.info["disease.CFR"] == approx(disease.CFR(region="BR"))
assert m.info["disease.IFR"] == approx(disease.IFR(region="BR"))
assert m.info["disease.infectious_period"] == approx(infectious_period)
assert set(m.info["disease"]) == {
"R0",
"case_fatality_ratio",
"critical_delay",
"critical_period",
"death_delay",
"hospital_fatality_ratio",
"hospitalization_overflow_bias",
"hospitalization_period",
"hospitalization_table",
"icu_fatality_ratio",
"icu_period",
"incubation_period",
"infection_fatality_ratio",
"infectious_period",
"mortality_table",
"prob_aggravate_to_icu",
"prob_critical",
"prob_severe",
"prob_symptoms",
"rho",
"serial_period",
"severe_delay",
"severe_period",
"symptom_delay",
}
# Region
br = mundi.region("BR")
keys = {
"population",
"age_distribution",
"age_pyramid",
"hospital_capacity",
"icu_capacity",
}
assert m.info["region.population"] == br.population
assert all(m.info["region.age_distribution"] == br.age_distribution)
assert all(m.info["region.age_pyramid"] == br.age_pyramid)
assert set(m.info["region"]) == keys
def test_load_country(self):
br = mundi.region("BR")
assert isinstance(br, Region)
assert br.id == "BR"
assert br["name"] == "Brazil"
assert br["type"] == "country"
assert br["short_code"] == "BR"
assert br["numeric_code"] == "076"
assert br["long_code"] == "BRA"
assert br["country_code"] is None
assert br["parent_id"] == "XSA"
ar = mundi.region("ar")
assert isinstance(ar, Region)
assert ar["name"] == "Argentina"
assert ar["type"] == "country"
assert ar["short_code"] == "AR"
assert ar["numeric_code"] == "032"
assert ar["long_code"] == "ARG"
assert ar["country_code"] is None
assert br["parent_id"] == "XSA"
def sari_br_state_dataframe(region: Region) -> pd.DataFrame:
"""
Return the full table of SARI hospital vigilance for the given region.
"""
region = mundi.region(region)
content = sari_br_state_content(region.id)
lines = content.splitlines()
content = lines[0] + b"\n" + b"\n".join(lines[-1000:])
fd = io.BytesIO(content)
with st.spinner(f"Converting to CSV ({region.name})"):
chunks = []
date_columns = [
"dataNotificacao",
"dataInicioSintomas",
"dataNascimento",
"dataEncerramento",
"dataTeste",
]
for df in pd.read_csv(
fd,
index_col=0,
sep=";",
parse_dates=date_columns,
dtype=DTYPES,
converters=CONVERTERS,
engine="c",
chunksize=1000,
encoding="latin1",
):
df: pd.DataFrame = (df.astype(DTYPES).rename(
columns=RENAME).astype({
"status": Status.categories,
"gender": Gender.categories,
"evolution": Evolution.categories,
"test_status": Test.categories,
}))
def localtime(x):
if pd.isna(x):
return x
return x.time()
df["notification_time"] = df["notification_date"].apply(localtime)
df["notification_date"] = df["notification_date"].apply(
lambda x: x if pd.isna(x) else x.date())
df.index.name = "id"
chunks.append(df)
df = pd.concat(chunks)
return df
def show_results(parent_region, regions, columns, targets, days, disease=covid19):
"""
Show results from user input.
"""
parent_region = mundi.region(parent_region)
ax = parent_region.plot.cases_and_deaths(disease=disease, logy=True, grid=True)
st.pyplot(ax.get_figure())
if days and targets and columns:
df = get_dataframe(regions, tuple(days), tuple(targets), tuple(columns), 61)
st.subheader(_("Download results"))
st.dataframe_download(df, name="report-brazil.{ext}")
def healthcare_params(region,
title=__("Hospital capacity"),
occupancy=0.75,
where=st):
"""
Return a dictionary with hospital and icu capacities from user input.
Returns:
icu_capacity (float): surge system capacity of ICUs
icu_full_capacity (float): total system capacity of ICUs
hospital_capacity (float): surge system capacity of regular beds
hospital_full_capacity (float): total system capacity of regular beds
"""
region = mundi.region(region)
where.header(str(title))
def get(title, capacity, rate, key=None):
where.subheader(title)
total = where.number_input(_("Total capacity"),
min_value=0,
value=int(capacity),
key=key + "_total")
occupied = where.number_input(_("Occupied"),
min_value=0,
value=int(capacity * rate),
key=key + "_used")
if occupied > total:
where.warning(_("Using more beds than total capacity"))
msg = markdown(
OCCUPANCY_MSG.format(n=fmt(total - occupied),
rate=pc(occupied / total),
globalrate=pc(rate)))
html(f'<span style="font-size: smaller;">{msg}</span>', where=where)
return max(total - occupied, 0)
h_cap = safe_int(region.hospital_capacity)
icu_cap = safe_int(region.icu_capacity)
return {
"icu_full_capacity":
icu_cap,
"hospital_full_capacity":
h_cap,
"icu_capacity":
get(_("ICU beds"), icu_cap, occupancy, key="icu"),
"hospital_capacity":
get(_("Clinical beds"), h_cap, occupancy, key="hospital"),
}
def test_clinical_model_uses_region_IFR(self, region="BR"):
m = SEIR(region=region, disease=covid19)
br = mundi.region("BR")
m1 = m.clinical.crude_model()
m2 = m.clinical.delay_model()
m3 = m.clinical.overflow_model()
IFR = covid19.IFR(region=region)
CFR = covid19.CFR(region=region)
for m in [m1, m2, m3]:
assert m.region == br
assert m.IFR == m.infection_fatality_ratio == IFR
assert m.CFR == m.case_fatality_ratio == CFR
def test_simulation_params(self, en):
br = mundi.region("BR")
st = Driver([
out.header("Simulation options"),
ask.slider[10](...),
ask.date_input[today(10)](...),
out.subheader("Cases"),
ask.number_input[10](...),
ask.slider[10](...),
])
assert input.simulation_params(br, where=st) == {
"period": 70,
"date": today(10),
"daily_cases": 100,
}
assert st.is_empty()
def show(self):
parent_region = self.__datahandler.user_inputs["parent_region"]
columns = self.__datahandler.user_inputs["columns"]
targets = self.__datahandler.user_inputs["targets"]
days = self.__datahandler.user_inputs["days"]
disease = self.__datahandler.user_inputs["disease"]
parent_region = mundi.region(parent_region)
axes = parent_region.plot.cases_and_deaths(disease=disease, logy=True, grid=True)
st.pyplot(axes.get_figure())
if days and targets and columns:
df = self.__datahandler.get_dataframe(tuple(days), tuple(targets), tuple(columns))
st.subheader(_("Download results"))
st.dataframe_download(df, name="report-brazil.{ext}")
