def main(self, region="BR", disease=covid19):
st.css()
params = self.ask(region=region,
disease=disease,
secret_date=Secret.date)
if Secret.is_easter_egg_activated(params):
return
Debug = DebugCalc(st, DEBUG)
run_infectious_model(Debug)
def main(embed=False):
if not embed:
st.css(keep_menu=True)
st.sidebar.logo()
models = ["crude", "delay", "overflow"]
kind = st.sidebar.selectbox(_("Clinical model"), models)
m = SEAIR(region="BR", disease=covid19)
cm = m.clinical(kind)
cm.ui.summary_table(subheader=_("Parameters table"))
def __init__(self, embed=False, disease="covid-19", **kwargs):
super().__init__(embed=embed, **kwargs)
self.embed
if not self.embed:
self.css = st.css(keep_menu=True)
self.logo = True
self.where = st if self.embed else st.sidebar
self.disease = disease
def main(embed=False, disease=None):
"""
Run application.
"""
if not embed:
st.css(keep_menu=True)
st.sidebar.logo()
title = st.empty().title
title(_("Covid risk factors"))
else:
title = lambda *args: None
opts = sidebar(title,
where=st if embed else st.sidebar,
embed=embed,
disease=disease)
show_opts = extract_keys(SHOW_OPTS, opts)
clinical_opts = extract_keys(CLINICAL_OPTS, opts)
run_opts = extract_keys(RUN_OPTS, opts)
# Start model with known R0
region = opts["region"]
plot_opts = show_opts["plot_opts"]
st.header(_("Cases and deaths"))
region.ui.epidemic_summary()
region.ui.cases_and_deaths(title=None,
download=f"cases-{region.id}.csv",
**plot_opts)
model = start_model(**opts)
group = start_group(model, **run_opts)
show_outputs(model,
group,
clinical_opts=clinical_opts,
**opts,
**show_opts)
def main(embed=False, disease=None):
"""
Main interface of the API explorer.
"""
if not embed:
st.css(keep_menu=True)
st.sidebar.logo()
where = st if embed else st.sidebar
st.title(_("Pydemic-UI API explorer"))
where.header(_("Options"))
region = where.text_input(_("Mundi region code"), value="BR")
try:
region = mundi.region(region)
except LookupError:
where.error("Invalid mundi region code.")
return
opts = {
"model": _("A Pydemic Model"),
"region": _("A Mundi Region"),
"components": _("Input components"),
}
msg = _("What do you want to explore?")
opt = where.radio(msg, list(opts), format_func=opts.get)
if opt == "model":
model = SEAIR(region=region, disease="covid-19")
model.run(180)
obj = model.clinical.overflow_model()
elif opt == "region":
obj = region
else:
import pydemic_ui.components as obj
explore_object_attribute(opt, obj, where=where)
def main(embed=False, where=st, **kwargs):
"""
Main application function.
"""
st = where
if not embed:
st.css(keep_menu=True)
st.sidebar.logo()
st.title(_("Epidemic situation dashboard (Brazil)"))
options = sidebar(where=st.sidebar)
kwargs = extract_keys(("cmap", "static_table"), options)
kwargs["where"] = where
data = get_data()
data = data.loc[options.pop("regions")]
section_opt = options["section"]
if section_opt == "download":
download_data(data, **kwargs)
else:
section = SECTIONS[section_opt]
section.show(data, **kwargs)
def __init__(self, embed=False, **kwargs):
super().__init__(embed=embed, **kwargs)
if not embed:
self.css = st.css(keep_menu=True)
self.logo = True
self.where = st if self.embed else st.sidebar
def main(region="BR", disease=covid19):
st.css()
params = sidebar(
region=region,
disease=disease,
secret_date=datetime.date(1904, 11, 10),
secret_function=lambda: easter_egg(disease),
)
if params is None: # Secret function was activated
return
debug = False
if DEBUG and st.checkbox(_("Enable debug")):
st.info(_("Running in debug mode!"))
st.html(
"""
<ul>
<li><a href="#debug">{}</a></li>
</ul>""".format(
_("Debug section!")
)
)
debug = True
epidemiology = extract_keys(PARAMS, params)
clinical = extract_keys(CLINICAL, params)
# Run infections model
m = cm = results = None
try:
m = model(disease=disease, **epidemiology)
cm = m.clinical.overflow_model(icu_occupancy=0, hospital_occupancy=0, **clinical)
cm.extra_info = params
output(cm)
finally:
if debug:
if results:
st.html('<div style="height: 15rem"></div>')
st.html('<h2 id="debug">{}</h2>'.format(_("Debug information")))
st.subheader(_("Generic parameters"))
st.write(params)
st.subheader(_("Epidemiological parameters"))
st.write(epidemiology)
st.subheader(_("Clinical parameters"))
st.write(clinical)
st.subheader(_("Output"))
st.write(results)
if m:
st.line_chart(m.data)
if cm:
st.line_chart(cm[["infectious", "severe", "critical"]])
st.subheader(_("Distribution of deaths"))
df = cm[DEATH_DISTRIBUTION_COLUMNS]
df.columns = [DEATH_DISTRIBUTION_COL_NAMES[k] for k in df.columns]
st.area_chart(df)
def __init__(self, embed=False, where=st, **kwargs):
super().__init__(embed=embed, where=where, **kwargs)
if not embed:
self.css = st.css(keep_menu=True)
self.logo = True
@st.cache(allow_output_mutation=True)
def run_model(region, duration, R0, notification_rate):
m = models.SEAIR(region=region, disease=covid19, R0=R0)
data = info.get_seair_curves_for_region(
region, notification_rate=notification_rate)
m.set_data(data)
m.initial_cases = info.get_cases_for_region(region)["cases"].iloc[0]
m.run(duration)
return m.clinical.overflow_model()
#
# ASK INFO
#
st.css()
st.sidebar.logo()
code = st.sidebar.region_input("BR", healthcare_regions=True)
region = mundi.region(code)
params = covid19.params(region=region)
st.sidebar.subheader(_("Parameters"))
duration = 60 # st.sidebar.number_input(_("Duration (days)"), 1, 120, value=60)
notification = st.sidebar.slider(_("Ascertainment ratio"),
0.01,
0.50,
value=0.10)
R0 = st.sidebar.slider(_("R0"), 0.1, 5.0, value=params.R0)
st.sidebar.subheader(_("Options"))
logy = not st.sidebar.checkbox(_("Linear scale"))
