def options(where=st.sidebar):
st = where
opts = {
None: _("Brazil"),
"BR-1": _("North"),
"BR-2": _("Northeast"),
"BR-3": _("Southeast"),
"BR-4": _("South"),
"BR-5": _("Midwest"),
}
st.subheader(_("Region"))
opt = st.radio(_("Select region"), [*opts], format_func=opts.get)
if opt is None:
regs = regions("BR", type="region", parent_id="BR")
else:
regs = regions(type="state", parent_id=opt)
opts = {"cases": _("Cases"), "deaths": _("Deaths")}
msg = _("Cases or deaths?")
column = st.radio(msg, [*opts], format_func=opts.get)
st.subheader(_("Plotting options"))
lines = st.checkbox(_("Show Lines"))
logy = False
if lines:
logy = st.checkbox(_("Logarithm scale"))
return {"lines": lines, "logy": logy, "regions": regs, "column": column}
def options(where=st):
st = where
regs = regions("BR", type="state")
# Regions to highlight
st.subheader(_("Highlight"))
opts = {
"BR-1": _("North"),
"BR-2": _("Northeast"),
"BR-3": _("Southeast"),
"BR-4": _("South"),
"BR-5": _("Midwest"),
"select": _("Select states"),
# 'top5': _('Top 5'), NotImplemented
}
msg = _("Which states do you want to highlight?")
opt = st.radio(msg, [*opts], format_func=opts.get)
if opt == "select":
fmt = {r.id: r.name for r in regs}.get
ids = [r.id for r in regs]
msg = _("Select states to highlight")
select = set(
st.multiselect(msg, ids, format_func=fmt, default=[regs[0].id]))
highlight = [r for r in regs if r.id in select]
elif opt == "top5":
highlight = opt
else:
highlight = [r for r in regs if r.parent_id == opt]
# Options
st.subheader(_("Options"))
logy = not st.checkbox(_("Linear scale"))
column = "deaths" if st.checkbox(_("Plot deaths")) else "cases"
diff = st.checkbox(_("Plot new daily cases"))
population_adj = st.checkbox(_("Adjust for population"))
default = (20 if diff else 100) // (1 if column == "cases" else 10)
thresh = st.number_input(_("Minimum number of cases"),
min_value=0,
value=default)
default = 7 if diff else 0
smooth = st.number_input(_("Smooth over n days"),
min_value=0,
value=default)
return {
"regions": regs,
"highlight": highlight,
"diff": diff,
"thresh": thresh,
"smoothing": smooth,
"column": column,
"logy": logy,
"population_adj": population_adj,
}
def select_arguments(fn, where=st):
"""
Select arguments from a callable object.
This method only works if we are able to introspect the object signature.
"""
st = where
sig = inspect.Signature.from_callable(fn)
args = []
kwargs = {}
show_title = True
for k, v in sig.parameters.items():
if k == "where":
continue
if show_title:
st.subheader(_("Arguments"))
show_title = False
if v.annotation == str:
kwargs[k] = st.text_input(k)
elif v.annotation == bool:
kwargs[k] = st.checkbox(k)
elif v.annotation == float:
kwargs[k] = st.number_input(k)
elif v.annotation == int:
kwargs[k] = st.number_input(k)
else:
st.text(k)
return args, kwargs
def ask(self, parent_region="BR", where=st.sidebar):
st = where
scenario_kind = st.selectbox(_("Select scenario"), list(REGIONS_TYPES[parent_region]))
scenario = REGIONS_TYPES[parent_region][scenario_kind]
regions = self.__datahandler.get_regions(**scenario["query"])
if "filter" in scenario:
filtering = scenario["filter"]
format_func = filtering.pop("format_func", None)
if format_func is not None:
function = format_func
def format_func(x):
if x == "all":
return _("All")
return function(x)
field, message = filtering.popitem()
groups = sk.group_by(lambda x: getattr(x, field), regions)
key = st.selectbox(message, ["all", *groups], format_func=format_func)
if key != "all":
regions = groups[key]
message = _("Columns")
columns = st.multiselect(message, COLUMNS, default=COLUMNS_DEFAULT)
message = _("Isolation scores")
kwargs = {"default": TARGETS_DEFAULT, "format_func": lambda x: f"{x}%"}
targets = st.multiselect(message, TARGETS, **kwargs)
message = _("Show values for the given days")
days = st.multiselect(message, DAYS, default=DAYS_DEFAULT)
if any(not isinstance(d, int) for d in days):
day_max = sk.pipe(
days,
sk.remove(lambda d: isinstance(d, int)),
sk.map(lambda d: int(NUMBER.search(d).groups()[0])),
max,
)
days = list(range(1, day_max + 1))
message = _("Transpose data")
transpose = st.checkbox(message, value=False)
self.__datahandler.user_inputs = {
"parent_region": parent_region,
"regions": regions,
"columns": columns,
"targets": targets,
"days": days,
"scenario": scenario,
"transpose": transpose,
"disease": "covid-19"
}
def sidebar(where=st.sidebar) -> dict:
"""
Run sidebar that asks for user input.
"""
st = where
st.header(_("Brazilian Epidemiological indicators"))
st.subheader(_("Sections"))
opts = {k: v.title for k, v in SECTIONS.items()}
opts["download"] = _("Download data")
msg = _("Select a section")
section = st.radio(msg, list(opts), format_func=opts.get)
st.subheader(_("Filter results"))
regions = select_regions(where=st)
st.subheader(_("Options"))
opts = {
"static_table": st.checkbox(_("Static tables")),
"cmap": st.selectbox(_("Colormap"), COLOR_MAPS, index=COLOR_MAPS.index("BuPu")),
}
return {"regions": regions, "section": section, **opts}
def sidebar(parent_region="BR", where=st.sidebar):
"""
Collect input parameters for the app to run.
Returns:
Dictionary with the following keys:
parent_region, regions, columns, targets, days
"""
st = where
kind = st.selectbox(_("Select scenario"), list(REGIONS_TYPES[parent_region]))
scenario = REGIONS_TYPES[parent_region][kind]
regions = get_regions(**scenario["query"])
if "filter" in scenario:
filtering = scenario["filter"]
format_func = filtering.pop("format_func", None)
if format_func is not None:
fn = format_func
def format_func(x):
if x == "all":
return _("All")
return fn(x)
field, msg = filtering.popitem()
groups = sk.group_by(lambda x: getattr(x, field), regions)
key = st.selectbox(msg, ["all", *groups], format_func=format_func)
if key != "all":
regions = groups[key]
msg = _("Columns")
columns = st.multiselect(msg, COLUMNS, default=COLUMNS_DEFAULT)
msg = _("Isolation scores")
kwargs = {"default": TARGETS_DEFAULT, "format_func": lambda x: f"{x}%"}
targets = st.multiselect(msg, TARGETS, **kwargs)
msg = _("Show values for the given days")
days = st.multiselect(msg, DAYS, default=DAYS_DEFAULT)
if any(not isinstance(d, int) for d in days):
day_max = sk.pipe(
days,
sk.remove(lambda d: isinstance(d, int)),
sk.map(lambda d: int(NUMBER.search(d).groups()[0])),
max,
)
days = list(range(1, day_max + 1))
msg = _("Transpose data")
transpose = st.checkbox(msg, value=False)
return {
"parent_region": parent_region,
"regions": regions,
"columns": columns,
"targets": targets,
"days": days,
"scenario": scenario,
"transpose": transpose,
}
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 ask(title, **kwargs):
if embed:
return True
return st.checkbox(title, **kwargs)
st.subheader(_("Dataset"))
opts = {
"show": _("Show in screen"),
"csv": _("Comma separated values"),
"xlsx": _("Excel"),
}
mime = {"csv": "text/csv", "xls": "application/vnd.ms-excel"}
opt = st.radio(_("How do you want your data?"),
list(opts),
format_func=opts.get)
df = pd.concat(data, axis=1)
df.index = base.to_dates(df.index)
df = df.astype(int)
if not st.checkbox(_("Keep observed period")):
df = df.iloc[data_size:]
if opt == "show":
st.write(df)
else:
df.index = [d.strftime("%Y-%m-%d") for d in df.index]
if opt == "csv":
fd = io.StringIO()
df.to_csv(fd)
data = fd.getvalue().encode("utf8")
else:
fd = io.BytesIO()
df.to_excel(fd)
data = fd.getvalue()
data = base64.b64encode(data).decode("utf8")
mu, sigma = r_stats(data.values)
T = data.index
N = len(T)
x0 = data.iloc[0]
st.line_chart(
pd.DataFrame(
{
"data": np.log(data.values),
"mean": np.log(progression(mu, x0, N)),
"high": np.log(progression(mu + sigma, x0, N)),
"low": np.log(progression(mu - sigma, x0, N)),
},
index=T,
))
if st.checkbox("show?"):
r_mean = mu
r_sigma = sigma
r_sigma_rel = r_sigma / r_mean
st.experimental_show(r_mean)
st.experimental_show(r_sigma)
st.experimental_show(r_sigma_rel)
st.line_chart(
pd.DataFrame(
{
"approx": log_Zk(K, Y, approx=True),
"no-approx": log_Zk(K, Y, approx=False)
},
index=K,