def region_select_callback(attr, old, new):
new_lines = set(new) - set(old)
old_lines = set(old) - set(new)
for key in old_lines:
lines[key].visible = False
lines[f'{key}_prediction'].visible = False
bands[key].visible = False
for key in new_lines:
if key in lines.keys():
lines[key].visible = True
lines[f'{key}_prediction'].visible = True
bands[key].visible = True
else:
color = RGB(*hex_string_to_rgb(np.random.choice(Viridis256)))
darkened_color = color.darken(.15)
lightened_color = color.lighten(.15)
draw_prediction_line(key, line_color=darkened_color)
draw_prediction_band(key,
conf_level=confidence_level,
fill_color=lightened_color)
draw_data_line(key, line_color=color)
hover_tool.renderers = [
*hover_tool.renderers, lines[key],
lines[f'{key}_prediction']
]
def create_logistic_growth_subtab(params_getter, time_series_getter,
starting_regions, tab_title):
# Data Sources
params_df, params_CDS = params_getter()
time_series_df, time_series_CDS = time_series_getter()
dates = np.arange(START_DATE_STRING, '2020-07-01', dtype='datetime64[D]')
bands_CDS = ColumnDataSource({'date': dates})
lines_CDS = ColumnDataSource({'date': dates})
# Set up Figure
plot = figure(x_axis_type='datetime',
x_axis_label='Date',
y_axis_label='Number of Cases',
title='Logistic Growth Modeling',
active_scroll='wheel_zoom')
plot.yaxis.formatter.use_scientific = False
lines = {} # region, line pairs housing which have been drawn already
bands = {} # region, band pairs housing which have been drawn already
def logistic_function(x, L, x0, k):
return L / (1 + np.exp(-k * (x - x0)))
def z_star(conf_level):
return st.norm.ppf(1 - (1 - conf_level) / 2)
def get_offset_from_start_date(region):
subdf = time_series_df[region]
nonzero_subdf = subdf[subdf > 0]
offset = (nonzero_subdf.index[0] - pd.to_datetime(START_DATE)).days
return offset
def draw_prediction_line(region, **kwargs):
plot_params = {
'line_width': 4,
'line_alpha': 0.4,
'line_dash': 'dashed'
}
plot_params.update(kwargs)
L, x0, k, L_std, x0_std, k_std = params_CDS.data[region]
xs = np.arange(lines_CDS.data['date'].size)
offset = get_offset_from_start_date(region)
line = logistic_function(xs, L, x0 + offset, k)
lines_CDS.data[region] = line
lines[f'{region}_prediction'] = plot.line(x='date',
y=region,
source=lines_CDS,
name=region,
**plot_params)
def draw_prediction_band(region, conf_level, **kwargs):
plot_params = {'line_alpha': 0, 'fill_alpha': 0.4}
plot_params.update(kwargs)
L, x0, k, L_std, x0_std, k_std = params_CDS.data[region]
xs = np.arange(lines_CDS.data['date'].size)
offset = get_offset_from_start_date(region)
bands_CDS.data[f'{region}_lower'], bands_CDS.data[
f'{region}_upper'] = (logistic_function(
xs, L - L_std * z_star(conf_level), x0 + offset, k),
logistic_function(
xs, L + L_std * z_star(conf_level),
x0 + offset, k))
bands[region] = Band(base='date',
lower=f'{region}_lower',
upper=f'{region}_upper',
source=bands_CDS,
level='underlay',
**plot_params)
plot.add_layout(bands[region])
def draw_data_line(region, **kwargs):
plot_params = {
'line_width': 4,
}
plot_params.update(kwargs)
lines[region] = plot.line(x='date',
y=region,
source=time_series_CDS,
name=region,
**plot_params)
confidence_level = 0.95
for region, color in zip(starting_regions, viridis(len(starting_regions))):
color = RGB(*hex_string_to_rgb(color))
darkened_color = color.darken(.15)
lightened_color = color.lighten(.15)
# draw prediction band
draw_prediction_band(region, confidence_level, fill_color=color)
# draw prediction line
draw_prediction_line(region, line_color=darkened_color)
# draw data line
draw_data_line(region, line_color=color)
# Hover Tool
hover_tool = HoverTool(tooltips=[('Date', '@date{%F}'),
('Region', '$name'),
('Num. Cases', '@$name{0,0}')],
formatters={
'@date': 'datetime',
})
plot.add_tools(hover_tool)
hover_tool.renderers = list(lines.values())
# Legend
prediction_line_glyph = plot.line(line_color='black',
line_dash='dashed',
name='prediction_line_glyph',
line_width=4)
prediction_line_glyph.visible = False
data_line_glyph = plot.line(line_color='black',
name='data_line_glyph',
line_width=4)
data_line_glyph.visible = False
confidence_interval_glyph = plot.patch(
[0, 0, 1, 1],
[0, 1, 1, 0],
name='confidence_interval_glyph',
line_color='black',
line_width=1,
fill_alpha=0.3,
fill_color='black',
)
confidence_interval_glyph.visible = False
legend = Legend(items=[
LegendItem(label="Data",
renderers=[plot.select_one({'name': 'data_line_glyph'})]),
LegendItem(
label="Prediction",
renderers=[plot.select_one({'name': 'prediction_line_glyph'})]),
LegendItem(
label="95% Confidence Interval",
renderers=[plot.select_one({'name': 'confidence_interval_glyph'})])
],
location='top_left')
plot.add_layout(legend)
## Prevent legend glyphs from affecting plotting ranges
def fit_to_visible_lines():
plot.x_range.renderers = list(
filter(lambda line: line.visible, lines.values()))
plot.y_range.renderers = list(
filter(lambda line: line.visible, lines.values()))
# Region Selector
excluded_columns_set = {'index', 'parameters'}
labels = [
key for key in params_CDS.data.keys()
if key not in excluded_columns_set
]
def region_select_callback(attr, old, new):
new_lines = set(new) - set(old)
old_lines = set(old) - set(new)
for key in old_lines:
lines[key].visible = False
lines[f'{key}_prediction'].visible = False
bands[key].visible = False
for key in new_lines:
if key in lines.keys():
lines[key].visible = True
lines[f'{key}_prediction'].visible = True
bands[key].visible = True
else:
color = RGB(*hex_string_to_rgb(np.random.choice(Viridis256)))
darkened_color = color.darken(.15)
lightened_color = color.lighten(.15)
draw_prediction_line(key, line_color=darkened_color)
draw_prediction_band(key,
conf_level=confidence_level,
fill_color=lightened_color)
draw_data_line(key, line_color=color)
hover_tool.renderers = [
*hover_tool.renderers, lines[key],
lines[f'{key}_prediction']
]
region_select = MultiSelect(title='Select Regions to Show',
value=starting_regions,
options=labels,
sizing_mode='stretch_height')
region_select.on_change('value', region_select_callback)
# Final Setup
fit_to_visible_lines()
child = row(column([plot]), column([region_select]))
return Panel(child=child, title=tab_title)
