def top_deaths_per_time(deaths, interval=7):
threshold = 20
df_diff = utils.sort_columns_on_row(deaths).diff().iloc[1:]
df_buckets = utils.bucket_values(df_diff,
interval=interval,
limit=threshold)
deaths_sorted = utils.sort_columns_on_row(df_buckets)
deaths_merged = deaths_sorted[deaths_sorted.columns[0:threshold]]
deaths_merged['Other'] = deaths_sorted[
deaths_sorted.columns[threshold:]].sum(axis=1)
deaths_merged = deaths_merged.iloc[-1].sort_values(ascending=False)
fig = go.Figure(layout=go.Layout(title=go.layout.Title(
text=f'Number of deaths by country - Last {interval} day(s)'),
paper_bgcolor='rgba(0,0,0,0)',
plot_bgcolor='rgba(0,0,0,0)',
font=dict(family="Lato, Helvetica",
color="#333447"),
legend_orientation="v",
xaxis=go.layout.XAxis(
showgrid=False,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
),
yaxis=go.layout.YAxis(
showgrid=True,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
tickformat=',.0',
side='right',
range=[0, deaths_merged.max()]),
margin={
'l': 0,
'r': 0,
'pad': 0
}), )
text = zip(
deaths_merged.values,
[x for x in round(deaths_merged / deaths_merged.sum() * 1000) / 10],
)
fig.add_trace(
go.Bar(x=deaths_merged.index,
y=deaths_merged,
text=[f"{x[0]:.0f} ({str(x[1])}%)" for x in text],
textposition='auto',
marker=dict(
color=[utils.get_color(c)[0] for c in deaths_merged.index]),
orientation='v'))
return fig
def deaths_pie_chart(deaths):
threshold = 10
deaths_sorted = utils.sort_columns_on_row(deaths)
deaths_merged = deaths_sorted[deaths_sorted.columns[0:threshold]]
deaths_merged['Other'] = deaths_sorted[
deaths_sorted.columns[threshold:]].sum(axis=1)
deaths_merged = deaths_merged.iloc[-1].transpose()
fig = go.Figure(layout=go.Layout(
title=go.layout.Title(text=f'Distribution of deaths by country'),
paper_bgcolor='rgba(0,0,0,0)',
plot_bgcolor='rgba(0,0,0,0)',
font=dict(family="Lato, Helvetica", color="#333447"),
legend_orientation="h",
margin={
'l': 0,
'r': 0,
'pad': 0
}),
data=[
go.Pie(labels=deaths_merged.index,
values=deaths_merged.values,
hole=0.5,
marker=dict(colors=[
utils.get_color(c)[0]
for c in deaths_merged.index
]))
])
return fig
def deaths_area(deaths):
threshold = 15
deaths_sorted = utils.sort_columns_on_row(deaths)
deaths_upper = deaths_sorted[deaths_sorted.columns[0:threshold]]
deaths_lower = deaths_sorted[deaths_sorted.columns[threshold:]].sum(axis=1)
fig = go.Figure(layout=go.Layout(
title=go.layout.Title(text=f'Total deaths due to COVID-19'),
paper_bgcolor='rgba(0,0,0,0)',
plot_bgcolor='rgba(0,0,0,0)',
font=dict(family="Lato, Helvetica", color="#333447"),
yaxis=go.layout.YAxis(
showgrid=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
),
xaxis=go.layout.XAxis(
showgrid=True, gridwidth=1, gridcolor='rgb(220,220,220)',
nticks=5),
legend_orientation="h",
margin={
'l': 0,
'r': 0,
'pad': 0
}))
color, show = utils.get_color('Other', 1000, 1)
fig.add_trace(
go.Scatter(
x=deaths_lower.index,
y=deaths_lower.values,
hoverinfo='none',
hovertemplate='Total deaths: %{y}<br>Day: %{x}',
mode='lines',
name='Other',
line=dict(width=0, color=color),
stackgroup='one' # define stack group
))
for i, column in enumerate(deaths_upper.columns):
color, show = utils.get_color(column)
fig.add_trace(
go.Scatter(
x=deaths_upper[column].index,
y=deaths_upper[column].values,
mode='lines',
name=column,
hoverinfo='none',
hovertemplate='Total deaths: %{y}<br>Day: %{x}',
line=dict(width=0, color=color),
stackgroup='one' # define stack group
))
return fig
def animated_map(df, iso_alpha_path):
iso_alpha = pd.read_csv(iso_alpha_path, delimiter='\t')
limit = 25
df_flat = utils.sort_columns_on_row(df).iloc[:, :limit].diff().iloc[1:]
df_flat = df_flat.iloc[1:].transpose().reset_index().melt(
id_vars=['Country/Region'], var_name='Date', value_name='Count')
df_flat['Count'] = df_flat['Count'].clip(lower=0)
df_flat = df_flat.merge(iso_alpha, on='Country/Region', how='left')
fig = px.scatter_geo(df_flat,
locations="iso3",
hover_name="Country/Region",
size="Count",
animation_frame="Date",
color='Country/Region',
projection="natural earth")
return fig
def confirmed_cases_over_threshold(confirmed):
limit = 25
confirmed = confirmed.assign(EU=confirmed[[
'Austria', 'Belgium', 'Bulgaria', 'Croatia', 'Cyprus', 'Czechia',
'Denmark', 'Estonia', 'Finland', 'France', 'Germany', 'Greece',
'Hungary', 'Ireland', 'Italy', 'Latvia', 'Lithuania', 'Luxembourg',
'Malta', 'Netherlands', 'Poland', 'Portugal', 'Romania', 'Slovakia',
'Slovenia', 'Spain', 'Sweden'
]].sum(axis=1))
confirmed_over_threshold = utils.sort_columns_on_row(
confirmed).iloc[:, :limit]
fig = go.Figure(
layout=go.Layout(title=go.layout.Title(
text=f'Positive cases of COVID-19 - Top {limit} countries'),
paper_bgcolor=paper_bgcolor,
plot_bgcolor=plot_bgcolor,
font=dict(family="Lato, Helvetica", color="#333447"),
yaxis=go.layout.YAxis(showgrid=True,
automargin=True,
gridwidth=1,
nticks=5,
gridcolor='rgb(220,220,220)'),
xaxis=go.layout.XAxis(
showgrid=True,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
nticks=5,
),
margin={
'l': 0,
'r': 0,
'pad': 0
}))
for i, column in enumerate(confirmed_over_threshold):
color, show = utils.get_color(column, i, 8)
fig.add_trace(
go.Scatter(x=confirmed_over_threshold[column].index,
y=confirmed_over_threshold[column].values,
name=column,
hoverinfo='none',
hovertemplate='Positive cases: %{y}<br>Date: %{x}',
marker_color=color,
line=dict(width=1.5, dash='solid' if show else 'dot')))
return fig
def daily_change(df, interval=1):
limit = 10
df_diff = utils.sort_columns_on_row(df).diff().iloc[1:]
df_buckets = utils.bucket_values(df_diff, limit=limit, interval=interval)
fig = go.Figure(
layout=go.Layout(title=go.layout.Title(
text=f'Sum of new deaths every {interval} day due to COVID-19'),
paper_bgcolor=paper_bgcolor,
plot_bgcolor=plot_bgcolor,
font=dict(family="Lato, Helvetica", color="#333447"),
yaxis=go.layout.YAxis(showgrid=True,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
nticks=5),
xaxis=go.layout.XAxis(
showgrid=False,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
nticks=5,
),
margin={
'l': 0,
'r': 0,
'pad': 0
},
barmode='stack'))
for i, column in enumerate(df_buckets):
hovertemplate = 'New deaths: %{y}<br>Date: %{x}'
if (interval > 1):
hovertemplate = 'New deaths: %{y}<br>Date: %{x}+' + str(interval -
1)
color, show = utils.get_color(column)
fig.add_trace(
go.Bar(
x=df_buckets[column].index,
y=df_buckets[column].values,
name=column,
hoverinfo='none',
hovertemplate=hovertemplate,
marker_color=color,
))
return fig
def current_distribution(deaths):
threshold = 15
deaths_sorted = utils.sort_columns_on_row(deaths)
deaths_merged = deaths_sorted[deaths_sorted.columns[0:threshold]]
deaths_merged['Other'] = deaths_sorted[
deaths_sorted.columns[threshold:]].sum(axis=1)
deaths_merged = deaths_merged.iloc[-1].sort_values()
fig = go.Figure(layout=go.Layout(
title=go.layout.Title(text=f'Distribution of deaths by country'),
paper_bgcolor='rgba(0,0,0,0)',
plot_bgcolor='rgba(0,0,0,0)',
font=dict(family="Lato, Helvetica", color="#333447"),
legend_orientation="h",
yaxis=go.layout.YAxis(showgrid=False,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
side='right'),
xaxis=go.layout.XAxis(
showgrid=True,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
tickformat=',.0%',
range=[0, deaths_merged.max() / deaths_merged.sum()]),
margin={
'l': 0,
'r': 0,
'pad': 0
}), )
fig.add_trace(
go.Bar(y=deaths_merged.index,
x=deaths_merged / deaths_merged.sum(),
text=[
str(x) + '%'
for x in round(deaths_merged / deaths_merged.sum() * 1000) /
10
],
textposition='auto',
marker=dict(
color=[utils.get_color(c)[0] for c in deaths_merged.index]),
orientation='h'))
return fig
def calc_stats(deaths, confirmed):
stats = {}
over_5_deaths = utils.over_threshold(deaths, 5)
change = utils.sort_columns_on_row(over_5_deaths.diff())
stats['deaths'] = over_5_deaths.iloc[-1].to_dict()
stats['change_deaths'] = change.iloc[-1].to_dict()
stats['num_countries_over_5_deaths'] = len(
utils.over_threshold(deaths, 5).columns)
stats['num_countries_over_5_deaths_change'] = len(
utils.over_threshold(deaths, 5, -1).columns) - len(
utils.over_threshold(deaths, 5, -2).columns)
stats['num_countries_over_limit_confirmed'] = len(
utils.over_threshold(confirmed, 500).columns)
stats['num_countries_over_limit_confirmed_change'] = len(
utils.over_threshold(confirmed, 500, -1).columns) - len(
utils.over_threshold(confirmed, 500, -2).columns)
stats['total_deaths'] = int(deaths.iloc[-1].sum())
stats['total_deaths_change'] = int(deaths.iloc[-1].sum()) - int(
deaths.iloc[-2].sum())
stats['total_confirmed'] = int(confirmed.iloc[-1].sum())
stats['total_confirmed_change'] = int(confirmed.iloc[-1].sum()) - int(
confirmed.iloc[-2].sum())
stats['last_updated'] = date.today().strftime('%Y-%m-%d')
return stats
def countries_deaths_over_threshold(deaths):
limit = 25
confirmed_over_threshold = utils.sort_columns_on_row(
deaths).iloc[:, :limit]
fig = go.Figure(
layout=go.Layout(title=go.layout.Title(
text=f'Deaths due to COVID-19 - Top {limit} countries'),
paper_bgcolor=paper_bgcolor,
plot_bgcolor=plot_bgcolor,
font=dict(family="Lato, Helvetica", color="#333447"),
yaxis=go.layout.YAxis(showgrid=True,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)'),
xaxis=go.layout.XAxis(showgrid=True,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
nticks=5),
margin={
'l': 0,
'r': 0,
'pad': 0
}))
for i, column in enumerate(confirmed_over_threshold):
color, show = utils.get_color(column, i, 8)
fig.add_trace(
go.Scatter(x=confirmed_over_threshold[column].index,
y=confirmed_over_threshold[column].values,
name=column,
hoverinfo='none',
hovertemplate='Total deaths: %{y}<br>Date: %{x}',
marker_color=color,
line=dict(width=1.5, dash='solid' if show else 'dot')))
return fig
def rate_vs_total(df, x_lower, y_lower, type_name, limit=35, window=7):
df = utils.sort_columns_on_row(df)
df_diff = df.diff().iloc[1:]
df = df.iloc[1:]
confirmed = utils.bucket_values(df,
limit=limit,
include_other=False,
interval=window)
confirmed_diff = utils.bucket_values(df_diff,
limit=limit,
include_other=False,
interval=window)
fig = go.Figure(layout=go.Layout(title=go.layout.Title(
text=
f'Weekly {type_name} rate vs. total {type_name}s - Top {limit} countries'
),
paper_bgcolor=paper_bgcolor,
plot_bgcolor=plot_bgcolor,
font=dict(family="Lato, Helvetica",
color="#333447"),
yaxis=go.layout.YAxis(
type='log',
showgrid=True,
automargin=True,
title='New deaths',
gridwidth=1,
range=[
log(y_lower) / log(10),
log(confirmed_diff.max().max()) /
log(10)
],
gridcolor='rgb(220,220,220)'),
xaxis=go.layout.XAxis(
type='log',
title='Total deaths',
showgrid=True,
automargin=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
range=[
log(x_lower) / log(10),
log(confirmed.max().max()) /
log(10)
],
nticks=5),
margin={
'l': 0,
'r': 0,
'pad': 0
}))
for i, column in enumerate(confirmed):
confirmed_single = confirmed[confirmed_diff[column] > 0][column]
confirmed_diff_single = confirmed_diff[
confirmed_diff[column] > 0][column]
color, show = utils.get_color(column, i, 8)
fig.add_trace(
go.Scatter(x=confirmed_single.values,
y=confirmed_diff_single.values,
name=column,
hoverinfo='none',
mode='lines',
hovertemplate='New deaths: %{y}<br>Total deaths: %{x}',
marker_color=color,
line=dict(width=1.5, dash='solid' if show else 'dot')))
# fig.add_trace(go.Scatter(
# x=[2, 1000000],
# y=[1, 100000],
# name='Time of lockdown',
# mode="lines",
# marker_color="red",
# line=dict(dash="dot", width=4)
# ))
return fig
def deaths_over_threshold_and_aligned(deaths):
threshold = 5
align_on = 5
limit = 40
deaths = deaths.assign(EU=deaths[[
'Austria', 'Belgium', 'Bulgaria', 'Croatia', 'Cyprus', 'Czechia',
'Denmark', 'Estonia', 'Finland', 'France', 'Germany', 'Greece',
'Hungary', 'Ireland', 'Italy', 'Latvia', 'Lithuania', 'Luxembourg',
'Malta', 'Netherlands', 'Poland', 'Portugal', 'Romania', 'Slovakia',
'Slovenia', 'Spain', 'Sweden'
]].sum(axis=1))
deaths_over_threshold = utils.sort_columns_on_row(deaths).iloc[:, :limit]
fig = go.Figure(layout=go.Layout(
title=go.layout.
Title(text=
f'Number of deaths aligned on the {align_on}th registered death - Top {limit} countries'
),
paper_bgcolor='rgba(0,0,0,0)',
plot_bgcolor='rgba(0,0,0,0)',
font=dict(family="Lato, Helvetica", color="#333447"),
xaxis=go.layout.XAxis(
showgrid=False,
gridwidth=1,
gridcolor='rgb(220,220,220)',
title_text=f'Number of days since {align_on}th death',
range=[0, len(deaths) - 25]),
yaxis=go.layout.YAxis(exponentformat='none',
type='log',
showgrid=True,
gridwidth=1,
gridcolor='rgb(220,220,220)',
nticks=5),
margin={
'l': 0,
'r': 0,
'pad': 0
}))
fig.update_layout(updatemenus=[
dict(type="buttons",
direction='left',
buttons=[
dict(label="Logarithmic",
method="relayout",
args=["yaxis.type", 'log']),
dict(label="Linear",
method="relayout",
args=["yaxis.type", 'lin']),
],
pad={
"r": 0,
"t": 0,
"b": 20
},
showactive=True,
x=0,
xanchor="left",
y=-0.2,
yanchor="top")
])
for i, column in enumerate(deaths_over_threshold):
x, y = utils.get_from_first_occurrence(deaths_over_threshold, column,
align_on)
color, show = utils.get_color(column, i, 8)
fig.add_trace(
go.Scatter(x=x,
y=y,
name=column,
mode='lines',
hoverinfo='none',
hovertemplate='Total deaths: %{y}<br>Day: %{x}',
marker_color=color,
line=dict(width=1.5, dash='solid' if show else 'dot')))
return fig