chore: fix up zh notebook

d5ad80af · Rok Roškar · f274f293 · d5ad80af
Unverified Commit d5ad80af authored 3 years ago by Rok Roškar
--- a/notebooks/openzh-covid-19.ipynb
+++ b/notebooks/openzh-covid-19.ipynb
@@ -187,7 +187,7 @@
   "metadata": {},
   "outputs": [],
   "source": [
-    "since_100th_case = helper.make_since_df(df, 'positive', 'canton', start_case=15000)\n",
+    "since_100th_case = helper.make_since_df(df, 'positive', 'canton', start_case=20000)\n",
    "\n",
    "base = alt.Chart(since_100th_case, title=\"Switzerland: total cases since 1000th case\").encode(alt.Y(scale=alt.Scale(type='log')))\n",
    "\n",

 %% Cell type:code id: tags:

 ``` python
 %load_ext autoreload
 %autoreload 2
 ```

 %% Cell type:code id: tags:

 ``` python
 from pathlib import Path

 import altair as alt
 import pandas as pd
 from IPython.display import display, HTML

 from covid_19_utils import helper, plotting
 from covid_19_utils.converters import CaseConverter
 ```

 %% Cell type:code id: tags:parameters

 ``` python
 save_figures = False
 data_path = '../data/openzh-covid-19'
 atlas_path = '../data/atlas'
 ```

 %% Cell type:code id: tags:

 ``` python
 html_credits=HTML('''
 <p style="font-size: smaller">Data Sources:
  <a href="https://github.com/openZH/covid_19">OpenData Zuerich</a>,
  <a href="https://www.bfs.admin.ch">Federal Statistical Office</a>
 <br>
 Analysis:
  <a href="https://renkulab.io/projects/covid-19/covid-19-public-data">Covid-19 Public Data Collaboration Project</a>
 </p>''')
 ```

 %% Cell type:markdown id: tags:

 ## Summary data for Covid-19 cases in Switzerland

 The data for Switzerland comes from the effort initiated by [OpenData Zürich](https://github.com/openZH/covid_19) and collected during the [Case data #covid19mon hackathon challenge](https://db.schoolofdata.ch/project/73).

 Below we make plots of total cases, total cases per 10k population and total deaths. You can click on the canton abbreviations in the legend to highlight individual lines.

 %% Cell type:code id: tags:

 ``` python
 # read in cantonal data and produce one dataframe
 converter = CaseConverter(atlas_path)
 df = converter.read_convert(data_path)
 df["canton"] = df.apply(lambda row: row["region_iso"][3:], axis=1)
 ```

 %% Cell type:markdown id: tags:

 ### Total cases

 %% Cell type:code id: tags:

 ``` python
 startdate = "2021-06-01"
 ```

 %% Cell type:code id: tags:

 ``` python
 base = alt.Chart(df[df['date'] > startdate])
 base.configure_header(titleFontSize=25)
 base.configure_axis(labelFontSize=15, titleFontSize=15)

 # cumul = generate_canton_chart(base, 'positive', 'Cases', 'Cases')
 cumul = plotting.generate_region_chart(
    base,
    column='positive',
    region_column='canton',
    ytitle='Cases',
    legend_title='Canton',
    tooltip_title='Cases')
 cumul_100k = plotting.generate_region_chart(
    base,
    column='positive_100k',
    region_column='canton',
    ytitle='Cases per 100k population',
    legend_title='Canton',
    tooltip_title='Cases/100k')

 chart = alt.hconcat(
    cumul, cumul_100k, title='Covid-19 cases in Switzerland by Canton'
 ).configure_title(
    anchor='middle'
 )

 display(chart)
 if save_figures:
    chart.save(str(Path(figures_path) / 'switzerland-cases-by-canton.html'))

 display(html_credits)
 ```

 %% Cell type:markdown id: tags:

 ### Deaths

 %% Cell type:code id: tags:

 ``` python
 base = alt.Chart(df[df['date'] > startdate])
 base.configure_header(titleFontSize=25)
 base.configure_axis(labelFontSize=15, titleFontSize=15)

 deaths = plotting.generate_region_chart(
    base,
    column='deceased',
    region_column='canton',
    ytitle='Deaths',
    tooltip_title='Deaths',
    legend_title='Canton'
 )
 deaths_10k = plotting.generate_region_chart(
    base,
    column='deceased_100k',
    region_column='canton',
    ytitle='Deaths per 100k population',
    tooltip_title='Deaths/100k',
    legend_title='Canton'
 )

 chart = alt.hconcat(
    deaths, deaths_10k, title='Covid-19 deaths in Switzerland by Canton'
 ).configure_title(
    anchor='middle'
 )
 display(chart)
 display(html_credits)

 if save_figures:
    chart.save(str(Path(figures_path) / 'switzerland-deaths-by-canton.html'))
 ```

 %% Cell type:code id: tags:

 ``` python
-since_100th_case = helper.make_since_df(df, 'positive', 'canton', start_case=15000)
+since_100th_case = helper.make_since_df(df, 'positive', 'canton', start_case=20000)

 base = alt.Chart(since_100th_case, title="Switzerland: total cases since 1000th case").encode(alt.Y(scale=alt.Scale(type='log')))

 lineChart = plotting.make_region_since_chart(
    base,
    'positive',
    'sinceDay0',
    'canton',
    'Days since 1000th case',
    'Cumulative positive cases',
    'Cases',
    'Canton'
 ).properties(
    width=450,
    height=450
 )

 lineChart
 ```

 %% Cell type:code id: tags:

 ``` python
 ```