From dae10602d084adb4690f5dcb1e34f9ec0fa8ed0a Mon Sep 17 00:00:00 2001
From: Rok Roskar <rokroskar@gmail.com>
Date: Fri, 3 Apr 2020 18:15:51 +0200
Subject: [PATCH] feat: add spain standardizer
---
notebooks/process/standardize_datasets.ipynb | 529 +++---------------
.../covid_19_dashboard/__init__.py | 2 +-
.../covid_19_dashboard/converters/spain.py | 91 +++
3 files changed, 179 insertions(+), 443 deletions(-)
create mode 100644 src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py
diff --git a/notebooks/process/standardize_datasets.ipynb b/notebooks/process/standardize_datasets.ipynb
index dff7b67c7..8a294aab2 100644
--- a/notebooks/process/standardize_datasets.ipynb
+++ b/notebooks/process/standardize_datasets.ipynb
@@ -1,4 +1,27 @@
{
+ "nbformat": 4,
+ "nbformat_minor": 2,
+ "metadata": {
+ "language_info": {
+ "name": "python",
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "version": "3.7.7-final"
+ },
+ "orig_nbformat": 2,
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "npconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": 3,
+ "kernelspec": {
+ "name": "python37764bitvenvvenv814492364d964019a25eb1cf3dc3e99c",
+ "display_name": "Python 3.7.7 64-bit ('.venv': venv)"
+ }
+ },
"cells": [
{
"cell_type": "code",
@@ -33,24 +56,34 @@
"import pandas as pd\n",
"\n",
"from covid_19_dashboard import helper, plotting\n",
- "from covid_19_dashboard.converters import CaseConverter"
+ "from covid_19_dashboard.converters import CaseConverter\n",
+ "from covid_19_dashboard.converters.switzerland import OpenZHCaseConverter\n",
+ "from covid_19_dashboard.converters.covidtracking import CovidtrackingCaseConverter\n",
+ "from covid_19_dashboard.converters.spain import SpainCaseConverter"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": "using: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.italy.ItalyCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.spain.SpainCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.switzerland.OpenZHCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.italy.ItalyCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.italy.ItalyCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.spain.SpainCaseConverter'>\n"
+ }
+ ],
"source": [
- "# read in cantonal data and produce one dataframe\n",
"df_list = []\n",
- "\n",
- "for f in Path('../../data/openzh-covid-19').glob('COVID19_Fallzahlen_Kanton_*total.csv'):\n",
- " df_list.append(pd.read_csv(f))\n",
- "\n",
- "df_ch = pd.concat(df_list)\n",
- "\n",
- "df_ch['date'] = pd.to_datetime(df_ch['date'], dayfirst=True)"
+ "for path in [\n",
+ " '../../data/openzh-covid-19', \n",
+ " '../../data/covid-19-italy', \n",
+ " '../../data/covidtracking/', \n",
+ " '../../data/covid-19-spain'\n",
+ "]:\n",
+ " df_list.append(CaseConverter.read_convert(path))\n",
+ "df_all = pd.concat(df_list).reset_index(drop=True)\n",
+ "df_all['date'] = pd.to_datetime(df_all.date)"
]
},
{
@@ -59,393 +92,75 @@
"metadata": {},
"outputs": [],
"source": [
- "df_ita = pd.read_csv('../../data/covid-19-italy/dpc-covid19-ita-regioni.csv')"
+ "df_esp = SpainCaseConverter.read_data('../../data/covid-19-spain')"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
- "outputs": [],
- "source": [
- "df_usa = pd.read_json('../../data/covidtracking/states-daily.json')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {},
- "outputs": [],
- "source": [
- "df_all = pd.DataFrame()\n",
- "for df in [df_ch, df_ita, df_usa]:\n",
- " df_all = df_all.append(CaseConverter.convert(df))\n",
- "df_all['date'] = pd.to_datetime(df_all.date)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {},
"outputs": [
{
+ "output_type": "execute_result",
"data": {
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- " <th>1271</th>\n",
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- " <td>US-WY</td>\n",
- " <td>Wyoming</td>\n",
- " <td>0.0</td>\n",
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- " date country region_iso region_label tested positive deceased \\\n",
- "0 2020-02-28 CHE CH-VS Valais NaN 1.0 NaN \n",
- "1 2020-02-29 CHE CH-VS Valais NaN 1.0 NaN \n",
- "2 2020-03-01 CHE CH-VS Valais NaN 2.0 NaN \n",
- "3 2020-03-02 CHE CH-VS Valais NaN 3.0 NaN \n",
- "4 2020-03-03 CHE CH-VS Valais NaN 3.0 NaN \n",
- "... ... ... ... ... ... ... ... \n",
- "1267 2020-03-11 USA US-WY Wyoming 0.0 0.0 NaN \n",
- "1268 2020-03-10 USA US-WY Wyoming 0.0 0.0 NaN \n",
- "1269 2020-03-09 USA US-WY Wyoming 0.0 0.0 NaN \n",
- "1270 2020-03-08 USA US-WY Wyoming 0.0 0.0 NaN \n",
- "1271 2020-03-07 USA US-WY Wyoming 0.0 0.0 NaN \n",
- "\n",
- " population positive_100k deceased_100k \n",
- "0 343955 0.290736 NaN \n",
- "1 343955 0.290736 NaN \n",
- "2 343955 0.581471 NaN \n",
- "3 343955 0.872207 NaN \n",
- "4 343955 0.872207 NaN \n",
- "... ... ... ... \n",
- "1267 586107 0.000000 NaN \n",
- "1268 586107 0.000000 NaN \n",
- "1269 586107 0.000000 NaN \n",
- "1270 586107 0.000000 NaN \n",
- "1271 586107 0.000000 NaN \n",
- "\n",
- "[2481 rows x 10 columns]"
- ]
+ "text/plain": " date country region_iso region_label tested positive deceased \\\n0 2020-02-27 ESP ES-AN AndalucÃa None 1 NaN \n1 2020-02-28 ESP ES-AN AndalucÃa None 6 NaN \n2 2020-02-29 ESP ES-AN AndalucÃa None 8 NaN \n3 2020-03-01 ESP ES-AN AndalucÃa None 12 NaN \n4 2020-03-02 ESP ES-AN AndalucÃa None 12 NaN \n.. ... ... ... ... ... ... ... \n622 2020-03-26 ESP ES-RI La Rioja None 995 43.0 \n623 2020-03-27 ESP ES-RI La Rioja None 1236 55.0 \n624 2020-03-28 ESP ES-RI La Rioja None 1436 65.0 \n625 2020-03-29 ESP ES-RI La Rioja None 1629 68.0 \n626 2020-03-30 ESP ES-RI La Rioja None 1733 71.0 \n\n population positive_100k deceased_100k \n0 8409738 0.011891 NaN \n1 8409738 0.071346 NaN \n2 8409738 0.095128 NaN \n3 8409738 0.142692 NaN \n4 8409738 0.142692 NaN \n.. ... ... ... \n622 315675 315.197592 13.621604 \n623 315675 391.541934 17.422982 \n624 315675 454.898234 20.590797 \n625 315675 516.037063 21.541142 \n626 315675 548.982339 22.491486 \n\n[627 rows x 10 columns]",
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},
- "execution_count": 7,
"metadata": {},
- "output_type": "execute_result"
+ "execution_count": 5
}
],
"source": [
- "df_all"
+ "\n",
+ "SpainCaseConverter.convert(df_esp)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
+ "outputs": [],
+ "source": [
+ "regions = ['Lombardy', 'Ticino', 'Zürich', 'Madrid', 'New York', 'Washington', 'Louisiana']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
"outputs": [
{
+ "output_type": "execute_result",
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+ "text/plain": "alt.Chart(...)"
},
- "execution_count": 8,
"metadata": {},
- "output_type": "execute_result"
+ "execution_count": 9
}
],
"source": [
- "base = alt.Chart(df_all[df_all.region_label.isin(['Lombardy', 'Veneto', 'Ticino', 'Zürich'])])\n",
- "base.mark_line().encode(x='date', y='positive', color='region_label')"
+ "base = alt.Chart(df_all[df_all.region_label.isin(regions)])\n",
+ "base.mark_line().encode(alt.X('date'), alt.Y('positive', scale=alt.Scale(type='linear')), color='region_label')"
]
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 10,
"metadata": {},
"outputs": [
{
+ "output_type": "execute_result",
"data": {
- "text/html": [
- "\n",
- "<div id=\"altair-viz-c13488b9b1104537ab20c91e60b1ae78\"></div>\n",
- "<script type=\"text/javascript\">\n",
- " (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-c13488b9b1104537ab20c91e60b1ae78\");\n",
- " const paths = {\n",
- " \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
- " \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
- " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
- " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
- " };\n",
- "\n",
- " function loadScript(lib) {\n",
- " return new Promise(function(resolve, reject) {\n",
- " var s = document.createElement('script');\n",
- " s.src = paths[lib];\n",
- " s.async = true;\n",
- " s.onload = () => resolve(paths[lib]);\n",
- " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
- " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
- " });\n",
- " }\n",
- "\n",
- " function showError(err) {\n",
- " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
- " throw err;\n",
- " }\n",
- "\n",
- " function displayChart(vegaEmbed) {\n",
- " vegaEmbed(outputDiv, spec, embedOpt)\n",
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+ "text/plain": "alt.HConcatChart(...)"
},
- "execution_count": 9,
"metadata": {},
- "output_type": "execute_result"
+ "execution_count": 10
}
],
"source": [
- "since_df_positive = helper.make_since_df(df_all[df_all.region_label.isin(['Lombardy', 'Ticino', 'Vaud', 'Geneva','Zürich'])], region_column='region_label', start_case=100)\n",
+ "since_df_positive = helper.make_since_df(df_all[df_all.region_label.isin(regions)], region_column='region_label', start_case=100)\n",
"base = alt.Chart(since_df_positive).properties(height=300,width=300)\n",
"days_log = plotting.make_region_since_chart(base, 'positive', 'sinceDay0', 'region_label', 'Days since 100th case', 'Cases', 'Cases', 'Region')\n",
"days_log_100k = plotting.make_region_since_chart(base, 'positive_100k', 'sinceDay0', 'region_label', 'Days since 100th case', 'Cases/100k', 'Cases/100k', 'Region')\n",
@@ -454,103 +169,33 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 11,
"metadata": {},
"outputs": [
{
+ "output_type": "execute_result",
"data": {
- "text/html": [
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- " function displayChart(vegaEmbed) {\n",
- " vegaEmbed(outputDiv, spec, embedOpt)\n",
- " .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
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- "\n",
- " if(typeof define === \"function\" && define.amd) {\n",
- " requirejs.config({paths});\n",
- " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
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],
"source": [
- "since_df_deceased = helper.make_since_df(df_all[df_all.region_label.isin(['Lombardy', 'Ticino', 'Vaud', 'Geneva','Zürich'])], column='deceased', region_column='region_label', start_case=10)\n",
+ "since_df_deceased = helper.make_since_df(df_all[df_all.region_label.isin(regions)], column='deceased', region_column='region_label', start_case=10)\n",
"base = alt.Chart(since_df_deceased).properties(height=300,width=300)\n",
"days_log = plotting.make_region_since_chart(base, 'deceased', 'sinceDay0', 'region_label', 'Days since 10th death', 'Deaths', 'Deaths', 'Region')\n",
- "days_log_100k = plotting.make_region_since_chart(base, 'deceased_100k', 'sinceDay0', 'region_label', 'Days since 100th case', 'Deaths/100k', 'Deaths/100k', 'Region')\n",
+ "days_log_100k = plotting.make_region_since_chart(base, 'deceased_100k', 'sinceDay0', 'region_label', 'Days since 10th death', 'Deaths/100k', 'Deaths/100k', 'Region')\n",
"alt.hconcat(days_log, days_log_100k)"
]
- }
- ],
- "metadata": {
- "file_extension": ".py",
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
},
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.7.3"
- },
- "mimetype": "text/x-python",
- "name": "python",
- "npconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": 3
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ]
+}
\ No newline at end of file
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py
index e14fd9fba..0e0779519 100644
--- a/src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/__init__.py
@@ -4,6 +4,6 @@ __author__ = """Chandrasekhar Ramakrishnan"""
__email__ = 'cramakri@ethz.ch'
__version__ = '0.1.0'
-from .converters import italy, switzerland, covidtracking
+from .converters import covidtracking, italy, spain, switzerland
from .helper import *
\ No newline at end of file
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py
new file mode 100644
index 000000000..df0f2c391
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py
@@ -0,0 +1,91 @@
+"""
+Converters for covid-19 data from Spain.
+"""
+
+from pathlib import Path
+
+import pandas as pd
+
+from . import CaseConverter
+from .. import helper
+
+# regional populations extracted from wikidata and wikipedia
+# Wikidata is missing information for Aragón
+# Query:
+
+# SELECT DISTINCT ?region_iso ?regionLabel (MAX(?population_cnt) as ?population)
+# {
+# ?country wdt:P298 "ESP" .
+# ?region wdt:P300 ?region_iso .
+# OPTIONAL{?region wdt:P1082 ?population_cnt}
+# ?country wdt:P150 ?region .
+# SERVICE wikibase:label { bd:serviceParam wikibase:language "es" }
+# }
+# GROUP BY ?region_iso ?regionLabel
+# ORDER BY ?regionLabel
+
+region_populations = [
+ {"region_iso": "ES-AN", "region_label": "AndalucÃa", "population": "8409738"},
+ {"region_iso": "ES-AR", "region_label": "Aragón", "population": "1308563"},
+ {"region_iso": "ES-AS", "region_label": "Asturias", "population": "1028244"},
+ {"region_iso": "ES-IB", "region_label": "Baleares", "population": "1150839"},
+ {"region_iso": "ES-CN", "region_label": "Canarias", "population": "2127685"},
+ {"region_iso": "ES-CB", "region_label": "Cantabria", "population": "580229"},
+ {"region_iso": "ES-CM", "region_label": "Castilla-La Mancha", "population": "2106331"},
+ {"region_iso": "ES-CL", "region_label": "Castilla y León", "population": "2418694"},
+ {"region_iso": "ES-CT", "region_label": "Cataluña", "population": "7619494"},
+ {"region_iso": "ES-CE", "region_label": "Ceuta", "population": "84777"},
+ {"region_iso": "ES-VC", "region_label": "C. Valenciana", "population": "5003769"},
+ {"region_iso": "ES-EX", "region_label": "Extremadura", "population": "1070586"},
+ {"region_iso": "ES-GA", "region_label": "Galicia", "population": "2708339"},
+ {"region_iso": "ES-MD", "region_label": "Madrid", "population": "6661949"},
+ {"region_iso": "ES-ML", "region_label": "Melilla", "population": "86487"},
+ {"region_iso": "ES-MC", "region_label": "Murcia", "population": "1478509"},
+ {"region_iso": "ES-NA", "region_label": "Navarra", "population": "647554"},
+ {"region_iso": "ES-PV", "region_label": "PaÃs Vasco", "population": "2167707"},
+ {"region_iso": "ES-RI", "region_label": "La Rioja", "population": "315675"},
+]
+
+
+class SpainCaseConverter(CaseConverter):
+ """
+ Converter for data from https://github.com/datadista/datasets
+ """
+
+ conversion_dict = {
+ "fecha": "date",
+ "total_casos": "positive",
+ "total_fallecidos": "deceased",
+ "CCAA": "region_label",
+ }
+
+ column_list = ["fecha", "CCAA", "cod_ine"]
+
+ @classmethod
+ def convert(cls, df):
+ # rename the existing columns
+ df_conv = df.rename(columns=cls.conversion_dict)
+
+ # calculate incidence rates
+ merged = df_conv.merge(pd.DataFrame(region_populations))
+ merged["population"] = merged.population.astype(int)
+ merged["positive_100k"] = merged["positive"] / merged["population"] * 100000
+ merged["deceased_100k"] = merged["deceased"] / merged["population"] * 100000
+
+ merged['country'] = 'ESP'
+ merged['tested'] = None
+ return merged[CaseConverter.common_columns]
+
+ @classmethod
+ def read_data(cls, path):
+ """Read data for Spain."""
+ df_c = pd.read_csv(Path(path) / "ccaa_covid19_casos_long.csv").rename(
+ columns={"total": "total_casos"}
+ )
+ df_f = pd.read_csv(Path(path) / "ccaa_covid19_fallecidos_long.csv").rename(
+ columns={"total": "total_fallecidos"}
+ )
+ return df_c.merge(df_f, how="outer")
+
+
+SpainCaseConverter._register()
--
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