From abbcd8c80bbaf2b459212042bee8cabc5b585405 Mon Sep 17 00:00:00 2001
From: Rok Roskar <rokroskar@gmail.com>
Date: Tue, 31 Mar 2020 22:41:11 +0200
Subject: [PATCH] chore: refactor dataframe and plotting
---
notebooks/examples/italy-covid-19.ipynb | 248 +++++++++++++-
notebooks/openzh-covid-19-dashboard.ipynb | 313 ++++++++++++++----
.../covid_19_dashboard/helper.py | 176 +++++++---
.../covid_19_dashboard/plotting.py | 163 +++++++++
4 files changed, 773 insertions(+), 127 deletions(-)
create mode 100644 src/covid-19/covid_19_dashboard/covid_19_dashboard/plotting.py
diff --git a/notebooks/examples/italy-covid-19.ipynb b/notebooks/examples/italy-covid-19.ipynb
index 2c80958..810c3db 100644
--- a/notebooks/examples/italy-covid-19.ipynb
+++ b/notebooks/examples/italy-covid-19.ipynb
@@ -32,6 +32,7 @@
"\n",
"from IPython.display import display, HTML\n",
"\n",
+ "from covid_19_dashboard import helper, plotting\n",
"from covid_19_dashboard.italy_utils import get_region_populations, prepare_dataframe"
]
},
@@ -104,10 +105,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-283197ecbf04499cbe673c8d8f180d54\"></div>\n",
+ "<div id=\"altair-viz-468aa5f5d41740288c8f71f1c8421509\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-283197ecbf04499cbe673c8d8f180d54\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-468aa5f5d41740288c8f71f1c8421509\");\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",
@@ -148,7 +149,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 10}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"tests\", \"title\": \"Tests (blue)\"}}}, {\"mark\": {\"type\": \"point\", \"color\": \"orange\", \"filled\": true, \"opacity\": 1, \"size\": 100}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases\", \"title\": \"Cases (orange)\"}}}]}, {\"mark\": {\"type\": \"bar\", \"size\": 10}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"New cases per day\"}}}], \"data\": {\"name\": \"data-d6920cc33bf5baef75219a92fc17aa0b\"}, \"title\": \"Total and daily tests and cases nationwide\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-d6920cc33bf5baef75219a92fc17aa0b\": [{\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 101, \"intensive_care\": 26, \"total_hospitalised\": 127, \"home_confinement\": 94, \"total_current_positive\": 221, \"new_current_positive\": 221, \"recovered\": 1, \"dead\": 7, \"total_cases\": 229, \"tests\": 4324, \"New cases per day\": null}, {\"date\": \"2020-02-25T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 114, \"intensive_care\": 35, \"total_hospitalised\": 150, \"home_confinement\": 162, \"total_current_positive\": 311, \"new_current_positive\": 90, \"recovered\": 1, \"dead\": 10, \"total_cases\": 322, \"tests\": 8623, \"New cases per day\": 93.0}, {\"date\": \"2020-02-26T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 128, \"intensive_care\": 36, \"total_hospitalised\": 164, \"home_confinement\": 221, \"total_current_positive\": 385, \"new_current_positive\": 74, \"recovered\": 3, \"dead\": 12, \"total_cases\": 400, \"tests\": 9587, \"New cases per day\": 78.0}, {\"date\": \"2020-02-27T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 248, \"intensive_care\": 56, \"total_hospitalised\": 304, \"home_confinement\": 284, \"total_current_positive\": 588, \"new_current_positive\": 203, \"recovered\": 45, \"dead\": 17, \"total_cases\": 650, \"tests\": 12014, \"New cases per day\": 250.0}, {\"date\": \"2020-02-28T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 345, \"intensive_care\": 64, \"total_hospitalised\": 409, \"home_confinement\": 412, \"total_current_positive\": 821, \"new_current_positive\": 233, \"recovered\": 46, \"dead\": 21, \"total_cases\": 888, \"tests\": 15695, \"New cases per day\": 238.0}, {\"date\": \"2020-02-29T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 401, \"intensive_care\": 105, \"total_hospitalised\": 506, \"home_confinement\": 543, \"total_current_positive\": 1049, \"new_current_positive\": 228, \"recovered\": 50, \"dead\": 29, \"total_cases\": 1128, \"tests\": 18661, \"New cases per day\": 240.0}, {\"date\": \"2020-03-01T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 639, \"intensive_care\": 140, \"total_hospitalised\": 779, \"home_confinement\": 798, \"total_current_positive\": 1577, \"new_current_positive\": 528, \"recovered\": 83, \"dead\": 34, \"total_cases\": 1694, \"tests\": 21127, \"New cases per day\": 566.0}, {\"date\": \"2020-03-02T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 742, \"intensive_care\": 166, \"total_hospitalised\": 908, \"home_confinement\": 927, \"total_current_positive\": 1835, \"new_current_positive\": 258, \"recovered\": 149, \"dead\": 52, \"total_cases\": 2036, \"tests\": 23345, \"New cases per day\": 342.0}, {\"date\": \"2020-03-03T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 1034, \"intensive_care\": 229, \"total_hospitalised\": 1263, \"home_confinement\": 1000, \"total_current_positive\": 2263, \"new_current_positive\": 428, \"recovered\": 160, \"dead\": 79, \"total_cases\": 2502, \"tests\": 25856, \"New cases per day\": 466.0}, {\"date\": \"2020-03-04T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 1346, \"intensive_care\": 295, \"total_hospitalised\": 1641, \"home_confinement\": 1065, \"total_current_positive\": 2706, \"new_current_positive\": 443, \"recovered\": 276, \"dead\": 107, \"total_cases\": 3089, \"tests\": 29837, \"New cases per day\": 587.0}, {\"date\": \"2020-03-05T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 1790, \"intensive_care\": 351, \"total_hospitalised\": 2141, \"home_confinement\": 1155, \"total_current_positive\": 3296, \"new_current_positive\": 590, \"recovered\": 414, \"dead\": 148, \"total_cases\": 3858, \"tests\": 32362, \"New cases per day\": 769.0}, {\"date\": \"2020-03-06T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 2394, \"intensive_care\": 462, \"total_hospitalised\": 2856, \"home_confinement\": 1060, \"total_current_positive\": 3916, \"new_current_positive\": 620, \"recovered\": 523, \"dead\": 197, \"total_cases\": 4636, \"tests\": 36359, \"New cases per day\": 778.0}, {\"date\": \"2020-03-07T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 2651, \"intensive_care\": 567, \"total_hospitalised\": 3218, \"home_confinement\": 1843, \"total_current_positive\": 5061, \"new_current_positive\": 1145, \"recovered\": 589, \"dead\": 233, \"total_cases\": 5883, \"tests\": 42062, \"New cases per day\": 1247.0}, {\"date\": \"2020-03-08T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 3557, \"intensive_care\": 650, \"total_hospitalised\": 4207, \"home_confinement\": 2180, \"total_current_positive\": 6387, \"new_current_positive\": 1326, \"recovered\": 622, \"dead\": 366, \"total_cases\": 7375, \"tests\": 49937, \"New cases per day\": 1492.0}, {\"date\": \"2020-03-09T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 4316, \"intensive_care\": 733, \"total_hospitalised\": 5049, \"home_confinement\": 2936, \"total_current_positive\": 7985, \"new_current_positive\": 1598, \"recovered\": 724, \"dead\": 463, \"total_cases\": 9172, \"tests\": 53826, \"New cases per day\": 1797.0}, {\"date\": \"2020-03-10T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 5038, \"intensive_care\": 877, \"total_hospitalised\": 5915, \"home_confinement\": 2599, \"total_current_positive\": 8514, \"new_current_positive\": 529, \"recovered\": 1004, \"dead\": 631, \"total_cases\": 10149, \"tests\": 60761, \"New cases per day\": 977.0}, {\"date\": \"2020-03-11T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 5838, \"intensive_care\": 1028, \"total_hospitalised\": 6866, \"home_confinement\": 3724, \"total_current_positive\": 10590, \"new_current_positive\": 2076, \"recovered\": 1045, \"dead\": 827, \"total_cases\": 12462, \"tests\": 73154, \"New cases per day\": 2313.0}, {\"date\": \"2020-03-12T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 6650, \"intensive_care\": 1153, \"total_hospitalised\": 7803, \"home_confinement\": 5036, \"total_current_positive\": 12839, \"new_current_positive\": 2249, \"recovered\": 1258, \"dead\": 1016, \"total_cases\": 15113, \"tests\": 86011, \"New cases per day\": 2651.0}, {\"date\": \"2020-03-13T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 7426, \"intensive_care\": 1328, \"total_hospitalised\": 8754, \"home_confinement\": 6201, \"total_current_positive\": 14955, \"new_current_positive\": 2116, \"recovered\": 1439, \"dead\": 1266, \"total_cases\": 17660, \"tests\": 97488, \"New cases per day\": 2547.0}, {\"date\": \"2020-03-14T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 8372, \"intensive_care\": 1518, \"total_hospitalised\": 9890, \"home_confinement\": 7860, \"total_current_positive\": 17750, \"new_current_positive\": 2795, \"recovered\": 1966, \"dead\": 1441, \"total_cases\": 21157, \"tests\": 109170, \"New cases per day\": 3497.0}, {\"date\": \"2020-03-15T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 9663, \"intensive_care\": 1672, \"total_hospitalised\": 11335, \"home_confinement\": 9268, \"total_current_positive\": 20603, \"new_current_positive\": 2853, \"recovered\": 2335, \"dead\": 1809, \"total_cases\": 24747, \"tests\": 124899, \"New cases per day\": 3590.0}, {\"date\": \"2020-03-16T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 11025, \"intensive_care\": 1851, \"total_hospitalised\": 12876, \"home_confinement\": 10197, \"total_current_positive\": 23073, \"new_current_positive\": 2470, \"recovered\": 2749, \"dead\": 2158, \"total_cases\": 27980, \"tests\": 137962, \"New cases per day\": 3233.0}, {\"date\": \"2020-03-17T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 12894, \"intensive_care\": 2060, \"total_hospitalised\": 14954, \"home_confinement\": 11108, \"total_current_positive\": 26062, \"new_current_positive\": 2989, \"recovered\": 2941, \"dead\": 2503, \"total_cases\": 31506, \"tests\": 148657, \"New cases per day\": 3526.0}, {\"date\": \"2020-03-18T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 14363, \"intensive_care\": 2257, \"total_hospitalised\": 16620, \"home_confinement\": 12090, \"total_current_positive\": 28710, \"new_current_positive\": 2648, \"recovered\": 4025, \"dead\": 2978, \"total_cases\": 35713, \"tests\": 165541, \"New cases per day\": 4207.0}, {\"date\": \"2020-03-19T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 15757, \"intensive_care\": 2498, \"total_hospitalised\": 18255, \"home_confinement\": 14935, \"total_current_positive\": 33190, \"new_current_positive\": 4480, \"recovered\": 4440, \"dead\": 3405, \"total_cases\": 41035, \"tests\": 182777, \"New cases per day\": 5322.0}, {\"date\": \"2020-03-20T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 16020, \"intensive_care\": 2655, \"total_hospitalised\": 18675, \"home_confinement\": 19185, \"total_current_positive\": 37860, \"new_current_positive\": 4670, \"recovered\": 5129, \"dead\": 4032, \"total_cases\": 47021, \"tests\": 206886, \"New cases per day\": 5986.0}, {\"date\": \"2020-03-21T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 17708, \"intensive_care\": 2857, \"total_hospitalised\": 20565, \"home_confinement\": 22116, \"total_current_positive\": 42681, \"new_current_positive\": 4821, \"recovered\": 6072, \"dead\": 4825, \"total_cases\": 53578, \"tests\": 233222, \"New cases per day\": 6557.0}, {\"date\": \"2020-03-22T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 19846, \"intensive_care\": 3009, \"total_hospitalised\": 22855, \"home_confinement\": 23783, \"total_current_positive\": 46638, \"new_current_positive\": 3957, \"recovered\": 7024, \"dead\": 5476, \"total_cases\": 59138, \"tests\": 258402, \"New cases per day\": 5560.0}, {\"date\": \"2020-03-23T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 20692, \"intensive_care\": 3204, \"total_hospitalised\": 23896, \"home_confinement\": 26522, \"total_current_positive\": 50418, \"new_current_positive\": 3780, \"recovered\": 7432, \"dead\": 6077, \"total_cases\": 63927, \"tests\": 275468, \"New cases per day\": 4789.0}, {\"date\": \"2020-03-24T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 21937, \"intensive_care\": 3396, \"total_hospitalised\": 25333, \"home_confinement\": 28697, \"total_current_positive\": 54030, \"new_current_positive\": 3612, \"recovered\": 8326, \"dead\": 6820, \"total_cases\": 69176, \"tests\": 296964, \"New cases per day\": 5249.0}, {\"date\": \"2020-03-25T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 23112, \"intensive_care\": 3489, \"total_hospitalised\": 26601, \"home_confinement\": 30920, \"total_current_positive\": 57521, \"new_current_positive\": 3491, \"recovered\": 9362, \"dead\": 7503, \"total_cases\": 74386, \"tests\": 324445, \"New cases per day\": 5210.0}, {\"date\": \"2020-03-26T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 24753, \"intensive_care\": 3612, \"total_hospitalised\": 28365, \"home_confinement\": 33648, \"total_current_positive\": 62013, \"new_current_positive\": 4492, \"recovered\": 10361, \"dead\": 8165, \"total_cases\": 80539, \"tests\": 361060, \"New cases per day\": 6153.0}, {\"date\": \"2020-03-27T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 26029, \"intensive_care\": 3732, \"total_hospitalised\": 29761, \"home_confinement\": 36653, \"total_current_positive\": 66414, \"new_current_positive\": 4401, \"recovered\": 10950, \"dead\": 9134, \"total_cases\": 86498, \"tests\": 394079, \"New cases per day\": 5959.0}, {\"date\": \"2020-03-28T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 26676, \"intensive_care\": 3856, \"total_hospitalised\": 30532, \"home_confinement\": 39533, \"total_current_positive\": 70065, \"new_current_positive\": 3651, \"recovered\": 12384, \"dead\": 10023, \"total_cases\": 92472, \"tests\": 429526, \"New cases per day\": 5974.0}, {\"date\": \"2020-03-29T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 27386, \"intensive_care\": 3906, \"total_hospitalised\": 31292, \"home_confinement\": 42588, \"total_current_positive\": 73880, \"new_current_positive\": 3815, \"recovered\": 13030, \"dead\": 10779, \"total_cases\": 97689, \"tests\": 454030, \"New cases per day\": 5217.0}]}}, {\"mode\": \"vega-lite\"});\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 10}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"tests\", \"title\": \"Tests (blue)\"}}}, {\"mark\": {\"type\": \"point\", \"color\": \"orange\", \"filled\": true, \"opacity\": 1, \"size\": 100}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases\", \"title\": \"Cases (orange)\"}}}]}, {\"mark\": {\"type\": \"bar\", \"size\": 10}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"New cases per day\"}}}], \"data\": {\"name\": \"data-469d9a3356d65b3bf4fd7777ed05b486\"}, \"title\": \"Total and daily tests and cases nationwide\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-469d9a3356d65b3bf4fd7777ed05b486\": [{\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 101, \"intensive_care\": 26, \"total_hospitalised\": 127, \"home_confinement\": 94, \"total_current_positive\": 221, \"new_current_positive\": 221, \"recovered\": 1, \"dead\": 7, \"total_cases\": 229, \"tests\": 4324, \"New cases per day\": null}, {\"date\": \"2020-02-25T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 114, \"intensive_care\": 35, \"total_hospitalised\": 150, \"home_confinement\": 162, \"total_current_positive\": 311, \"new_current_positive\": 90, \"recovered\": 1, \"dead\": 10, \"total_cases\": 322, \"tests\": 8623, \"New cases per day\": 93.0}, {\"date\": \"2020-02-26T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 128, \"intensive_care\": 36, \"total_hospitalised\": 164, \"home_confinement\": 221, \"total_current_positive\": 385, \"new_current_positive\": 74, \"recovered\": 3, \"dead\": 12, \"total_cases\": 400, \"tests\": 9587, \"New cases per day\": 78.0}, {\"date\": \"2020-02-27T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 248, \"intensive_care\": 56, \"total_hospitalised\": 304, \"home_confinement\": 284, \"total_current_positive\": 588, \"new_current_positive\": 203, \"recovered\": 45, \"dead\": 17, \"total_cases\": 650, \"tests\": 12014, \"New cases per day\": 250.0}, {\"date\": \"2020-02-28T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 345, \"intensive_care\": 64, \"total_hospitalised\": 409, \"home_confinement\": 412, \"total_current_positive\": 821, \"new_current_positive\": 233, \"recovered\": 46, \"dead\": 21, \"total_cases\": 888, \"tests\": 15695, \"New cases per day\": 238.0}, {\"date\": \"2020-02-29T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 401, \"intensive_care\": 105, \"total_hospitalised\": 506, \"home_confinement\": 543, \"total_current_positive\": 1049, \"new_current_positive\": 228, \"recovered\": 50, \"dead\": 29, \"total_cases\": 1128, \"tests\": 18661, \"New cases per day\": 240.0}, {\"date\": \"2020-03-01T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 639, \"intensive_care\": 140, \"total_hospitalised\": 779, \"home_confinement\": 798, \"total_current_positive\": 1577, \"new_current_positive\": 528, \"recovered\": 83, \"dead\": 34, \"total_cases\": 1694, \"tests\": 21127, \"New cases per day\": 566.0}, {\"date\": \"2020-03-02T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 742, \"intensive_care\": 166, \"total_hospitalised\": 908, \"home_confinement\": 927, \"total_current_positive\": 1835, \"new_current_positive\": 258, \"recovered\": 149, \"dead\": 52, \"total_cases\": 2036, \"tests\": 23345, \"New cases per day\": 342.0}, {\"date\": \"2020-03-03T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 1034, \"intensive_care\": 229, \"total_hospitalised\": 1263, \"home_confinement\": 1000, \"total_current_positive\": 2263, \"new_current_positive\": 428, \"recovered\": 160, \"dead\": 79, \"total_cases\": 2502, \"tests\": 25856, \"New cases per day\": 466.0}, {\"date\": \"2020-03-04T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 1346, \"intensive_care\": 295, \"total_hospitalised\": 1641, \"home_confinement\": 1065, \"total_current_positive\": 2706, \"new_current_positive\": 443, \"recovered\": 276, \"dead\": 107, \"total_cases\": 3089, \"tests\": 29837, \"New cases per day\": 587.0}, {\"date\": \"2020-03-05T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 1790, \"intensive_care\": 351, \"total_hospitalised\": 2141, \"home_confinement\": 1155, \"total_current_positive\": 3296, \"new_current_positive\": 590, \"recovered\": 414, \"dead\": 148, \"total_cases\": 3858, \"tests\": 32362, \"New cases per day\": 769.0}, {\"date\": \"2020-03-06T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 2394, \"intensive_care\": 462, \"total_hospitalised\": 2856, \"home_confinement\": 1060, \"total_current_positive\": 3916, \"new_current_positive\": 620, \"recovered\": 523, \"dead\": 197, \"total_cases\": 4636, \"tests\": 36359, \"New cases per day\": 778.0}, {\"date\": \"2020-03-07T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 2651, \"intensive_care\": 567, \"total_hospitalised\": 3218, \"home_confinement\": 1843, \"total_current_positive\": 5061, \"new_current_positive\": 1145, \"recovered\": 589, \"dead\": 233, \"total_cases\": 5883, \"tests\": 42062, \"New cases per day\": 1247.0}, {\"date\": \"2020-03-08T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 3557, \"intensive_care\": 650, \"total_hospitalised\": 4207, \"home_confinement\": 2180, \"total_current_positive\": 6387, \"new_current_positive\": 1326, \"recovered\": 622, 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{\"date\": \"2020-03-28T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 576, \"intensive_care\": 123, \"total_hospitalised\": 699, \"home_confinement\": 1464, \"total_current_positive\": 2163, \"new_current_positive\": 166, \"recovered\": 267, \"dead\": 184, \"total_cases\": 2614, \"tests\": 14729, \"total_cases_100k\": 243.78051919468493, \"tests_100k\": 1373.620224643655, \"dead_100k\": 17.159761106282335}, {\"date\": \"2020-03-29T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 590, \"intensive_care\": 131, \"total_hospitalised\": 721, \"home_confinement\": 1606, \"total_current_positive\": 2327, \"new_current_positive\": 164, \"recovered\": 288, \"dead\": 193, \"total_cases\": 2808, \"tests\": 16087, \"total_cases_100k\": 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"</script>"
],
"text/plain": [
@@ -340,8 +341,8 @@
"base = alt.Chart(df_regions).encode(alt.X('date'))\n",
"death = base.mark_line(color='black').encode(alt.Y('dead', title='Deaths'))\n",
"total = base.mark_bar(color='orange', size=5).encode(alt.Y('total_cases', title=\"Total cases\")).properties(\n",
- " width=200,\n",
- " height=200)\n",
+ " width=150,\n",
+ " height=150)\n",
"totals = alt.layer(total, death)\n",
"chart = totals.facet(facet='region', \n",
" columns=5, \n",
@@ -363,10 +364,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-dd5c31e402ca49e787e5846e76187f9d\"></div>\n",
+ "<div id=\"altair-viz-16a607b068ee4387ad56c95f585147d0\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-dd5c31e402ca49e787e5846e76187f9d\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-16a607b068ee4387ad56c95f585147d0\");\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",
@@ -407,7 +408,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"data\": {\"name\": \"data-ad3f583db58caf31837f49afe6b50082\"}, \"facet\": {\"type\": \"nominal\", \"field\": \"region\"}, \"spec\": {\"layer\": [{\"mark\": {\"type\": \"bar\", \"color\": \"orange\", \"size\": 5}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases_100k\", \"title\": \"Total cases\"}}, \"height\": 200, \"width\": 200}, {\"mark\": {\"type\": \"line\", \"color\": \"black\"}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"dead_100k\", \"title\": \"Deaths\"}}}]}, \"align\": \"each\", \"columns\": 5, \"title\": \"Total cases (orange) and deaths (black) by region per 100k population\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-ad3f583db58caf31837f49afe6b50082\": [{\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"region\": \"Abruzzo\", \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_current_positive\": 0, \"new_current_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 5, \"total_cases_100k\": 0.0, \"tests_100k\": 0.3821312376237246, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 17, \"region\": \"Basilicata\", \"latitude\": 40.63947052, \"longitude\": 15.80514834, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_current_positive\": 0, \"new_current_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 0, \"total_cases_100k\": 0.0, \"tests_100k\": 0.0, \"dead_100k\": 0.0}, 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0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 12, \"region\": \"Lazio\", \"latitude\": 41.89277044, \"longitude\": 12.48366722, \"hospitalised_with_symptoms\": 1, \"intensive_care\": 1, \"total_hospitalised\": 2, \"home_confinement\": 0, \"total_current_positive\": 2, \"new_current_positive\": 2, \"recovered\": 1, \"dead\": 0, \"total_cases\": 3, \"tests\": 124, \"total_cases_100k\": 0.051028374838112484, \"tests_100k\": 2.1091728266419825, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 7, \"region\": \"Liguria\", \"latitude\": 44.41149315, \"longitude\": 8.9326992, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_current_positive\": 0, \"new_current_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 1, \"total_cases_100k\": 0.0, \"tests_100k\": 0.06448950110921942, \"dead_100k\": 0.0}, {\"date\": 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{\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 14, \"region\": \"Molise\", \"latitude\": 41.55774754, \"longitude\": 14.65916051, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_current_positive\": 0, \"new_current_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 0, \"total_cases_100k\": 0.0, \"tests_100k\": 0.0, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 1, \"region\": \"Piemonte\", \"latitude\": 45.0732745, \"longitude\": 7.680687483, \"hospitalised_with_symptoms\": 2, \"intensive_care\": 0, \"total_hospitalised\": 2, \"home_confinement\": 1, \"total_current_positive\": 3, \"new_current_positive\": 3, \"recovered\": 0, \"dead\": 0, \"total_cases\": 3, \"tests\": 141, \"total_cases_100k\": 0.0688641049525687, \"tests_100k\": 3.236612932770729, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 16, \"region\": \"Puglia\", \"latitude\": 41.12559576, \"longitude\": 16.86736689, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_current_positive\": 0, \"new_current_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 0, \"total_cases_100k\": 0.0, \"tests_100k\": 0.0, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 20, \"region\": \"Sardegna\", \"latitude\": 39.21531192, \"longitude\": 9.110616306, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_current_positive\": 0, \"new_current_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 1, \"total_cases_100k\": 0.0, \"tests_100k\": 0.06099082027164091, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 19, 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{\"date\": \"2020-03-15T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 123, \"intensive_care\": 23, \"total_hospitalised\": 146, \"home_confinement\": 420, \"total_current_positive\": 566, \"new_current_positive\": 197, \"recovered\": 5, \"dead\": 11, \"total_cases\": 582, \"tests\": 2503, \"total_cases_100k\": 54.277070455740876, \"tests_100k\": 233.42870678817766, \"dead_100k\": 1.0258552835277484}, {\"date\": \"2020-03-16T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 126, \"intensive_care\": 30, \"total_hospitalised\": 156, \"home_confinement\": 446, \"total_current_positive\": 602, \"new_current_positive\": 36, \"recovered\": 5, \"dead\": 12, \"total_cases\": 619, \"tests\": 2746, \"total_cases_100k\": 57.7276745912433, 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{\"date\": \"2020-03-28T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 576, \"intensive_care\": 123, \"total_hospitalised\": 699, \"home_confinement\": 1464, \"total_current_positive\": 2163, \"new_current_positive\": 166, \"recovered\": 267, \"dead\": 184, \"total_cases\": 2614, \"tests\": 14729, \"total_cases_100k\": 243.78051919468493, \"tests_100k\": 1373.620224643655, \"dead_100k\": 17.159761106282335}, {\"date\": \"2020-03-29T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 590, \"intensive_care\": 131, \"total_hospitalised\": 721, \"home_confinement\": 1606, \"total_current_positive\": 2327, \"new_current_positive\": 164, \"recovered\": 288, \"dead\": 193, \"total_cases\": 2808, \"tests\": 16087, \"total_cases_100k\": 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"</script>"
],
"text/plain": [
@@ -442,8 +443,8 @@
"base = alt.Chart(df_regions).encode(alt.X('date'))\n",
"death = base.mark_line(color='black').encode(alt.Y('dead_100k', title='Deaths'))\n",
"total = base.mark_bar(color='orange', size=5).encode(alt.Y('total_cases_100k', title=\"Total cases\")).properties(\n",
- " width=200,\n",
- " height=200)\n",
+ " width=150,\n",
+ " height=150)\n",
"totals = alt.layer(total, death)\n",
"chart = totals.facet(facet='region', \n",
" columns=5, \n",
@@ -477,10 +478,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-302cda8eab454dc0a453fca37f0968a3\"></div>\n",
+ "<div id=\"altair-viz-ca04680f37484d38a337525fdcd8380a\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-302cda8eab454dc0a453fca37f0968a3\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-ca04680f37484d38a337525fdcd8380a\");\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",
@@ -521,7 +522,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"data\": {\"name\": \"data-fa1eaeb9d63b2afbbe8a4ae16ad313bd\"}, \"facet\": {\"type\": \"nominal\", \"field\": \"region\"}, \"spec\": {\"layer\": [{\"mark\": {\"type\": \"bar\", \"color\": \"orange\"}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases_diff\", \"title\": \"N\"}}, \"height\": 200, \"width\": 200}, {\"mark\": {\"type\": \"line\", \"color\": \"black\"}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"dead_diff\"}}, \"height\": 200, \"width\": 200}]}, \"align\": \"each\", \"columns\": 5, \"title\": \"Daily new cases (orange) and deaths (black) by region\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-fa1eaeb9d63b2afbbe8a4ae16ad313bd\": [{\"region\": 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\"intensive_care\": 8, \"total_hospitalised\": 24, \"home_confinement\": 45, \"total_current_positive\": 69, \"new_current_positive\": 27, \"recovered\": 0, \"dead\": 2, \"total_cases\": 71, \"tests\": 4900, \"total_cases_100k\": 1.4410924048747082, \"tests_100k\": 99.45567301247986, \"dead_100k\": 0.04059415224999178, \"total_cases_diff\": 28.0, \"dead_diff\": 1.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-25T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 12, \"intensive_care\": 7, \"total_hospitalised\": 19, \"home_confinement\": 23, \"total_current_positive\": 42, \"new_current_positive\": 10, \"recovered\": 0, \"dead\": 1, \"total_cases\": 43, \"tests\": 3780, \"total_cases_100k\": 0.8727742733748233, \"tests_100k\": 76.72294775248447, \"dead_100k\": 0.02029707612499589, \"total_cases_diff\": 10.0, \"dead_diff\": 0.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 12, \"intensive_care\": 4, \"total_hospitalised\": 16, \"home_confinement\": 16, \"total_current_positive\": 32, \"new_current_positive\": 32, \"recovered\": 0, \"dead\": 1, \"total_cases\": 33, \"tests\": 2200, \"total_cases_100k\": 0.6698035121248644, \"tests_100k\": 44.65356747499096, \"dead_100k\": 0.02029707612499589, \"total_cases_diff\": null, \"dead_diff\": null}]}}, {\"mode\": \"vega-lite\"});\n",
"</script>"
],
"text/plain": [
@@ -553,8 +554,8 @@
"source": [
"# make the daily charts\n",
"base = alt.Chart(tdf_diff).encode(alt.X('date')).properties(\n",
- " width=200,\n",
- " height=200,\n",
+ " width=150,\n",
+ " height=150,\n",
")\n",
"daily_new = base.mark_bar(color='orange').encode(alt.Y('total_cases_diff', title='N'))\n",
"daily_dead = base.mark_line(color='black').encode(alt.Y('dead_diff'))\n",
@@ -569,6 +570,217 @@
"display(chart)\n",
"display(html_credits)"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Rates of growth\n",
+ "\n",
+ "How quickly is the infection spreading? The charts below show data for all of the regions of Italy framed by some illustrative guiding lines to give an idea of how the rate of infection is evolving. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-b45b745dcba14e69a75cf93b76249f5b\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-b45b745dcba14e69a75cf93b76249f5b\");\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",
+ " .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",
+ " }\n",
+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"layer\": [{\"data\": {\"name\": \"data-3a642d6fd66161f771384604e4a0e040\"}, \"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"region\", \"legend\": {\"title\": \"Region\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector001\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"region\", \"title\": \"Region\"}, {\"type\": \"quantitative\", \"field\": \"total_cases\", \"title\": \"Cases\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"quantitative\", \"axis\": {\"title\": \"Days since 100th case\"}, \"field\": \"sinceDay0\"}, \"y\": {\"type\": \"quantitative\", \"axis\": {\"title\": \"Cumulative cases\"}, \"field\": \"total_cases\", \"scale\": {\"type\": \"log\"}}}, \"height\": 450, \"selection\": {\"selector001\": {\"type\": \"multi\", \"fields\": [\"region\"], \"bind\": \"legend\"}}, \"title\": \"Italy: total cases since 100th case\", \"width\": 450}, {\"layer\": [{\"data\": {\"name\": \"data-c37b0600efa89cfc8e618f4bf8a6529f\"}, \"mark\": {\"type\": \"line\", \"clip\": true, \"opacity\": 0.2}, \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"doubling period\"}, \"x\": {\"type\": \"quantitative\", \"field\": \"day\", \"scale\": {\"domain\": [1, 40]}}, \"y\": {\"type\": \"quantitative\", \"field\": \"case\", \"scale\": {\"domain\": [100, 50000]}}}}, {\"data\": {\"name\": \"data-aa59bf214a8c09741dbfe3c84b0574e7\"}, \"mark\": {\"type\": \"text\", \"align\": \"right\", \"baseline\": \"bottom\", \"dx\": 0, \"opacity\": 0.5, \"size\": 15}, \"encoding\": {\"text\": {\"type\": \"nominal\", \"field\": \"labelText\"}, \"x\": {\"type\": \"quantitative\", \"field\": \"labelX\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"labelY\"}}}]}], \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": 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{\"index\": 34, \"day\": 34, \"case\": 2898.3157256445006, \"doubling period\": \"every week\"}, {\"index\": 35, \"day\": 35, \"case\": 3200.0, \"doubling period\": \"every week\"}, {\"index\": 36, \"day\": 36, \"case\": 3533.0864437562004, \"doubling period\": \"every week\"}, {\"index\": 37, \"day\": 37, \"case\": 3900.843693454321, \"doubling period\": \"every week\"}, {\"index\": 38, \"day\": 38, \"case\": 4306.88061642354, \"doubling period\": \"every week\"}, {\"index\": 39, \"day\": 39, \"case\": 4755.181725238234, \"doubling period\": \"every week\"}, {\"index\": 40, \"day\": 40, \"case\": 5250.146278448883, \"doubling period\": \"every week\"}], \"data-aa59bf214a8c09741dbfe3c84b0574e7\": [{\"labelX\": 12, \"labelY\": 50000, \"labelText\": \"doubles every day\"}, {\"labelX\": 35, \"labelY\": 70000, \"labelText\": \"doubles every 3 days\"}, {\"labelX\": 40, \"labelY\": 2000, \"labelText\": \"doubles every week\"}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 15,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "since_100th_case = helper.make_since_df(df_regions, column='total_cases', region_column='region')\n",
+ "\n",
+ "base = alt.Chart(since_100th_case, title=\"Italy: total cases since 100th case\").mark_line(interpolate='basis')\n",
+ "\n",
+ "lineChart = plotting.make_region_since_chart(\n",
+ " base,\n",
+ " 'total_cases',\n",
+ " 'sinceDay0',\n",
+ " 'region',\n",
+ " 'Days since 100th case',\n",
+ " 'Cumulative cases', \n",
+ " 'Cases',\n",
+ " 'Region'\n",
+ ").properties(\n",
+ " width=450,\n",
+ " height=450\n",
+ ")\n",
+ "\n",
+ "lineChart + plotting.make_rule_chart(max_case=50000, max_days=40, pos_day=(12,50000), pos_3days=(35,70000), pos_week=(40,2000))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-0f415258007d4cdca8193448c0e93b1a\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-0f415258007d4cdca8193448c0e93b1a\");\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",
+ " .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",
+ " }\n",
+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"layer\": [{\"data\": {\"name\": \"data-98a9722b5b09c454fbe481c131fe0e3b\"}, \"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"region\", \"legend\": {\"title\": \"Region\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector002\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"region\", \"title\": \"Region\"}, {\"type\": \"quantitative\", \"field\": \"dead\", \"title\": \"Deaths\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"quantitative\", \"axis\": {\"title\": \"Days since 10th death\"}, \"field\": \"sinceDay0\"}, \"y\": {\"type\": \"quantitative\", \"axis\": {\"title\": \"Cumulative deaths\"}, \"field\": \"dead\", \"scale\": {\"type\": \"log\"}}}, \"height\": 450, \"selection\": {\"selector002\": {\"type\": \"multi\", \"fields\": [\"region\"], \"bind\": \"legend\"}}, \"title\": \"Italy: total deaths since 10th death\", \"width\": 450}, {\"layer\": [{\"data\": {\"name\": \"data-e6a039ecd947cfb0fd9bc1afc28ed1fb\"}, \"mark\": {\"type\": \"line\", \"clip\": true, \"opacity\": 0.2}, \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"doubling period\"}, \"x\": {\"type\": \"quantitative\", \"field\": \"day\", \"scale\": {\"domain\": [1, 40]}}, \"y\": {\"type\": \"quantitative\", \"field\": \"case\", \"scale\": {\"domain\": [10, 50000]}}}}, {\"data\": {\"name\": \"data-8aca84b2cb38af04a943b70d0d659a8e\"}, \"mark\": {\"type\": \"text\", \"align\": \"right\", \"baseline\": \"bottom\", \"dx\": 0, \"opacity\": 0.5, \"size\": 15}, \"encoding\": {\"text\": {\"type\": \"nominal\", \"field\": \"labelText\"}, \"x\": {\"type\": \"quantitative\", \"field\": \"labelX\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"labelY\"}}}]}], \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-98a9722b5b09c454fbe481c131fe0e3b\": 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{\"index\": 32, \"day\": 32, \"case\": 237.7590862619117, \"doubling period\": \"every week\"}, {\"index\": 33, \"day\": 33, \"case\": 262.50731392244415, \"doubling period\": \"every week\"}, {\"index\": 34, \"day\": 34, \"case\": 289.83157256445, \"doubling period\": \"every week\"}, {\"index\": 35, \"day\": 35, \"case\": 320.0, \"doubling period\": \"every week\"}, {\"index\": 36, \"day\": 36, \"case\": 353.3086443756201, \"doubling period\": \"every week\"}, {\"index\": 37, \"day\": 37, \"case\": 390.08436934543215, \"doubling period\": \"every week\"}, {\"index\": 38, \"day\": 38, \"case\": 430.68806164235406, \"doubling period\": \"every week\"}, {\"index\": 39, \"day\": 39, \"case\": 475.5181725238234, \"doubling period\": \"every week\"}, {\"index\": 40, \"day\": 40, \"case\": 525.0146278448883, \"doubling period\": \"every week\"}], \"data-8aca84b2cb38af04a943b70d0d659a8e\": [{\"labelX\": 12, \"labelY\": 50000, \"labelText\": \"doubles every day\"}, {\"labelX\": 35, \"labelY\": 20000, \"labelText\": \"doubles every 3 days\"}, {\"labelX\": 40, \"labelY\": 100, \"labelText\": \"doubles every week\"}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "since_10th_death = helper.make_since_df(df_regions, start_case=10, column='dead', region_column='region')\n",
+ "\n",
+ "base = alt.Chart(since_10th_death, title=\"Italy: total deaths since 10th death\")\n",
+ "lineChart = plotting.make_region_since_chart(\n",
+ " base,\n",
+ " 'dead',\n",
+ " 'sinceDay0',\n",
+ " 'region',\n",
+ " 'Days since 10th death',\n",
+ " 'Cumulative deaths', \n",
+ " 'Deaths',\n",
+ " 'Region'\n",
+ ").properties(\n",
+ " width=450,\n",
+ " height=450\n",
+ ")\n",
+ "\n",
+ "rule_chart = plotting.make_rule_chart(\n",
+ " start_case=10, \n",
+ " max_case=50000, \n",
+ " max_days=40, \n",
+ " pos_day=(12,50000), \n",
+ " pos_3days=(35,20000), \n",
+ " pos_week=(40,100)) \n",
+ "\n",
+ "lineChart + rule_chart"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {
diff --git a/notebooks/openzh-covid-19-dashboard.ipynb b/notebooks/openzh-covid-19-dashboard.ipynb
index 075f70f..7a3fe57 100644
--- a/notebooks/openzh-covid-19-dashboard.ipynb
+++ b/notebooks/openzh-covid-19-dashboard.ipynb
@@ -2,7 +2,17 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "%load_ext autoreload\n",
+ "%autoreload 2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
"metadata": {
"jupyter": {
"source_hidden": true
@@ -19,7 +29,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 3,
"metadata": {
"jupyter": {
"source_hidden": true
@@ -36,7 +46,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 4,
"metadata": {
"jupyter": {
"source_hidden": true
@@ -67,7 +77,7 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 5,
"metadata": {
"jupyter": {
"source_hidden": true
@@ -88,7 +98,7 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 6,
"metadata": {
"jupyter": {
"source_hidden": true
@@ -97,57 +107,16 @@
"outputs": [],
"source": [
"# read in population data\n",
- "df_pop = pd.read_excel(\n",
- " Path(data_path) / '../ch-population-statistics/ch-population-by-age-canton.xls', \n",
- " header=1, \n",
- " skipfooter=5\n",
- ")\n",
- "df_pop = df_pop.where(\n",
- " df_pop.Region.str.startswith('-')\n",
- ").dropna().sort_values('Region').reset_index(drop=True)\n",
+ "from covid_19_dashboard import helper, plotting\n",
"\n",
- "# match the cantons in the two datasets\n",
- "df_pop['abbreviation_canton_and_fl'] = ['AG', 'AI', 'AR', 'BL', 'BS', 'BE', 'FR', 'GE', 'GL', 'GR', 'JU', 'LU', 'NE', 'NW', 'OW', 'SH', 'SZ', 'SO', 'SG', 'TG', 'TI', 'UR', 'VS', 'VD', 'ZG', 'ZH']\n",
- "\n",
- "pop_d = df_pop[['abbreviation_canton_and_fl', 'Total']].set_index('abbreviation_canton_and_fl').to_dict()\n",
- "\n",
- "\n",
- "# calculate cases and deaths per 10k\n",
+ "population = {key[3:]: value for (key,value) in helper.get_region_populations('CHE').items()}\n",
"\n",
"for x in ['conf', 'deceased']:\n",
- " df[f'ncumul_{x}_10k'] = df.apply(\n",
- " lambda row: row[f'ncumul_{x}']/pop_d['Total'][row.abbreviation_canton_and_fl]*10000, axis=1\n",
+ " df[f'ncumul_{x}_100k'] = df.apply(\n",
+ " lambda row: row[f'ncumul_{x}']/population[row.abbreviation_canton_and_fl]*100000, axis=1\n",
" )"
]
},
- {
- "cell_type": "code",
- "execution_count": 10,
- "metadata": {
- "jupyter": {
- "source_hidden": true
- }
- },
- "outputs": [],
- "source": [
- "def generate_canton_chart(column, title, tooltip_title):\n",
- " \"\"\"Produce a canton chart given a column name\"\"\"\n",
- " selection = alt.selection_multi(fields=['abbreviation_canton_and_fl'], bind='legend')\n",
- " chart = base.mark_line().encode(\n",
- " alt.X('date', title='Date'), \n",
- " alt.Y(column, \n",
- " title=title, scale=alt.Scale(type='linear')),\n",
- " color=alt.Color('abbreviation_canton_and_fl', legend=alt.Legend(title=\"Canton\")),\n",
- " tooltip=[alt.Tooltip('abbreviation_canton_and_fl',title='Canton'),\n",
- " alt.Tooltip(column,title=tooltip_title),\n",
- " alt.Tooltip('date',title='Date')],\n",
- " opacity=alt.condition(selection, alt.value(1), alt.value(0.2))\n",
- " ).add_selection(\n",
- " selection\n",
- " )\n",
- " return chart"
- ]
- },
{
"cell_type": "markdown",
"metadata": {},
@@ -157,7 +126,7 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 7,
"metadata": {
"jupyter": {
"source_hidden": true
@@ -168,10 +137,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-5771810cda31478ba62c12691bb8a3cf\"></div>\n",
+ "<div id=\"altair-viz-0e82592a43b94700a9f153cfd4ba6544\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-5771810cda31478ba62c12691bb8a3cf\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-0e82592a43b94700a9f153cfd4ba6544\");\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",
@@ -212,7 +181,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector001\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"title\": \"Cases\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Cases\"}}, \"selection\": {\"selector001\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}, {\"mark\": \"line\", \"encoding\": 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55.74481263549086, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-26T00:00:00\", \"time\": \"18:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 11.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 68.13254877671105, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-27T00:00:00\", \"time\": \"18:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 12.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 74.32641684732116, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-28T00:00:00\", \"time\": \"18:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 13.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 80.52028491793125, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-30T00:00:00\", \"time\": \"12:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 14.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 86.71415298854134, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-01T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 0.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.suedostschweiz.ch/ereignisse/2020-03-02/kantone-gehen-unterschiedlich-mit-dem-corona-virus-um\", \"TotalPosTests1\": null, 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\"ncumul_deceased\": null, \"source\": \"https://www.suedostschweiz.ch/ereignisse/2020-03-20/die-zahl-der-corona-faelle-im-glarnerland-steigt-stark-an\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 42.076083459149075, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-22T00:00:00\", \"time\": \"13:30\", \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 31.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.gl.ch/verwaltung/finanzen-und-gesundheit/gesundheit/coronavirus.html/4817#Fallzahlen\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 76.72697571962478, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-24T00:00:00\", \"time\": 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"</script>"
],
"text/plain": [
@@ -243,15 +212,28 @@
}
],
"source": [
- "base = alt.Chart(df.where(df.ncumul_conf>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
+ "base = alt.Chart(df)\n",
"base.configure_header(titleFontSize=25)\n",
"base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
"\n",
- "cumul = generate_canton_chart('ncumul_conf', 'Cases', 'Cases')\n",
- "cumul_10k = generate_canton_chart('ncumul_conf_10k', 'Cases per 10k population', 'Cases/10k')\n",
+ "# cumul = generate_canton_chart(base, 'ncumul_conf', 'Cases', 'Cases')\n",
+ "cumul = plotting.generate_region_chart(\n",
+ " base, \n",
+ " column='ncumul_conf', \n",
+ " region_column='abbreviation_canton_and_fl',\n",
+ " ytitle='Cases', \n",
+ " legend_title='Canton',\n",
+ " tooltip_title='Cases')\n",
+ "cumul_100k = plotting.generate_region_chart(\n",
+ " base, \n",
+ " column='ncumul_conf_100k', \n",
+ " region_column='abbreviation_canton_and_fl',\n",
+ " ytitle='Cases per 100k population', \n",
+ " legend_title='Canton',\n",
+ " tooltip_title='Cases/100k')\n",
"\n",
"chart = alt.hconcat(\n",
- " cumul, cumul_10k, title='Covid-19 cases in Switzerland by Canton'\n",
+ " cumul, cumul_100k, title='Covid-19 cases in Switzerland by Canton'\n",
").configure_title(\n",
" anchor='middle'\n",
")\n",
@@ -272,7 +254,7 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 8,
"metadata": {
"jupyter": {
"source_hidden": true
@@ -283,10 +265,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-104a418bbf5146d09c3630e163c6956f\"></div>\n",
+ "<div id=\"altair-viz-325c8436249b4e13948e2223ab7b8055\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-104a418bbf5146d09c3630e163c6956f\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-325c8436249b4e13948e2223ab7b8055\");\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",
@@ -327,7 +309,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector003\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_deceased\", \"title\": \"Deaths\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_deceased\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Deaths\"}}, \"selection\": {\"selector003\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}, {\"mark\": \"line\", 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\"abbreviation_canton_and_fl\": \"GR\", \"ncumul_tested\": null, \"ncumul_conf\": 497.0, \"ncumul_hosp\": 63.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 12.0, \"source\": \"https://www.gr.ch/DE/institutionen/verwaltung/djsg/ga/coronavirus/info/Seiten/Start.aspx\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 250.53055010863045, \"ncumul_deceased_100k\": 6.049027366807978}, {\"date\": \"2020-03-14T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 2.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/aktuelles/erste-bestaetigte-coronavirus-faelle-auch-in-innerrhoden\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 12.387736141220191, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-16T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 4.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"Kantonaler F\\u00fchrungsstab Appenzell Innerrhoden\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 24.775472282440383, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-17T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 5.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"Kantonaler F\\u00fchrungsstab Appenzell Innerrhoden\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 30.96934035305048, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-19T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 6.0, \"ncumul_hosp\": 1.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"Kantonaler F\\u00fchrungsstab Appenzell Innerrhoden\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 37.16320842366058, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-24T00:00:00\", \"time\": \"17:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 8.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 49.550944564880766, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-25T00:00:00\", \"time\": \"17:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 9.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 55.74481263549086, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-26T00:00:00\", \"time\": \"18:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 11.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 68.13254877671105, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-27T00:00:00\", \"time\": \"18:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 12.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 74.32641684732116, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-28T00:00:00\", \"time\": \"18:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 13.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 80.52028491793125, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-30T00:00:00\", \"time\": \"12:00\", \"abbreviation_canton_and_fl\": \"AI\", \"ncumul_tested\": null, \"ncumul_conf\": 14.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.ai.ch/themen/gesundheit-alter-und-soziales/gesundheitsfoerderung-und-praevention/uebertragbare-krankheiten/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 86.71415298854134, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-01T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 0.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.suedostschweiz.ch/ereignisse/2020-03-02/kantone-gehen-unterschiedlich-mit-dem-corona-virus-um\", \"TotalPosTests1\": null, 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\"ncumul_deceased\": null, \"source\": \"https://www.suedostschweiz.ch/ereignisse/2020-03-20/die-zahl-der-corona-faelle-im-glarnerland-steigt-stark-an\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 42.076083459149075, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-22T00:00:00\", \"time\": \"13:30\", \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 31.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.gl.ch/verwaltung/finanzen-und-gesundheit/gesundheit/coronavirus.html/4817#Fallzahlen\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 76.72697571962478, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-24T00:00:00\", \"time\": 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\"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 99.00254931564487, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-26T00:00:00\", \"time\": \"13:30\", \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 43.0, \"ncumul_hosp\": 2.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.gl.ch/verwaltung/finanzen-und-gesundheit/gesundheit/coronavirus.html/4817#Fallzahlen\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 106.42774051431824, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-27T00:00:00\", \"time\": \"13:30\", \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 44.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.gl.ch/verwaltung/finanzen-und-gesundheit/gesundheit/coronavirus.html/4817#Fallzahlen\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 108.90280424720937, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-28T00:00:00\", \"time\": \"13:30\", \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 47.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.gl.ch/verwaltung/finanzen-und-gesundheit/gesundheit/coronavirus.html/4817#Fallzahlen\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 116.32799544588272, \"ncumul_deceased_100k\": 2.475063732891122}, {\"date\": \"2020-03-30T00:00:00\", \"time\": \"13:30\", \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 50.0, \"ncumul_hosp\": 1.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.gl.ch/verwaltung/finanzen-und-gesundheit/gesundheit/coronavirus.html/4817#Fallzahlen\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 123.7531866445561, \"ncumul_deceased_100k\": 2.475063732891122}]}}, {\"mode\": \"vega-lite\"});\n",
"</script>"
],
"text/plain": [
@@ -358,12 +340,26 @@
}
],
"source": [
- "base = alt.Chart(df.where(df.ncumul_deceased>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
+ "base = alt.Chart(df)\n",
"base.configure_header(titleFontSize=25)\n",
"base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
"\n",
- "deaths = generate_canton_chart('ncumul_deceased', 'Deaths', 'Deaths')\n",
- "deaths_10k = generate_canton_chart('ncumul_deceased_10k', 'Deaths per 10k population', 'Deaths/10k')\n",
+ "deaths = plotting.generate_region_chart(\n",
+ " base, \n",
+ " column='ncumul_deceased', \n",
+ " region_column='abbreviation_canton_and_fl',\n",
+ " ytitle='Deaths', \n",
+ " tooltip_title='Deaths',\n",
+ " legend_title='Canton'\n",
+ ")\n",
+ "deaths_10k = plotting.generate_region_chart(\n",
+ " base, \n",
+ " column='ncumul_deceased_100k', \n",
+ " region_column='abbreviation_canton_and_fl',\n",
+ " ytitle='Deaths per 10k population', \n",
+ " tooltip_title='Deaths/100k',\n",
+ " legend_title='Canton'\n",
+ ")\n",
"\n",
"chart = alt.hconcat(\n",
" deaths, deaths_10k, title='Covid-19 deaths in Switzerland by Canton'\n",
@@ -376,6 +372,193 @@
"if save_figures:\n",
" chart.save(str(Path(figures_path) / 'switzerland-deaths-by-canton.html'))\n"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-b2da12acdfda4c739d02eecd67f9100c\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-b2da12acdfda4c739d02eecd67f9100c\");\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",
+ " .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",
+ " }\n",
+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
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\"labelY\": 8000, \"labelText\": \"doubles every 3 days\"}, {\"labelX\": 20, \"labelY\": 300, \"labelText\": \"doubles every week\"}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "since_100th_case = helper.make_since_df(df, 'ncumul_conf', 'abbreviation_canton_and_fl')\n",
+ "\n",
+ "base = alt.Chart(since_100th_case, title=\"Switzerland: total cases since 100th case\").encode(alt.Y(scale=alt.Scale(type='log')))\n",
+ "\n",
+ "lineChart = plotting.make_region_since_chart(\n",
+ " base, \n",
+ " 'ncumul_conf', \n",
+ " 'sinceDay0', \n",
+ " 'abbreviation_canton_and_fl', \n",
+ " 'Days since 100th case',\n",
+ " 'Cumulative positive cases',\n",
+ " 'Cases',\n",
+ " 'Canton'\n",
+ ").properties(\n",
+ " width=450,\n",
+ " height=450\n",
+ ")\n",
+ "\n",
+ "\n",
+ "lineChart + plotting.make_rule_chart(max_days=20, pos_day=(9,5000), pos_3days=(19,8000))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
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\"ncumul_deceased\": 14.0, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 189.26894506548823, \"ncumul_deceased_100k\": 4.070299893881467, \"sinceDay0\": 3}, {\"index\": 26, \"date\": \"2020-03-26T00:00:00\", \"time\": \"15:00\", \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 715.0, \"ncumul_hosp\": 96.0, \"ncumul_ICU\": 11.0, \"ncumul_vent\": 9.0, \"ncumul_released\": null, \"ncumul_deceased\": 15.0, \"source\": \"https://www.vs.ch/de/web/coronavirus\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 207.87603029466064, \"ncumul_deceased_100k\": 4.361035600587287, \"sinceDay0\": 4}, {\"index\": 27, \"date\": \"2020-03-27T00:00:00\", \"time\": \"15:00\", \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 808.0, \"ncumul_hosp\": 104.0, \"ncumul_ICU\": 15.0, \"ncumul_vent\": 14.0, \"ncumul_released\": null, \"ncumul_deceased\": 20.0, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2027.03.2020.pdf\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 234.91445101830183, \"ncumul_deceased_100k\": 5.8147141341163815, \"sinceDay0\": 5}, {\"index\": 28, \"date\": \"2020-03-28T00:00:00\", \"time\": \"15:00\", \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 902.0, \"ncumul_hosp\": 110.0, \"ncumul_ICU\": 19.0, \"ncumul_vent\": 15.0, \"ncumul_released\": null, \"ncumul_deceased\": 21.0, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2028.03.2020.pdf\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 262.2436074486488, \"ncumul_deceased_100k\": 6.1054498408222, \"sinceDay0\": 6}, {\"index\": 29, \"date\": \"2020-03-29T00:00:00\", \"time\": \"15:00\", \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 964.0, \"ncumul_hosp\": 112.0, \"ncumul_ICU\": 23.0, \"ncumul_vent\": 14.0, \"ncumul_released\": null, \"ncumul_deceased\": 21.0, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2029.03.2020.pdf\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 280.26922126440957, \"ncumul_deceased_100k\": 6.1054498408222, \"sinceDay0\": 7}, {\"index\": 30, \"date\": \"2020-03-30T00:00:00\", \"time\": \"15:00\", \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 1000.0, \"ncumul_hosp\": 122.0, \"ncumul_ICU\": 21.0, \"ncumul_vent\": 16.0, \"ncumul_released\": null, \"ncumul_deceased\": 26.0, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2030.03.2020.pdf\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 290.7357067058191, \"ncumul_deceased_100k\": 7.559128374351295, \"sinceDay0\": 8}, {\"index\": 22, \"date\": \"2020-03-27T00:00:00\", \"time\": \"9:30\", \"abbreviation_canton_and_fl\": \"ZH\", \"ncumul_tested\": null, \"ncumul_conf\": 1578.0, \"ncumul_hosp\": 156.0, \"ncumul_ICU\": null, \"ncumul_vent\": 37.0, \"ncumul_released\": null, \"ncumul_deceased\": 11.0, \"source\": \"https://gd.zh.ch/internet/gesundheitsdirektion/de/themen/coronavirus.html#title-content-internet-gesundheitsdirektion-de-themen-coronavirus-jcr-content-contentPar-textimage_7\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 103.74971728530778, \"ncumul_deceased_100k\": 0.723223631266404, \"sinceDay0\": 0}, {\"index\": 23, \"date\": \"2020-03-28T00:00:00\", \"time\": \"14:00\", \"abbreviation_canton_and_fl\": \"ZH\", \"ncumul_tested\": null, \"ncumul_conf\": 1720.0, \"ncumul_hosp\": 187.0, \"ncumul_ICU\": null, \"ncumul_vent\": 42.0, \"ncumul_released\": null, \"ncumul_deceased\": 15.0, \"source\": \"https://gd.zh.ch/internet/gesundheitsdirektion/de/themen/coronavirus.html#title-content-internet-gesundheitsdirektion-de-themen-coronavirus-jcr-content-contentPar-textimage_7\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 113.08587688892862, \"ncumul_deceased_100k\": 0.9862140426360054, \"sinceDay0\": 1}, {\"index\": 24, \"date\": \"2020-03-29T00:00:00\", \"time\": \"14:00\", \"abbreviation_canton_and_fl\": \"ZH\", \"ncumul_tested\": null, \"ncumul_conf\": 1758.0, \"ncumul_hosp\": 194.0, \"ncumul_ICU\": null, \"ncumul_vent\": 46.0, \"ncumul_released\": null, \"ncumul_deceased\": 15.0, \"source\": \"https://gd.zh.ch/internet/gesundheitsdirektion/de/themen/coronavirus.html#title-content-internet-gesundheitsdirektion-de-themen-coronavirus-jcr-content-contentPar-textimage_7\", \"TotalPosTests1\": null, \"ninst_ICU_intub\": null, \"ncumul_ICF\": null, \"ncumul_deceased_suspect\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 115.58428579693985, \"ncumul_deceased_100k\": 0.9862140426360054, \"sinceDay0\": 2}, {\"index\": 25, \"date\": \"2020-03-30T00:00:00\", \"time\": \"17:00\", \"abbreviation_canton_and_fl\": \"ZH\", \"ncumul_tested\": null, 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\"day\": 18, \"case\": 59.43977156547795, \"doubling period\": \"every week\"}, {\"index\": 19, \"day\": 19, \"case\": 65.62682848061104, \"doubling period\": \"every week\"}, {\"index\": 20, \"day\": 20, \"case\": 72.45789314111254, \"doubling period\": \"every week\"}], \"data-693dc947621cd64b3e9caa057255ea5b\": [{\"labelX\": 6, \"labelY\": 200, \"labelText\": \"doubles every day\"}, {\"labelX\": 18, \"labelY\": 150, \"labelText\": \"doubles every 3 days\"}, {\"labelX\": 20, \"labelY\": 30, \"labelText\": \"doubles every week\"}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "since_10th_death = helper.make_since_df(\n",
+ " df, \n",
+ " column='ncumul_deceased', \n",
+ " region_column='abbreviation_canton_and_fl', \n",
+ " start_case=10\n",
+ ")\n",
+ "\n",
+ "base = alt.Chart(since_10th_death, title=\"Switzerland: total deaths since 10th death\")\n",
+ "lineChart = plotting.make_region_since_chart(\n",
+ " base,\n",
+ " 'ncumul_deceased',\n",
+ " 'sinceDay0',\n",
+ " 'abbreviation_canton_and_fl',\n",
+ " 'Days since 10th death',\n",
+ " 'Cumulative deaths', \n",
+ " 'Deaths',\n",
+ " 'Canton'\n",
+ ").properties(\n",
+ " width=450,\n",
+ " height=450\n",
+ ")\n",
+ "\n",
+ "rule_chart = plotting.make_rule_chart(\n",
+ " start_case=10, \n",
+ " max_case=200,\n",
+ " max_days=20, \n",
+ " pos_day=(6, 200),\n",
+ " pos_3days=(18, 150),\n",
+ " pos_week=(20,30)\n",
+ ") \n",
+ "lineChart + rule_chart"
+ ]
}
],
"metadata": {
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py
index 879186f..05deeed 100644
--- a/src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/helper.py
@@ -10,7 +10,7 @@ import os
def read_jhu_covid_df(ts_folder, name):
filename = os.path.join(ts_folder, f"time_series_covid19_{name}_global.csv")
df = pd.read_csv(filename)
- df = df.set_index(['Province/State', 'Country/Region', 'Lat', 'Long'])
+ df = df.set_index(["Province/State", "Country/Region", "Lat", "Long"])
df.columns = pd.to_datetime(df.columns)
return df
@@ -27,7 +27,7 @@ def read_jhu_frames_map(ts_folder):
def read_rates_covid_df(rates_folder, name):
filename = os.path.join(rates_folder, f"ts_rates_19-covid-{name}.csv")
df = pd.read_csv(filename).drop("Unnamed: 0", axis=1)
- df = df.set_index(['Country/Region'])
+ df = df.set_index(["Country/Region"])
df.columns = pd.to_datetime(df.columns)
return df
@@ -42,41 +42,56 @@ def read_rates_frames_map(rates_folder):
def read_geodata(geodata_path):
geodata_df = pd.read_csv(geodata_path)
- geodata_df = geodata_df.drop('Unnamed: 0', axis=1)
- geodata_df = geodata_df.rename({'name_jhu':'Country/Region'}, axis=1)
- geodata_df = geodata_df.set_index('Country/Region')
+ geodata_df = geodata_df.drop("Unnamed: 0", axis=1)
+ geodata_df = geodata_df.rename({"name_jhu": "Country/Region"}, axis=1)
+ geodata_df = geodata_df.set_index("Country/Region")
return geodata_df
def latest_jhu_country_ser(jhu_frames_map, name):
- return jhu_frames_map[name].iloc[:,-1].groupby(level='Country/Region').sum()
+ return jhu_frames_map[name].iloc[:, -1].groupby(level="Country/Region").sum()
def countries_with_number_of_cases(jhu_frames_map, name, count):
- case_count_ser = latest_jhu_country_ser(jhu_frames_map, 'confirmed')
+ case_count_ser = latest_jhu_country_ser(jhu_frames_map, "confirmed")
countries_over_thresh = case_count_ser[case_count_ser > count - 1].index
return countries_over_thresh
def latest_rates_ser(rates_frames_map, name):
- return rates_frames_map[name].iloc[:,-1]
+ return rates_frames_map[name].iloc[:, -1]
def compute_map_df(rates_frames_map, jhu_frames_map, geodata_df, countries_over_thresh):
- map_df = pd.concat([
- latest_rates_ser(rates_frames_map, 'confirmed'),
- latest_rates_ser(rates_frames_map, 'deaths')], axis=1)
- nominal_df = pd.concat([
- latest_jhu_country_ser(jhu_frames_map, 'confirmed'),
- latest_jhu_country_ser(jhu_frames_map, 'deaths')], axis=1)
- map_df = pd.concat([map_df, nominal_df, geodata_df[['Longitude', 'Latitude']]], axis=1)
+ map_df = pd.concat(
+ [
+ latest_rates_ser(rates_frames_map, "confirmed"),
+ latest_rates_ser(rates_frames_map, "deaths"),
+ ],
+ axis=1,
+ )
+ nominal_df = pd.concat(
+ [
+ latest_jhu_country_ser(jhu_frames_map, "confirmed"),
+ latest_jhu_country_ser(jhu_frames_map, "deaths"),
+ ],
+ axis=1,
+ )
+ map_df = pd.concat(
+ [map_df, nominal_df, geodata_df[["Longitude", "Latitude"]]], axis=1
+ )
# Restrict to countries with 100 or more cases
map_df = map_df.loc[countries_over_thresh].dropna()
map_df = map_df.reset_index()
- map_df.columns = ['Country/Region',
- 'Confirmed/100k', 'Deaths/100k',
- 'Confirmed', 'Deaths',
- 'Long', 'Lat']
+ map_df.columns = [
+ "Country/Region",
+ "Confirmed/100k",
+ "Deaths/100k",
+ "Confirmed",
+ "Deaths",
+ "Long",
+ "Lat",
+ ]
return map_df
@@ -86,41 +101,114 @@ def map_of_variable(map_df, variable, title):
graticule = alt.graticule()
# Source of land data
- source = alt.topo_feature(data.world_110m.url, 'countries')
+ source = alt.topo_feature(data.world_110m.url, "countries")
# Layering and configuring the components
- p = alt.layer(
- alt.Chart(sphere).mark_geoshape(fill='#cae6ef'),
- alt.Chart(graticule).mark_geoshape(stroke='white', strokeWidth=0.5),
- alt.Chart(source).mark_geoshape(fill='#dddddd', stroke='#aaaaaa'),
- alt.Chart(map_df).mark_circle(opacity=0.6).encode(
- longitude='Long:Q',
- latitude='Lat:Q',
- size=alt.Size(f'{variable}:Q', title="Cases"),
- color=alt.value('steelblue'),
- tooltip=["Country/Region:N",
- "Confirmed:Q", "Deaths:Q",
- "Confirmed/100k:Q", "Deaths/100k:Q"]
+ p = (
+ alt.layer(
+ alt.Chart(sphere).mark_geoshape(fill="#cae6ef"),
+ alt.Chart(graticule).mark_geoshape(stroke="white", strokeWidth=0.5),
+ alt.Chart(source).mark_geoshape(fill="#dddddd", stroke="#aaaaaa"),
+ alt.Chart(map_df)
+ .mark_circle(opacity=0.6)
+ .encode(
+ longitude="Long:Q",
+ latitude="Lat:Q",
+ size=alt.Size(f"{variable}:Q", title="Cases"),
+ color=alt.value("steelblue"),
+ tooltip=[
+ "Country/Region:N",
+ "Confirmed:Q",
+ "Deaths:Q",
+ "Confirmed/100k:Q",
+ "Deaths/100k:Q",
+ ],
+ ),
)
- ).project(
- 'naturalEarth1'
- ).properties(width=600, height=400, title=f"{title} cases per 100k inhabitants"
- ).configure_view(stroke=None)
+ .project("naturalEarth1")
+ .properties(width=600, height=400, title=f"{title} cases per 100k inhabitants")
+ .configure_view(stroke=None)
+ )
return p
def growth_df(rates_frames_map, geodata_df, name, countries_over_thresh, cutoff):
- latest_confirmed_ser = rates_frames_map['confirmed'].iloc[:,-1]
- countries_over_1 = latest_confirmed_ser[latest_confirmed_ser >= cutoff].reset_index()['Country/Region']
+ latest_confirmed_ser = rates_frames_map["confirmed"].iloc[:, -1]
+ countries_over_1 = latest_confirmed_ser[
+ latest_confirmed_ser >= cutoff
+ ].reset_index()["Country/Region"]
- confirmed_rate_df = rates_frames_map['confirmed']
+ confirmed_rate_df = rates_frames_map["confirmed"]
confirmed_rate_df = confirmed_rate_df.loc[
- confirmed_rate_df.index.isin(countries_over_1) &
- confirmed_rate_df.index.isin(countries_over_thresh)]
+ confirmed_rate_df.index.isin(countries_over_1)
+ & confirmed_rate_df.index.isin(countries_over_thresh)
+ ]
confirmed_rate_df = confirmed_rate_df.join(
- geodata_df[['Longitude', 'Latitude', 'region_un']]).set_index(
- ['Longitude', 'Latitude', 'region_un'], append=True)
+ geodata_df[["Longitude", "Latitude", "region_un"]]
+ ).set_index(["Longitude", "Latitude", "region_un"], append=True)
confirmed_rate_df = confirmed_rate_df.stack().reset_index()
confirmed_rate_df = confirmed_rate_df.rename(
- {'region_un': 'Geo Region', 'level_4': 'Date', 0: 'Confirmed/100k'}, axis=1)
+ {"region_un": "Geo Region", "level_4": "Date", 0: "Confirmed/100k"}, axis=1
+ )
return confirmed_rate_df
+
+
+def get_region_populations(country_iso3):
+ import sys
+ from SPARQLWrapper import SPARQLWrapper, JSON
+
+ endpoint_url = "https://query.wikidata.org/sparql"
+
+ query = """
+ SELECT DISTINCT ?population ?region_iso ?regionLabel
+ {{
+ # select country by its iso-3
+ ?country wdt:P298 "{country_iso3}" .
+ # region has an iso ?iso
+ ?region wdt:P300 ?region_iso .
+ # region has a population of ?population
+ ?region wdt:P1082 ?population .
+ # country contains region ?region
+ ?country wdt:P150 ?region .
+ # country is an instance of sovereign state
+ ?country wdt:P31 wd:Q3624078 .
+
+ SERVICE wikibase:label {{ bd:serviceParam wikibase:language "en" }}
+ }}
+ """
+
+ def get_results(endpoint_url, query):
+ user_agent = "WDQS-example Python/%s.%s" % (
+ sys.version_info[0],
+ sys.version_info[1],
+ )
+ # TODO adjust user agent; see https://w.wiki/CX6
+ sparql = SPARQLWrapper(endpoint_url, agent=user_agent)
+ sparql.setQuery(query)
+ sparql.setReturnFormat(JSON)
+ return sparql.query().convert()
+
+ results = get_results(endpoint_url, query.format(country_iso3=country_iso3))
+
+ return {
+ result["region_iso"]["value"]: int(result["population"]["value"])
+ for result in results["results"]["bindings"]
+ }
+
+
+def make_since_df(df, column="positive", region_column="state", start_case=100):
+ """Make dataframe shifted by date of case 100."""
+
+ # make dataframe with only points >=100 positives
+ since_df = df.loc[df[column] >= start_case]
+
+ # group since_df dataframe by region and then increasing order of date
+ since_df = since_df.sort_values(by=[region_column, "date"])
+ since_df = since_df.reset_index()
+
+ # add a column for the number of days since the 100th case for each state
+ for _, df in since_df.groupby(region_column):
+ since_df.loc[df.index, "sinceDay0"] = range(0, len(df))
+ since_df = since_df.astype({"sinceDay0": "int32"})
+
+ return since_df
\ No newline at end of file
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/plotting.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/plotting.py
new file mode 100644
index 0000000..87a977d
--- /dev/null
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/plotting.py
@@ -0,0 +1,163 @@
+"""Simple functions to help with common charts."""
+
+import altair as alt
+import pandas as pd
+
+
+def make_rule_chart(
+ start_case=100,
+ max_case=10000,
+ max_days=100,
+ pos_day=(9, 30000),
+ pos_3days=(28, 31000),
+ pos_week=(20, 300),
+):
+ """
+ Make dataframe with lines to indicate doubling every day, 3 days, week.
+
+ start_case: case starting point
+ max_case: maxium number of cases to plot
+ max_days: maximum number of days to show
+ pos_day: position of the "doubles every day" label
+ pos_3days: position of "doubles every three days" label
+ pos_week: position of "doubles every week" label
+ """
+ days = {"day": range(max_days + 1)}
+ logRuleDay_df = pd.DataFrame(days, columns=["day"])
+ logRuleDay_df["case"] = start_case * pow(2, logRuleDay_df["day"])
+ logRuleDay_df["doubling period"] = "every day"
+
+ logRule3Days_df = pd.DataFrame(days, columns=["day"])
+ logRule3Days_df["case"] = start_case * pow(2, (logRule3Days_df["day"]) / 3)
+ logRule3Days_df["doubling period"] = "three days"
+
+ logRuleWeek_df = pd.DataFrame(days, columns=["day"])
+ logRuleWeek_df["case"] = start_case * pow(2, (logRuleWeek_df["day"]) / 7)
+ logRuleWeek_df["doubling period"] = "every week"
+
+ logRules_df = pd.concat([logRuleDay_df, logRule3Days_df, logRuleWeek_df])
+ logRules_df = logRules_df.reset_index()
+
+ ruleChart = (
+ alt.Chart(logRules_df)
+ .mark_line(opacity=0.2, clip=True)
+ .encode(
+ alt.X("day:Q", scale=alt.Scale(domain=[1, max_days])),
+ alt.Y("case", scale=alt.Scale(domain=[start_case, max_case])),
+ color=alt.Color("doubling period")
+ )
+ )
+
+ # make dataframe for text labels on chart - hand edit these label locations
+ textLabels_df = pd.DataFrame(
+ [
+ [*pos_day, "doubles every day"],
+ [*pos_3days, "doubles every 3 days"],
+ [*pos_week, "doubles every week"],
+ ],
+ columns=["labelX", "labelY", "labelText"],
+ )
+
+ labelChart = (
+ alt.Chart(textLabels_df)
+ .mark_text(align="right", baseline="bottom", dx=0, size=15, opacity=0.5)
+ .encode(x="labelX", y="labelY", text="labelText")
+ )
+ return ruleChart + labelChart
+
+
+def generate_region_chart(
+ base,
+ column,
+ region_column,
+ ytitle,
+ tooltip_title,
+ legend_title=None,
+ scale_type="linear",
+):
+ """
+ Produce a regional chart given a column name.
+
+ base: chart base - create with alt.Chart()
+ column: name of column to use for y-axis
+ region_column: column to use for regions
+ ytitle: name of y-axis
+ tooltip_title: tooltip title for y-axis values
+ legend_title: legend title
+ scale_type: "linear" or "log"
+ """
+
+ if legend_title is None:
+ legend_title = region_column
+
+ color = alt.Color(region_column, legend=alt.Legend(title=legend_title))
+
+ selection = alt.selection_multi(fields=[region_column], bind="legend")
+ opacity = alt.condition(selection, alt.value(1), alt.value(0.2))
+
+ tooltip = [
+ alt.Tooltip(region_column, title=legend_title),
+ alt.Tooltip(column, title=tooltip_title),
+ alt.Tooltip("date", title="Date"),
+ ]
+ chart = (
+ base.mark_line()
+ .encode(
+ alt.X("date", title="Date"),
+ alt.Y(column, title=ytitle, scale=alt.Scale(type=scale_type)),
+ color=color,
+ opacity=opacity,
+ tooltip=tooltip,
+ )
+ .add_selection(selection)
+ )
+
+ return chart
+
+
+def make_region_since_chart(
+ base,
+ column,
+ time_column,
+ region_column,
+ xtitle,
+ ytitle,
+ tooltip_title,
+ legend_title,
+
+):
+ """
+ Make chart "days since X case".
+
+ base: chart base - create with alt.Chart()
+ column: name of column to use for y-axis
+ time_column: column that encodes the time since X case
+ region_column: column to use for regions
+ xtitle: as it says on the tin
+ ytitle: as it says on the tin
+ tooltip_title: as it says on the tin
+ legend_title: as it says on the tin
+ scale_type: "linear" or "log"
+ """
+
+ selection = alt.selection_multi(fields=[region_column], bind='legend')
+ opacity=alt.condition(selection, alt.value(1), alt.value(0.2))
+
+ lineChart = base.mark_line().encode(
+ alt.X(time_column,
+ axis=alt.Axis(title=xtitle)
+ ),
+ alt.Y(column,
+ axis = alt.Axis(title=ytitle),
+ scale=alt.Scale(type='log'),
+ ),
+ tooltip=[alt.Tooltip(region_column,title=legend_title),
+ alt.Tooltip(column,title=tooltip_title),
+ alt.Tooltip('date',title='Date')],
+ color = alt.Color(region_column, legend=alt.Legend(title=legend_title)),
+ opacity=opacity
+ ).add_selection(
+ selection
+ )
+
+ return lineChart
--
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