diff --git a/.renku/workflow/4cc7ffe9d5a045efb048ef2222a40ffa_papermill.cwl b/.renku/workflow/4cc7ffe9d5a045efb048ef2222a40ffa_papermill.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..1ca535dda41f95c17c85bc3c6cf2a2a7c67fb1ea
--- /dev/null
+++ b/.renku/workflow/4cc7ffe9d5a045efb048ef2222a40ffa_papermill.cwl
@@ -0,0 +1,113 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ inputBinding:
+ position: 1
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_2:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ inputBinding:
+ position: 2
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_3:
+ default: rates_folder
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_rates
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_5:
+ default: geodata_path
+ inputBinding:
+ position: 5
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_6:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ inputBinding:
+ position: 6
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_7:
+ default:
+ class: File
+ path: ../../notebooks/Dashboard.ipynb
+ inputBinding:
+ position: 7
+ prefix: --inject-paths
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_8:
+ default: runs/Dashboard.run.ipynb
+ inputBinding:
+ position: 8
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_8)
+ streamable: false
+ type: File
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: $(inputs.input_2)
+ entryname: data/covid-19_jhu-csse
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/covid-19_rates
+ writable: false
+ - entry: $(inputs.input_6)
+ entryname: data/geodata/geo_data.csv
+ writable: false
+ - entry: $(inputs.input_7)
+ entryname: notebooks/Dashboard.ipynb
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
index 190e010a7c08454474636230fddb9c678c05e4aa..97ed85143c3d9761aef8bb6b781fd8d2526c70b4 100644
--- a/runs/Dashboard.run.ipynb
+++ b/runs/Dashboard.run.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.318369,
- "end_time": "2020-03-13T17:58:07.699048",
+ "duration": 0.328323,
+ "end_time": "2020-03-15T16:37:29.576519",
"exception": false,
- "start_time": "2020-03-13T17:58:07.380679",
+ "start_time": "2020-03-15T16:37:29.248196",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.02116,
- "end_time": "2020-03-13T17:58:07.739632",
+ "duration": 0.023318,
+ "end_time": "2020-03-15T16:37:29.619560",
"exception": false,
- "start_time": "2020-03-13T17:58:07.718472",
+ "start_time": "2020-03-15T16:37:29.596242",
"status": "completed"
},
"tags": [
@@ -39,6 +39,7 @@
"source": [
"ts_folder = \"../data/covid-19_jhu-csse/\"\n",
"rates_folder = \"../data/covid-19_rates/\"\n",
+ "geodata_path = \"../data/geodata/geo_data.csv\"\n",
"out_folder = None\n",
"PAPERMILL_OUTPUT_PATH = None"
]
@@ -48,10 +49,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021777,
- "end_time": "2020-03-13T17:58:07.771101",
+ "duration": 0.021164,
+ "end_time": "2020-03-15T16:37:29.651150",
"exception": false,
- "start_time": "2020-03-13T17:58:07.749324",
+ "start_time": "2020-03-15T16:37:29.629986",
"status": "completed"
},
"tags": [
@@ -61,10 +62,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/ajs106te/notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"notebooks/Dashboard.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
- "ts_folder = \"/tmp/ajs106te/data/covid-19_jhu-csse\"\n",
- "rates_folder = \"/tmp/ajs106te/data/covid-19_rates\"\n"
+ "ts_folder = \"./data/covid-19_jhu-csse/\"\n",
+ "rates_folder = \"./data/covid-19_rates/\"\n",
+ "geodata_path = \"./data/geodata/geo_data.csv\"\n"
]
},
{
@@ -72,10 +74,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.020625,
- "end_time": "2020-03-13T17:58:07.801350",
+ "duration": 0.018422,
+ "end_time": "2020-03-15T16:37:29.679468",
"exception": false,
- "start_time": "2020-03-13T17:58:07.780725",
+ "start_time": "2020-03-15T16:37:29.661046",
"status": "completed"
},
"tags": []
@@ -90,10 +92,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.088499,
- "end_time": "2020-03-13T17:58:07.900202",
+ "duration": 0.081996,
+ "end_time": "2020-03-15T16:37:29.770910",
"exception": false,
- "start_time": "2020-03-13T17:58:07.811703",
+ "start_time": "2020-03-15T16:37:29.688914",
"status": "completed"
},
"tags": []
@@ -120,10 +122,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.046747,
- "end_time": "2020-03-13T17:58:07.960957",
+ "duration": 0.058057,
+ "end_time": "2020-03-15T16:37:29.848129",
"exception": false,
- "start_time": "2020-03-13T17:58:07.914210",
+ "start_time": "2020-03-15T16:37:29.790072",
"status": "completed"
},
"tags": []
@@ -150,17 +152,20 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.019568,
- "end_time": "2020-03-13T17:58:07.999627",
+ "duration": 0.032963,
+ "end_time": "2020-03-15T16:37:29.896281",
"exception": false,
- "start_time": "2020-03-13T17:58:07.980059",
+ "start_time": "2020-03-15T16:37:29.863318",
"status": "completed"
},
"tags": []
},
"outputs": [],
"source": [
- "# Compile data needed for the visualizations"
+ "geodata_df = pd.read_csv(geodata_path)\n",
+ "geodata_df = geodata_df.drop('Unnamed: 0', axis=1)\n",
+ "geodata_df = geodata_df.rename({'name_jhu':'Country/Region'}, axis=1)\n",
+ "geodata_df = geodata_df.set_index('Country/Region')"
]
},
{
@@ -168,30 +173,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.03619,
- "end_time": "2020-03-13T17:58:08.046674",
+ "duration": 0.03569,
+ "end_time": "2020-03-15T16:37:29.945698",
"exception": false,
- "start_time": "2020-03-13T17:58:08.010484",
- "status": "completed"
- },
- "tags": []
- },
- "outputs": [],
- "source": [
- "# Compute geospatial coordinates\n",
- "country_coords_df = jhu_frames_map['confirmed'].reset_index([2,3])[['Lat', 'Long']]\n",
- "country_coords_df = country_coords_df.groupby(level='Country/Region').mean()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 9,
- "metadata": {
- "papermill": {
- "duration": 0.036248,
- "end_time": "2020-03-13T17:58:08.099308",
- "exception": false,
- "start_time": "2020-03-13T17:58:08.063060",
+ "start_time": "2020-03-15T16:37:29.910008",
"status": "completed"
},
"tags": []
@@ -199,7 +184,11 @@
"outputs": [],
"source": [
"# Identify countries with 100 or more cases\n",
- "case_count_ser = jhu_frames_map['confirmed'].iloc[:,-1].groupby(level='Country/Region').sum()\n",
+ "def latest_jhu_country_ser(name):\n",
+ " return jhu_frames_map[name].iloc[:,-1].groupby(level='Country/Region').sum()\n",
+ "\n",
+ "\n",
+ "case_count_ser = latest_jhu_country_ser('confirmed')\n",
"countries_over_thresh = case_count_ser[case_count_ser > 99].index"
]
},
@@ -207,10 +196,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009486,
- "end_time": "2020-03-13T17:58:08.127085",
+ "duration": 0.008775,
+ "end_time": "2020-03-15T16:37:29.967726",
"exception": false,
- "start_time": "2020-03-13T17:58:08.117599",
+ "start_time": "2020-03-15T16:37:29.958951",
"status": "completed"
},
"tags": []
@@ -218,18 +207,20 @@
"source": [
"# Questions About COVID-19 and Its Spread\n",
"\n",
- "These plots should be taken with a large grain of salt. I am not an epidemiologist, so the analyses shown here are completely naive. There are large discrepencies in the data from different countries for a variety of reasons (rates of testing, demographics, etc.) so that make direct comparisons inaccurate. Nonetheless, I think there is a lot of interesting information in this data."
+ "Understanding the spread, distribution, and deadliness of COVID-19 is difficult, despite the data available about it. Differences in rates of testing, quality of data, demographics, etc. make it difficult to compare data between countries. \n",
+ "\n",
+ "All this needs to be considered when looking at the plots below. But despite those caveats, I found it helpful to plot the raw data, even though direct comparisons between countries might not be inaccurate."
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.043858,
- "end_time": "2020-03-13T17:58:08.178940",
+ "duration": 0.041164,
+ "end_time": "2020-03-15T16:37:30.016520",
"exception": false,
- "start_time": "2020-03-13T17:58:08.135082",
+ "start_time": "2020-03-15T16:37:29.975356",
"status": "completed"
},
"tags": []
@@ -238,7 +229,7 @@
{
"data": {
"text/html": [
- "<em>Data up to Mar 12 2020</em>"
+ "<em>Data up to Mar 13 2020; countries with 100 or more confirmed cases.</em>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
@@ -250,17 +241,17 @@
],
"source": [
"data_ts = jhu_frames_map['confirmed'].iloc[:,-1].name.strftime(\"%b %d %Y\")\n",
- "display(HTML(f\"<em>Data up to {data_ts}</em>\"))"
+ "display(HTML(f\"<em>Data up to {data_ts}; countries with 100 or more confirmed cases.</em>\"))"
]
},
{
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009732,
- "end_time": "2020-03-13T17:58:08.205403",
+ "duration": 0.008127,
+ "end_time": "2020-03-15T16:37:30.039436",
"exception": false,
- "start_time": "2020-03-13T17:58:08.195671",
+ "start_time": "2020-03-15T16:37:30.031309",
"status": "completed"
},
"tags": []
@@ -271,13 +262,13 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.215996,
- "end_time": "2020-03-13T17:58:08.429475",
+ "duration": 0.189114,
+ "end_time": "2020-03-15T16:37:30.236186",
"exception": false,
- "start_time": "2020-03-13T17:58:08.213479",
+ "start_time": "2020-03-15T16:37:30.047072",
"status": "completed"
},
"tags": []
@@ -290,47 +281,58 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.040087,
- "end_time": "2020-03-13T17:58:08.490379",
+ "duration": 0.046044,
+ "end_time": "2020-03-15T16:37:30.300949",
"exception": false,
- "start_time": "2020-03-13T17:58:08.450292",
+ "start_time": "2020-03-15T16:37:30.254905",
"status": "completed"
},
"tags": []
},
"outputs": [],
"source": [
+ "def latest_rates_ser(name):\n",
+ " return rates_frames_map[name].iloc[:,-1]\n",
+ "\n",
+ "\n",
"# Compile the basic df\n",
"map_df = pd.concat([\n",
- " rates_frames_map['confirmed'].iloc[:,-1],\n",
- " rates_frames_map['deaths'].iloc[:,-1],\n",
- " rates_frames_map['recovered'].iloc[:,-1],\n",
- " country_coords_df], axis=1)\n",
+ " latest_rates_ser('confirmed'),\n",
+ " latest_rates_ser('deaths'),\n",
+ " latest_rates_ser('recovered')], axis=1)\n",
+ "nominal_df = pd.concat([\n",
+ " latest_jhu_country_ser('confirmed'),\n",
+ " latest_jhu_country_ser('deaths'),\n",
+ " latest_jhu_country_ser('recovered')], axis=1)\n",
+ "map_df = pd.concat([map_df, nominal_df, geodata_df[['Longitude', 'Latitude']]], axis=1)\n",
"# Restrict to countries with 100 or more cases\n",
"map_df = map_df.loc[countries_over_thresh].dropna()\n",
"map_df = map_df.reset_index()\n",
- "map_df.columns = ['Country/Region', 'Confirmed', 'Deaths', 'Recovered', 'Lat', 'Long']"
+ "map_df.columns = ['Country/Region', \n",
+ " 'Confirmed/100k', 'Deaths/100k', 'Recovered/100k', \n",
+ " 'Confirmed', 'Deaths', 'Recovered',\n",
+ " 'Long', 'Lat']"
]
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 12,
"metadata": {
"papermill": {
- "duration": 0.034884,
- "end_time": "2020-03-13T17:58:08.543325",
+ "duration": 0.031175,
+ "end_time": "2020-03-15T16:37:30.349234",
"exception": false,
- "start_time": "2020-03-13T17:58:08.508441",
+ "start_time": "2020-03-15T16:37:30.318059",
"status": "completed"
},
"tags": []
},
"outputs": [],
"source": [
- "def map_of_variable(map_df, variable):\n",
+ "def map_of_variable(map_df, variable, title):\n",
" # Data generators for the background\n",
" sphere = alt.sphere()\n",
" graticule = alt.graticule()\n",
@@ -348,24 +350,26 @@
" latitude='Lat:Q',\n",
" size=alt.Size(f'{variable}:Q', title=\"Cases\"),\n",
" color=alt.value('steelblue'),\n",
- " tooltip=[\"Country/Region:N\", \"Confirmed:Q\", \"Deaths:Q\", \"Recovered:Q\"]\n",
+ " tooltip=[\"Country/Region:N\", \n",
+ " \"Confirmed:Q\", \"Deaths:Q\", \"Recovered:Q\",\n",
+ " \"Confirmed/100k:Q\", \"Deaths/100k:Q\", \"Recovered/100k:Q\"]\n",
" )\n",
" ).project(\n",
" 'naturalEarth1'\n",
- " ).properties(width=600, height=400, title=f\"{variable} cases per 100,000\"\n",
+ " ).properties(width=600, height=400, title=f\"{title} cases per 100k inhabitants\"\n",
" ).configure_view(stroke=None)\n",
" return p"
]
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 13,
"metadata": {
"papermill": {
- "duration": 0.103115,
- "end_time": "2020-03-13T17:58:08.660915",
+ "duration": 0.113317,
+ "end_time": "2020-03-15T16:37:30.476323",
"exception": false,
- "start_time": "2020-03-13T17:58:08.557800",
+ "start_time": "2020-03-15T16:37:30.363006",
"status": "completed"
},
"tags": []
@@ -375,10 +379,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-9d8bbc6305e34585bef05d17e261d227\"></div>\n",
+ "<div id=\"altair-viz-0d5ef06b0f5c47e49467448e93085b54\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-9d8bbc6305e34585bef05d17e261d227\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-0d5ef06b0f5c47e49467448e93085b54\");\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",
@@ -419,7 +423,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300, \"stroke\": null}}, \"layer\": [{\"data\": {\"sphere\": true}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#cae6ef\"}}, {\"data\": {\"graticule\": true}, \"mark\": {\"type\": \"geoshape\", \"stroke\": \"white\", \"strokeWidth\": 0.5}}, {\"data\": {\"url\": \"https://vega.github.io/vega-datasets/data/world-110m.json\", \"format\": {\"feature\": \"countries\", \"type\": \"topojson\"}}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#dddddd\", \"stroke\": \"#aaaaaa\"}}, {\"data\": {\"name\": \"data-af06d21f07e2679aa76ca6a14f5f1418\"}, \"mark\": {\"type\": \"circle\", \"opacity\": 0.6}, \"encoding\": {\"color\": {\"value\": \"steelblue\"}, \"latitude\": {\"field\": \"Lat\", \"type\": \"quantitative\"}, \"longitude\": {\"field\": \"Long\", \"type\": \"quantitative\"}, \"size\": {\"type\": \"quantitative\", \"field\": \"Confirmed\", \"title\": \"Cases\"}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"Country/Region\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, {\"type\": \"quantitative\", \"field\": \"Deaths\"}, {\"type\": \"quantitative\", \"field\": \"Recovered\"}]}}], \"height\": 400, \"projection\": {\"type\": \"naturalEarth1\"}, \"title\": \"Confirmed cases per 100,000\", \"width\": 600, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-af06d21f07e2679aa76ca6a14f5f1418\": [{\"Country/Region\": \"Australia\", \"Confirmed\": 0.5121563305983519, \"Deaths\": 0.012003663998398872, \"Recovered\": 0.0840256479887921, \"Lat\": -23.1315375, \"Long\": 140.0609875}, {\"Country/Region\": \"Austria\", \"Confirmed\": 3.4135722502347403, \"Deaths\": 0.01130321937163821, \"Recovered\": 0.04521287748655284, \"Lat\": 47.5162, \"Long\": 14.5501}, {\"Country/Region\": \"Bahrain\", \"Confirmed\": 12.424821863098854, \"Deaths\": 0.0, \"Recovered\": 2.230096231838256, \"Lat\": 26.0275, \"Long\": 50.55}, {\"Country/Region\": \"Belgium\", \"Confirmed\": 2.749064355071253, \"Deaths\": 0.026264946067559743, \"Recovered\": 0.008754982022519914, \"Lat\": 50.8333, \"Long\": 4.0}, {\"Country/Region\": \"Canada\", \"Confirmed\": 0.3157140090886777, \"Deaths\": 0.002698410334091263, \"Recovered\": 0.021587282672730104, \"Lat\": 50.795, \"Long\": -93.00628}, {\"Country/Region\": \"Denmark\", \"Confirmed\": 10.6426174560315, \"Deaths\": 0.0, \"Recovered\": 0.01724897480718234, \"Lat\": 59.07825, \"Long\": 1.2949999999999995}, {\"Country/Region\": \"France\", \"Confirmed\": 3.4096043718413016, \"Deaths\": 0.07165543338370511, \"Recovered\": 0.017913858345926282, \"Lat\": 27.399466666666665, \"Long\": -41.22323333333333}, {\"Country/Region\": \"Germany\", \"Confirmed\": 2.5057905104628087, \"Deaths\": 0.0036175993895035743, \"Recovered\": 0.03014666157919645, \"Lat\": 51.0, \"Long\": 9.0}, {\"Country/Region\": \"Iceland\", \"Confirmed\": 29.13110126875845, \"Deaths\": 0.0, \"Recovered\": 0.28282622591027623, \"Lat\": 64.9631, \"Long\": -19.0208}, {\"Country/Region\": \"Israel\", \"Confirmed\": 1.4745942051824668, \"Deaths\": 0.0, \"Recovered\": 0.045025777257479915, \"Lat\": 31.0, \"Long\": 35.0}, {\"Country/Region\": \"Italy\", \"Confirmed\": 20.62176968839136, \"Deaths\": 1.368496511980393, \"Recovered\": 1.7292368259002542, \"Lat\": 43.0, \"Long\": 12.0}, {\"Country/Region\": \"Japan\", \"Confirmed\": 0.5050221648616801, \"Deaths\": 0.012645312422201693, \"Recovered\": 0.09325917911373748, \"Lat\": 36.0, \"Long\": 138.0}, {\"Country/Region\": \"Malaysia\", \"Confirmed\": 0.4725870190495387, \"Deaths\": 0.0, \"Recovered\": 0.08246484896166446, \"Lat\": 2.5, \"Long\": 112.5}, {\"Country/Region\": \"Netherlands\", \"Confirmed\": 2.919154452694232, \"Deaths\": 0.02901743988761661, \"Recovered\": 0.0, \"Lat\": 52.1326, \"Long\": 5.2913}, {\"Country/Region\": \"Norway\", \"Confirmed\": 13.209552425740487, \"Deaths\": 0.0, \"Recovered\": 0.018817026247493568, \"Lat\": 60.472, \"Long\": 8.4689}, {\"Country/Region\": \"Qatar\", \"Confirmed\": 9.418778672002537, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Lat\": 25.3548, \"Long\": 51.1839}, {\"Country/Region\": \"Singapore\", \"Confirmed\": 3.156769426014192, \"Deaths\": 0.0, \"Recovered\": 1.7025273308840587, \"Lat\": 1.2833, \"Long\": 103.8333}, {\"Country/Region\": \"Spain\", \"Confirmed\": 4.873324698324187, \"Deaths\": 0.11771315696435232, \"Recovered\": 0.3916637768086632, \"Lat\": 40.0, \"Long\": -4.0}, {\"Country/Region\": \"Sweden\", \"Confirmed\": 5.882251851706369, \"Deaths\": 0.009820119952765223, \"Recovered\": 0.009820119952765223, \"Lat\": 63.0, \"Long\": 16.0}, {\"Country/Region\": \"Switzerland\", \"Confirmed\": 7.655688464204314, \"Deaths\": 0.04696741389082401, \"Recovered\": 0.04696741389082401, \"Lat\": 46.8182, \"Long\": 8.2275}, {\"Country/Region\": \"US\", \"Confirmed\": 0.508302424745612, \"Deaths\": 0.012226155736515023, \"Recovered\": 0.0036678467209545055, \"Lat\": 38.88347448559672, \"Long\": -94.14907777777768}]}}, {\"mode\": \"vega-lite\"});\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300, \"stroke\": null}}, \"layer\": [{\"data\": {\"sphere\": true}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#cae6ef\"}}, {\"data\": {\"graticule\": true}, \"mark\": {\"type\": \"geoshape\", \"stroke\": \"white\", \"strokeWidth\": 0.5}}, {\"data\": {\"url\": \"https://vega.github.io/vega-datasets/data/world-110m.json\", \"format\": {\"feature\": \"countries\", \"type\": \"topojson\"}}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#dddddd\", \"stroke\": \"#aaaaaa\"}}, {\"data\": {\"name\": \"data-95ea86d40d32f37e513861317827f4db\"}, \"mark\": {\"type\": \"circle\", \"opacity\": 0.6}, \"encoding\": {\"color\": {\"value\": \"steelblue\"}, \"latitude\": {\"field\": \"Lat\", \"type\": \"quantitative\"}, \"longitude\": {\"field\": \"Long\", \"type\": \"quantitative\"}, \"size\": {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\", \"title\": \"Cases\"}, \"tooltip\": [{\"type\": \"nominal\", 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\"Confirmed/100k\": 4.666004333928752, \"Deaths/100k\": 0.05803487977523322, \"Recovered/100k\": 0.0, \"Confirmed\": 804.0, \"Deaths\": 10.0, \"Recovered\": 0.0, \"Long\": 5.28144793, \"Lat\": 52.1007899}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 18.741758142503603, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 996.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572}, {\"Country/Region\": \"Portugal\", \"Confirmed/100k\": 1.0893074552785798, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.009725959422130177, \"Confirmed\": 112.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": -8.50104361, \"Lat\": 39.59550671}, {\"Country/Region\": \"Qatar\", \"Confirmed/100k\": 11.503851813132869, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 320.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 51.18479632, \"Lat\": 25.30601188}, {\"Country/Region\": \"Singapore\", \"Confirmed/100k\": 3.5469319393417886, 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\"Deaths/100k\": 0.12916038819976602, \"Recovered/100k\": 0.04696741389082401, \"Confirmed\": 1139.0, \"Deaths\": 11.0, \"Recovered\": 4.0, \"Long\": 8.20867471, \"Lat\": 46.79785878}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 0.6660198337466559, \"Deaths/100k\": 0.01436573299040515, \"Recovered/100k\": 0.0036678467209545055, \"Confirmed\": 2179.0, \"Deaths\": 47.0, \"Recovered\": 12.0, \"Long\": -112.4616737, \"Lat\": 45.6795472}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 1.2047107166959414, \"Deaths/100k\": 0.012032067083105532, \"Recovered/100k\": 0.028576159322375637, \"Confirmed\": 801.0, \"Deaths\": 8.0, \"Recovered\": 19.0, \"Long\": -2.86563164, \"Lat\": 54.12387156}]}}, {\"mode\": \"vega-lite\"});\n",
"</script>"
],
"text/plain": [
@@ -433,9 +437,10 @@
"data": {
"text/html": [
"\n",
- "<p style=\"font-size: smaller\">Data Source: \n",
- " <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a> and\n",
- " <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
+ " <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
+ " <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
"</p>"
],
"text/plain": [
@@ -447,23 +452,24 @@
}
],
"source": [
- "display(map_of_variable(map_df, 'Confirmed'))\n",
+ "display(map_of_variable(map_df, 'Confirmed/100k', 'Confirmed'))\n",
"display(HTML('''\n",
- "<p style=\"font-size: smaller\">Data Source: \n",
- " <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a> and\n",
- " <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
+ " <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
+ " <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
"</p>'''))"
]
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": 14,
"metadata": {
"papermill": {
- "duration": 0.048886,
- "end_time": "2020-03-13T17:58:08.727920",
+ "duration": 0.083778,
+ "end_time": "2020-03-15T16:37:30.576656",
"exception": false,
- "start_time": "2020-03-13T17:58:08.679034",
+ "start_time": "2020-03-15T16:37:30.492878",
"status": "completed"
},
"tags": []
@@ -473,10 +479,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-01c78ff6476e41d882dd62fc1875817d\"></div>\n",
+ "<div id=\"altair-viz-6a54aa46a40245ccbf20c582c4265681\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-01c78ff6476e41d882dd62fc1875817d\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-6a54aa46a40245ccbf20c582c4265681\");\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",
@@ -517,22 +523,25 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"layer\": [{\"mark\": \"bar\", \"encoding\": {\"x\": {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, \"y\": {\"type\": \"nominal\", \"field\": \"Country/Region\", \"sort\": \"-x\"}}}, {\"mark\": {\"type\": \"text\", \"align\": \"left\", \"baseline\": \"middle\", \"dx\": 3}, \"encoding\": {\"text\": {\"type\": \"quantitative\", \"field\": \"Confirmed\", \"format\": \".3\"}, \"x\": {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, \"y\": {\"type\": \"nominal\", \"field\": \"Country/Region\", \"sort\": \"-x\"}}}], \"data\": {\"name\": \"data-af06d21f07e2679aa76ca6a14f5f1418\"}, \"height\": 900, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-af06d21f07e2679aa76ca6a14f5f1418\": [{\"Country/Region\": \"Australia\", \"Confirmed\": 0.5121563305983519, \"Deaths\": 0.012003663998398872, \"Recovered\": 0.0840256479887921, \"Lat\": -23.1315375, \"Long\": 140.0609875}, {\"Country/Region\": \"Austria\", \"Confirmed\": 3.4135722502347403, \"Deaths\": 0.01130321937163821, \"Recovered\": 0.04521287748655284, \"Lat\": 47.5162, \"Long\": 14.5501}, {\"Country/Region\": \"Bahrain\", \"Confirmed\": 12.424821863098854, \"Deaths\": 0.0, \"Recovered\": 2.230096231838256, \"Lat\": 26.0275, \"Long\": 50.55}, {\"Country/Region\": \"Belgium\", \"Confirmed\": 2.749064355071253, \"Deaths\": 0.026264946067559743, \"Recovered\": 0.008754982022519914, \"Lat\": 50.8333, \"Long\": 4.0}, {\"Country/Region\": \"Canada\", \"Confirmed\": 0.3157140090886777, \"Deaths\": 0.002698410334091263, \"Recovered\": 0.021587282672730104, \"Lat\": 50.795, \"Long\": -93.00628}, {\"Country/Region\": \"Denmark\", \"Confirmed\": 10.6426174560315, \"Deaths\": 0.0, \"Recovered\": 0.01724897480718234, \"Lat\": 59.07825, \"Long\": 1.2949999999999995}, {\"Country/Region\": \"France\", \"Confirmed\": 3.4096043718413016, \"Deaths\": 0.07165543338370511, \"Recovered\": 0.017913858345926282, \"Lat\": 27.399466666666665, \"Long\": -41.22323333333333}, {\"Country/Region\": \"Germany\", \"Confirmed\": 2.5057905104628087, \"Deaths\": 0.0036175993895035743, \"Recovered\": 0.03014666157919645, \"Lat\": 51.0, \"Long\": 9.0}, {\"Country/Region\": \"Iceland\", \"Confirmed\": 29.13110126875845, \"Deaths\": 0.0, \"Recovered\": 0.28282622591027623, \"Lat\": 64.9631, \"Long\": -19.0208}, {\"Country/Region\": \"Israel\", \"Confirmed\": 1.4745942051824668, \"Deaths\": 0.0, \"Recovered\": 0.045025777257479915, \"Lat\": 31.0, \"Long\": 35.0}, {\"Country/Region\": \"Italy\", \"Confirmed\": 20.62176968839136, \"Deaths\": 1.368496511980393, \"Recovered\": 1.7292368259002542, \"Lat\": 43.0, \"Long\": 12.0}, {\"Country/Region\": \"Japan\", \"Confirmed\": 0.5050221648616801, \"Deaths\": 0.012645312422201693, \"Recovered\": 0.09325917911373748, \"Lat\": 36.0, \"Long\": 138.0}, {\"Country/Region\": \"Malaysia\", \"Confirmed\": 0.4725870190495387, \"Deaths\": 0.0, \"Recovered\": 0.08246484896166446, \"Lat\": 2.5, \"Long\": 112.5}, {\"Country/Region\": \"Netherlands\", \"Confirmed\": 2.919154452694232, \"Deaths\": 0.02901743988761661, \"Recovered\": 0.0, \"Lat\": 52.1326, \"Long\": 5.2913}, {\"Country/Region\": \"Norway\", \"Confirmed\": 13.209552425740487, \"Deaths\": 0.0, \"Recovered\": 0.018817026247493568, \"Lat\": 60.472, \"Long\": 8.4689}, {\"Country/Region\": \"Qatar\", \"Confirmed\": 9.418778672002537, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Lat\": 25.3548, \"Long\": 51.1839}, {\"Country/Region\": \"Singapore\", \"Confirmed\": 3.156769426014192, \"Deaths\": 0.0, \"Recovered\": 1.7025273308840587, \"Lat\": 1.2833, \"Long\": 103.8333}, {\"Country/Region\": \"Spain\", \"Confirmed\": 4.873324698324187, \"Deaths\": 0.11771315696435232, \"Recovered\": 0.3916637768086632, \"Lat\": 40.0, \"Long\": -4.0}, {\"Country/Region\": \"Sweden\", \"Confirmed\": 5.882251851706369, \"Deaths\": 0.009820119952765223, \"Recovered\": 0.009820119952765223, \"Lat\": 63.0, \"Long\": 16.0}, {\"Country/Region\": \"Switzerland\", \"Confirmed\": 7.655688464204314, \"Deaths\": 0.04696741389082401, \"Recovered\": 0.04696741389082401, \"Lat\": 46.8182, \"Long\": 8.2275}, {\"Country/Region\": \"US\", \"Confirmed\": 0.508302424745612, \"Deaths\": 0.012226155736515023, \"Recovered\": 0.0036678467209545055, \"Lat\": 38.88347448559672, \"Long\": -94.14907777777768}]}}, {\"mode\": \"vega-lite\"});\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"layer\": [{\"mark\": \"bar\", \"encoding\": {\"tooltip\": [{\"type\": \"nominal\", \"field\": \"Country/Region\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, {\"type\": \"quantitative\", \"field\": \"Deaths\"}, {\"type\": \"quantitative\", \"field\": \"Recovered\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, {\"type\": \"quantitative\", \"field\": \"Deaths/100k\"}, {\"type\": \"quantitative\", \"field\": \"Recovered/100k\"}], \"x\": {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, \"y\": {\"type\": \"nominal\", \"field\": \"Country/Region\", \"sort\": \"-x\"}}}, {\"mark\": {\"type\": \"text\", \"align\": \"left\", \"baseline\": \"middle\", \"dx\": 3}, \"encoding\": {\"text\": {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\", \"format\": \".3\"}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"Country/Region\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, {\"type\": \"quantitative\", \"field\": \"Deaths\"}, {\"type\": \"quantitative\", \"field\": \"Recovered\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, {\"type\": \"quantitative\", \"field\": \"Deaths/100k\"}, {\"type\": \"quantitative\", \"field\": \"Recovered/100k\"}], \"x\": {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, \"y\": {\"type\": \"nominal\", \"field\": \"Country/Region\", \"sort\": \"-x\"}}}], \"data\": {\"name\": \"data-95ea86d40d32f37e513861317827f4db\"}, \"height\": 900, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-95ea86d40d32f37e513861317827f4db\": [{\"Country/Region\": \"Australia\", \"Confirmed/100k\": 0.8002442665599246, \"Deaths/100k\": 0.012003663998398872, \"Recovered/100k\": 0.09202809065439137, \"Confirmed\": 200.0, \"Deaths\": 3.0, \"Recovered\": 23.0, \"Long\": 134.49100008, \"Lat\": -25.73288704}, {\"Country/Region\": \"Austria\", \"Confirmed/100k\": 5.696822563305657, \"Deaths/100k\": 0.01130321937163821, \"Recovered/100k\": 0.06781931622982926, \"Confirmed\": 504.0, \"Deaths\": 1.0, \"Recovered\": 6.0, \"Long\": 14.1264761, \"Lat\": 47.58549439}, {\"Country/Region\": \"Bahrain\", \"Confirmed/100k\": 12.042519651926579, \"Deaths/100k\": 0.0, \"Recovered/100k\": 2.8035495485966644, \"Confirmed\": 189.0, \"Deaths\": 0.0, \"Recovered\": 44.0, \"Long\": 50.54196932, \"Lat\": 26.04205135}, {\"Country/Region\": \"Belgium\", \"Confirmed/100k\": 4.894034950588631, \"Deaths/100k\": 0.026264946067559743, \"Recovered/100k\": 0.008754982022519914, \"Confirmed\": 559.0, \"Deaths\": 3.0, \"Recovered\": 1.0, \"Long\": 4.64065114, \"Lat\": 50.63981576}, {\"Country/Region\": \"Brazil\", \"Confirmed/100k\": 0.07208692453324421, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 151.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": -53.09783113, \"Lat\": -10.78777702}, {\"Country/Region\": \"Canada\", \"Confirmed/100k\": 0.5207931944796137, \"Deaths/100k\": 0.002698410334091263, \"Recovered/100k\": 0.021587282672730104, \"Confirmed\": 193.0, \"Deaths\": 1.0, \"Recovered\": 8.0, \"Long\": -98.30777028, \"Lat\": 61.36206324}, {\"Country/Region\": \"China\", \"Confirmed/100k\": 5.811966425653213, \"Deaths/100k\": 0.22832853460469724, \"Recovered/100k\": 4.609364341975832, \"Confirmed\": 80945.0, \"Deaths\": 3180.0, \"Recovered\": 64196.0, \"Long\": 103.81907349, \"Lat\": 36.56176546}, {\"Country/Region\": \"Czechia\", \"Confirmed/100k\": 1.3269720239476102, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 141.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 15.31240163, \"Lat\": 49.73341233}, {\"Country/Region\": \"Denmark\", \"Confirmed/100k\": 13.868175744974597, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.01724897480718234, \"Confirmed\": 804.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 10.02800992, \"Lat\": 55.98125296}, {\"Country/Region\": \"Finland\", \"Confirmed/100k\": 2.808963311314685, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.018122343943965717, \"Confirmed\": 155.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 26.2746656, \"Lat\": 64.49884603}, {\"Country/Region\": \"France\", \"Confirmed/100k\": 5.474176546209304, \"Deaths/100k\": 0.117932900777348, \"Recovered/100k\": 0.017913858345926282, \"Confirmed\": 3667.0, \"Deaths\": 79.0, \"Recovered\": 12.0, \"Long\": -2.76172945, \"Lat\": 42.17344011}, {\"Country/Region\": \"Germany\", \"Confirmed/100k\": 4.431559252141878, \"Deaths/100k\": 0.008441065242175007, \"Recovered/100k\": 0.055469857305721466, \"Confirmed\": 3675.0, \"Deaths\": 7.0, \"Recovered\": 46.0, \"Long\": 10.38578051, \"Lat\": 51.10698181}, {\"Country/Region\": \"Greece\", \"Confirmed/100k\": 1.771121179365357, \"Deaths/100k\": 0.009321690417712405, \"Recovered/100k\": 0.0, \"Confirmed\": 190.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 22.95555794, \"Lat\": 39.07469623}, {\"Country/Region\": \"Iceland\", \"Confirmed/100k\": 37.898714271977006, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.28282622591027623, \"Confirmed\": 134.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": -18.57396167, \"Lat\": 64.99575386}, {\"Country/Region\": \"Iran\", \"Confirmed/100k\": 13.892374852703725, \"Deaths/100k\": 0.6283597918241565, \"Recovered/100k\": 3.6173475175246668, \"Confirmed\": 11364.0, \"Deaths\": 514.0, \"Recovered\": 2959.0, \"Long\": 54.27407004, \"Lat\": 32.57503292}, {\"Country/Region\": \"Iraq\", \"Confirmed/100k\": 0.26279089130344285, \"Deaths/100k\": 0.023417010116148367, \"Recovered/100k\": 0.06244536030972898, \"Confirmed\": 101.0, \"Deaths\": 9.0, \"Recovered\": 24.0, \"Long\": 43.74353149, \"Lat\": 33.03970582}, {\"Country/Region\": \"Israel\", \"Confirmed/100k\": 1.8122875346135665, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.045025777257479915, \"Confirmed\": 161.0, \"Deaths\": 0.0, \"Recovered\": 4.0, \"Long\": 35.00444693, \"Lat\": 31.46110101}, {\"Country/Region\": \"Italy\", \"Confirmed/100k\": 29.22327497167319, \"Deaths/100k\": 2.0949414560667194, \"Recovered/100k\": 2.3812170262875267, \"Confirmed\": 17660.0, \"Deaths\": 1266.0, \"Recovered\": 1439.0, \"Long\": 12.07001339, \"Lat\": 42.79662641}, {\"Country/Region\": \"Japan\", \"Confirmed/100k\": 0.5540227504977115, \"Deaths/100k\": 0.01501630850136451, \"Recovered/100k\": 0.09325917911373748, \"Confirmed\": 701.0, \"Deaths\": 19.0, \"Recovered\": 118.0, \"Long\": 138.03089558, \"Lat\": 37.59230135}, {\"Country/Region\": \"Korea, South\", \"Confirmed/100k\": 15.452620201979823, \"Deaths/100k\": 0.12781964322981182, \"Recovered/100k\": 0.9876972431394551, \"Confirmed\": 7979.0, \"Deaths\": 66.0, \"Recovered\": 510.0, \"Long\": 127.83916086, \"Lat\": 36.38523983}, {\"Country/Region\": \"Malaysia\", \"Confirmed/100k\": 0.6248298171326115, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.08246484896166446, \"Confirmed\": 197.0, \"Deaths\": 0.0, \"Recovered\": 26.0, \"Long\": 109.69762284, \"Lat\": 3.78986846}, {\"Country/Region\": \"Netherlands\", \"Confirmed/100k\": 4.666004333928752, \"Deaths/100k\": 0.05803487977523322, \"Recovered/100k\": 0.0, \"Confirmed\": 804.0, \"Deaths\": 10.0, \"Recovered\": 0.0, \"Long\": 5.28144793, \"Lat\": 52.1007899}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 18.741758142503603, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 996.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572}, {\"Country/Region\": \"Portugal\", \"Confirmed/100k\": 1.0893074552785798, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.009725959422130177, \"Confirmed\": 112.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": -8.50104361, \"Lat\": 39.59550671}, {\"Country/Region\": \"Qatar\", \"Confirmed/100k\": 11.503851813132869, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 320.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 51.18479632, \"Lat\": 25.30601188}, {\"Country/Region\": \"Singapore\", \"Confirmed/100k\": 3.5469319393417886, \"Deaths/100k\": 0.0, \"Recovered/100k\": 1.7202619905807677, \"Confirmed\": 200.0, \"Deaths\": 0.0, \"Recovered\": 97.0, \"Long\": 103.81725592, \"Lat\": 1.35876087}, {\"Country/Region\": \"Slovenia\", \"Confirmed/100k\": 6.820252958828889, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 141.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 14.80444238, \"Lat\": 46.11554772}, {\"Country/Region\": \"Spain\", \"Confirmed/100k\": 11.197731586136207, \"Deaths/100k\": 0.28465181593197925, \"Recovered/100k\": 0.413066168984, \"Confirmed\": 5232.0, \"Deaths\": 133.0, \"Recovered\": 193.0, \"Long\": -3.64755047, \"Lat\": 40.24448698}, {\"Country/Region\": \"Sweden\", \"Confirmed/100k\": 7.993577641550892, \"Deaths/100k\": 0.009820119952765223, \"Recovered/100k\": 0.009820119952765223, \"Confirmed\": 814.0, \"Deaths\": 1.0, \"Recovered\": 1.0, \"Long\": 16.74558049, \"Lat\": 62.77966519}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 13.373971105412135, \"Deaths/100k\": 0.12916038819976602, \"Recovered/100k\": 0.04696741389082401, \"Confirmed\": 1139.0, \"Deaths\": 11.0, \"Recovered\": 4.0, \"Long\": 8.20867471, \"Lat\": 46.79785878}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 0.6660198337466559, \"Deaths/100k\": 0.01436573299040515, \"Recovered/100k\": 0.0036678467209545055, \"Confirmed\": 2179.0, \"Deaths\": 47.0, \"Recovered\": 12.0, \"Long\": -112.4616737, \"Lat\": 45.6795472}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 1.2047107166959414, \"Deaths/100k\": 0.012032067083105532, \"Recovered/100k\": 0.028576159322375637, \"Confirmed\": 801.0, \"Deaths\": 8.0, \"Recovered\": 19.0, \"Long\": -2.86563164, \"Lat\": 54.12387156}]}}, {\"mode\": \"vega-lite\"});\n",
"</script>"
],
"text/plain": [
"alt.LayerChart(...)"
]
},
- "execution_count": 15,
+ "execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"bars = alt.Chart(map_df).mark_bar().encode(\n",
- " x='Confirmed:Q',\n",
- " y=alt.Y(\"Country/Region:N\", sort='-x')\n",
+ " x='Confirmed/100k:Q',\n",
+ " y=alt.Y(\"Country/Region:N\", sort='-x'),\n",
+ " tooltip=[\"Country/Region:N\", \n",
+ " \"Confirmed:Q\", \"Deaths:Q\", \"Recovered:Q\",\n",
+ " \"Confirmed/100k:Q\", \"Deaths/100k:Q\", \"Recovered/100k:Q\"]\n",
")\n",
"\n",
"text = bars.mark_text(\n",
@@ -540,7 +549,7 @@
" baseline='middle',\n",
" dx=3 # Nudges text to right so it doesn't appear on top of the bar\n",
").encode(\n",
- " text=alt.Text('Confirmed:Q', format=\".3\")\n",
+ " text=alt.Text('Confirmed/100k:Q', format=\".3\")\n",
")\n",
"\n",
"(bars + text).properties(height=900)"
@@ -566,19 +575,20 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 2.508313,
- "end_time": "2020-03-13T17:58:09.048792",
+ "duration": 2.502575,
+ "end_time": "2020-03-15T16:37:30.908644",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/ajs106te/notebooks/Dashboard.ipynb",
+ "input_path": "notebooks/Dashboard.ipynb",
"output_path": "runs/Dashboard.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/ajs106te/notebooks/Dashboard.ipynb",
+ "PAPERMILL_INPUT_PATH": "notebooks/Dashboard.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
- "rates_folder": "/tmp/ajs106te/data/covid-19_rates",
- "ts_folder": "/tmp/ajs106te/data/covid-19_jhu-csse"
+ "geodata_path": "./data/geodata/geo_data.csv",
+ "rates_folder": "./data/covid-19_rates/",
+ "ts_folder": "./data/covid-19_jhu-csse/"
},
- "start_time": "2020-03-13T17:58:06.540479",
+ "start_time": "2020-03-15T16:37:28.406069",
"version": "1.1.0"
}
},