diff --git a/.renku/workflow/b1c0a33b463d406a820ff0a61fb3a526_papermill.cwl b/.renku/workflow/b1c0a33b463d406a820ff0a61fb3a526_papermill.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..335e476c4a827ba842a68d5ded0cab96ecc5ad9e
--- /dev/null
+++ b/.renku/workflow/b1c0a33b463d406a820ff0a61fb3a526_papermill.cwl
@@ -0,0 +1,91 @@
+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:
+ class: File
+ path: ../../notebooks/Dashboard.ipynb
+ inputBinding:
+ position: 5
+ prefix: --inject-paths
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_6:
+ default: runs/Dashboard.run.ipynb
+ inputBinding:
+ position: 6
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_6)
+ streamable: false
+ type: File
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"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_5)
+ entryname: notebooks/Dashboard.ipynb
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..8ee68b5da01772bb9e712ece6093a1cbf2df62c1
--- /dev/null
+++ b/runs/Dashboard.run.ipynb
@@ -0,0 +1,587 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "papermill": {
+ "duration": 0.35409,
+ "end_time": "2020-03-13T17:04:15.061697",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:14.707607",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import os\n",
+ "from IPython.display import display, HTML, Markdown"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "papermill": {
+ "duration": 0.02437,
+ "end_time": "2020-03-13T17:04:15.106586",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.082216",
+ "status": "completed"
+ },
+ "tags": [
+ "parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "ts_folder = \"../data/covid-19_jhu-csse/\"\n",
+ "rates_folder = \"../data/covid-19_rates/\"\n",
+ "out_folder = None\n",
+ "PAPERMILL_OUTPUT_PATH = None"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "papermill": {
+ "duration": 0.022646,
+ "end_time": "2020-03-13T17:04:15.137496",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.114850",
+ "status": "completed"
+ },
+ "tags": [
+ "injected-parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "# Parameters\n",
+ "PAPERMILL_INPUT_PATH = \"notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
+ "ts_folder = \"./data/covid-19_jhu-csse/\"\n",
+ "rates_folder = \"./data/covid-19_rates/\"\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "papermill": {
+ "duration": 0.021072,
+ "end_time": "2020-03-13T17:04:15.168525",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.147453",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Read in the data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "papermill": {
+ "duration": 0.065756,
+ "end_time": "2020-03-13T17:04:15.243131",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.177375",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "def read_jhu_covid_df(name):\n",
+ " filename = os.path.join(ts_folder, f\"time_series_19-covid-{name}.csv\")\n",
+ " df = pd.read_csv(filename)\n",
+ " df = df.set_index(['Province/State', 'Country/Region', 'Lat', 'Long'])\n",
+ " df.columns = pd.to_datetime(df.columns)\n",
+ " return df\n",
+ "\n",
+ "\n",
+ "jhu_frames_map = {\n",
+ " \"confirmed\": read_jhu_covid_df(\"Confirmed\"),\n",
+ " \"deaths\": read_jhu_covid_df(\"Deaths\"),\n",
+ " \"recovered\": read_jhu_covid_df(\"Recovered\")\n",
+ "}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "papermill": {
+ "duration": 0.038039,
+ "end_time": "2020-03-13T17:04:15.289236",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.251197",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "def read_rates_covid_df(name):\n",
+ " filename = os.path.join(rates_folder, f\"ts_rates_19-covid-{name}.csv\")\n",
+ " df = pd.read_csv(filename).drop(\"Unnamed: 0\", axis=1)\n",
+ " df = df.set_index(['Country/Region'])\n",
+ " df.columns = pd.to_datetime(df.columns)\n",
+ " return df\n",
+ "\n",
+ "\n",
+ "rates_frames_map = {\n",
+ " \"confirmed\": read_rates_covid_df(\"confirmed\"),\n",
+ " \"deaths\": read_rates_covid_df(\"deaths\"),\n",
+ " \"recovered\": read_rates_covid_df(\"recovered\")\n",
+ "}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "papermill": {
+ "duration": 0.017688,
+ "end_time": "2020-03-13T17:04:15.314301",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.296613",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Compile data needed for the visualizations"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "papermill": {
+ "duration": 0.040604,
+ "end_time": "2020-03-13T17:04:15.374996",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.334392",
+ "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": 0.034326,
+ "end_time": "2020-03-13T17:04:15.424734",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.390408",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "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",
+ "countries_over_thresh = case_count_ser[case_count_ser > 99].index"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.009134,
+ "end_time": "2020-03-13T17:04:15.448316",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.439182",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "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."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "papermill": {
+ "duration": 0.041449,
+ "end_time": "2020-03-13T17:04:15.498158",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.456709",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<em>Data up to Mar 10 2020</em>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "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>\"))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.009938,
+ "end_time": "2020-03-13T17:04:15.526404",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.516466",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## How are cases per 100,000 distributed geographically?"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "papermill": {
+ "duration": 0.199352,
+ "end_time": "2020-03-13T17:04:15.733984",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.534632",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "import altair as alt\n",
+ "from vega_datasets import data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "papermill": {
+ "duration": 0.045428,
+ "end_time": "2020-03-13T17:04:15.799713",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.754285",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# 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",
+ "# 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']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {
+ "papermill": {
+ "duration": 0.030132,
+ "end_time": "2020-03-13T17:04:15.844929",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.814797",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "def map_of_variable(map_df, variable):\n",
+ " # Data generators for the background\n",
+ " sphere = alt.sphere()\n",
+ " graticule = alt.graticule()\n",
+ "\n",
+ " # Source of land data\n",
+ " source = alt.topo_feature(data.world_110m.url, 'countries')\n",
+ "\n",
+ " # Layering and configuring the components\n",
+ " p = alt.layer(\n",
+ " alt.Chart(sphere).mark_geoshape(fill='#cae6ef'),\n",
+ " alt.Chart(graticule).mark_geoshape(stroke='white', strokeWidth=0.5),\n",
+ " alt.Chart(source).mark_geoshape(fill='#dddddd', stroke='#aaaaaa'),\n",
+ " alt.Chart(map_df).mark_circle(opacity=0.6).encode(\n",
+ " longitude='Long:Q',\n",
+ " 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",
+ " )\n",
+ " ).project(\n",
+ " 'naturalEarth1'\n",
+ " ).properties(width=600, height=400, title=f\"{variable} cases per 100,000\"\n",
+ " ).configure_view(stroke=None)\n",
+ " return p"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {
+ "papermill": {
+ "duration": 0.100208,
+ "end_time": "2020-03-13T17:04:15.958509",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.858301",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-b79eb79d0e8f4b50be1688903bb8f9f0\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-b79eb79d0e8f4b50be1688903bb8f9f0\");\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: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300, \"stroke\": null}}, \"layer\": [{\"data\": {\"sphere\": true}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#cae6ef\"}}, {\"data\": {\"graticule\": true}, \"mark\": {\"type\": \"geoshape\", \"stroke\": \"white\", \"strokeWidth\": 0.5}}, {\"data\": {\"url\": \"https://vega.github.io/vega-datasets/data/world-110m.json\", \"format\": {\"feature\": \"countries\", \"type\": \"topojson\"}}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#dddddd\", \"stroke\": \"#aaaaaa\"}}, {\"data\": {\"name\": \"data-433f706ddfa6221156e78c265aebad1f\"}, \"mark\": {\"type\": \"circle\", \"opacity\": 0.6}, \"encoding\": {\"color\": {\"value\": \"steelblue\"}, \"latitude\": {\"field\": \"Lat\", \"type\": \"quantitative\"}, \"longitude\": {\"field\": \"Long\", \"type\": \"quantitative\"}, \"size\": {\"type\": \"quantitative\", \"field\": \"Confirmed\", \"title\": \"Cases\"}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"Country/Region\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, {\"type\": \"quantitative\", \"field\": \"Deaths\"}, {\"type\": \"quantitative\", \"field\": \"Recovered\"}]}}], \"height\": 400, \"projection\": {\"type\": \"naturalEarth1\"}, \"title\": \"Confirmed cases per 100,000\", \"width\": 600, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-433f706ddfa6221156e78c265aebad1f\": [{\"Country/Region\": \"Australia\", \"Confirmed\": 0.4281306826095598, \"Deaths\": 0.012003663998398872, \"Recovered\": 0.0840256479887921, \"Lat\": -23.1315375, \"Long\": 140.0609875}, {\"Country/Region\": \"Austria\", \"Confirmed\": 2.057185925638154, \"Deaths\": 0.0, \"Recovered\": 0.04521287748655284, \"Lat\": 47.5162, \"Long\": 14.5501}, {\"Country/Region\": \"Bahrain\", \"Confirmed\": 7.00887387149166, \"Deaths\": 0.0, \"Recovered\": 1.4017747742983322, \"Lat\": 26.0275, \"Long\": 50.55}, {\"Country/Region\": \"Belgium\", \"Confirmed\": 2.3375802000128174, \"Deaths\": 0.0, \"Recovered\": 0.008754982022519914, \"Lat\": 50.8333, \"Long\": 4.0}, {\"Country/Region\": \"Denmark\", \"Confirmed\": 4.519231399481772, \"Deaths\": 0.0, \"Recovered\": 0.01724897480718234, \"Lat\": 56.2639, \"Long\": 9.5018}, {\"Country/Region\": \"France\", \"Confirmed\": 2.663193607427707, \"Deaths\": 0.04926311045129727, \"Recovered\": 0.017913858345926282, \"Lat\": 47.0, \"Long\": 2.0}, {\"Country/Region\": \"Germany\", \"Confirmed\": 1.7569474368355689, \"Deaths\": 0.0024117329263357162, \"Recovered\": 0.021705596337021446, \"Lat\": 51.0, \"Long\": 9.0}, {\"Country/Region\": \"Hong Kong SAR\", \"Confirmed\": 1.61052207757348, \"Deaths\": 0.040263051939337005, \"Recovered\": 0.8723661253523016, \"Lat\": 22.3, \"Long\": 114.2}, {\"Country/Region\": \"Iran (Islamic Republic of)\", \"Confirmed\": 9.831263513326588, \"Deaths\": 0.3557445514023921, \"Recovered\": 3.3386198277660917, \"Lat\": 32.0, \"Long\": 53.0}, {\"Country/Region\": \"Italy\", \"Confirmed\": 16.794281862259982, \"Deaths\": 1.0441611838689575, \"Recovered\": 1.198054987513669, \"Lat\": 43.0, \"Long\": 12.0}, {\"Country/Region\": \"Japan\", \"Confirmed\": 0.4591829073311989, \"Deaths\": 0.007903320263876057, \"Recovered\": 0.07982353466514817, \"Lat\": 36.0, \"Long\": 138.0}, {\"Country/Region\": \"Mainland China\", \"Confirmed\": 5.798467757569664, \"Deaths\": 0.2251692718617392, \"Recovered\": 4.315696509732684, \"Lat\": 33.40693612903227, \"Long\": 111.54290322580646}, {\"Country/Region\": \"Malaysia\", \"Confirmed\": 0.4091525198482584, \"Deaths\": 0.0, \"Recovered\": 0.07612139904153642, \"Lat\": 2.5, \"Long\": 112.5}, {\"Country/Region\": \"Netherlands\", \"Confirmed\": 2.216932407413909, \"Deaths\": 0.02321395191009329, \"Recovered\": 0.0, \"Lat\": 52.1326, \"Long\": 5.2913}, {\"Country/Region\": \"Norway\", \"Confirmed\": 7.526810498997428, \"Deaths\": 0.0, \"Recovered\": 0.018817026247493568, \"Lat\": 60.472, \"Long\": 8.4689}, {\"Country/Region\": \"Republic of Korea\", \"Confirmed\": 14.550136054326911, \"Deaths\": 0.10457970809711876, \"Recovered\": 0.4783553314812655, \"Lat\": 36.0, \"Long\": 128.0}, {\"Country/Region\": \"Singapore\", \"Confirmed\": 2.837545551473431, \"Deaths\": 0.0, \"Recovered\": 1.3833034563432978, \"Lat\": 1.2833, \"Long\": 103.8333}, {\"Country/Region\": \"Spain\", \"Confirmed\": 3.6277054737195855, \"Deaths\": 0.07490837261367876, \"Recovered\": 0.06848765496107773, \"Lat\": 40.0, \"Long\": -4.0}, {\"Country/Region\": \"Sweden\", \"Confirmed\": 3.4861425832316537, \"Deaths\": 0.0, \"Recovered\": 0.009820119952765223, \"Lat\": 63.0, \"Long\": 16.0}, {\"Country/Region\": \"Switzerland\", \"Confirmed\": 5.7652500550986465, \"Deaths\": 0.035225560418118015, \"Recovered\": 0.035225560418118015, \"Lat\": 46.8182, \"Long\": 8.2275}, {\"Country/Region\": \"UK\", \"Confirmed\": 0.5745312032182892, \"Deaths\": 0.009024050312329149, \"Recovered\": 0.027072150936987446, \"Lat\": 55.0, \"Long\": -3.0}, {\"Country/Region\": \"US\", \"Confirmed\": 0.5104420019995022, \"Deaths\": 0.017116618031121033, \"Recovered\": 0.004584808401193134, \"Lat\": 38.77302746113991, \"Long\": -93.61047823834195}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "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>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "display(map_of_variable(map_df, '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>'''))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {
+ "papermill": {
+ "duration": 0.062654,
+ "end_time": "2020-03-13T17:04:16.037936",
+ "exception": false,
+ "start_time": "2020-03-13T17:04:15.975282",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-a0d74fce564e44529149f3e190cf879e\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-a0d74fce564e44529149f3e190cf879e\");\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: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"layer\": [{\"mark\": \"bar\", \"encoding\": {\"x\": {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, \"y\": {\"type\": \"nominal\", \"field\": \"Country/Region\", \"sort\": \"-x\"}}}, {\"mark\": {\"type\": \"text\", \"align\": \"left\", \"baseline\": \"middle\", \"dx\": 3}, \"encoding\": {\"text\": {\"type\": \"quantitative\", \"field\": \"Confirmed\", \"format\": \".3\"}, \"x\": {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, \"y\": {\"type\": \"nominal\", \"field\": \"Country/Region\", \"sort\": \"-x\"}}}], \"data\": {\"name\": \"data-433f706ddfa6221156e78c265aebad1f\"}, \"height\": 900, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-433f706ddfa6221156e78c265aebad1f\": [{\"Country/Region\": \"Australia\", \"Confirmed\": 0.4281306826095598, \"Deaths\": 0.012003663998398872, \"Recovered\": 0.0840256479887921, \"Lat\": -23.1315375, \"Long\": 140.0609875}, {\"Country/Region\": \"Austria\", \"Confirmed\": 2.057185925638154, \"Deaths\": 0.0, \"Recovered\": 0.04521287748655284, \"Lat\": 47.5162, \"Long\": 14.5501}, {\"Country/Region\": \"Bahrain\", \"Confirmed\": 7.00887387149166, \"Deaths\": 0.0, \"Recovered\": 1.4017747742983322, \"Lat\": 26.0275, \"Long\": 50.55}, {\"Country/Region\": \"Belgium\", \"Confirmed\": 2.3375802000128174, \"Deaths\": 0.0, \"Recovered\": 0.008754982022519914, \"Lat\": 50.8333, \"Long\": 4.0}, {\"Country/Region\": \"Denmark\", \"Confirmed\": 4.519231399481772, \"Deaths\": 0.0, \"Recovered\": 0.01724897480718234, \"Lat\": 56.2639, \"Long\": 9.5018}, {\"Country/Region\": \"France\", \"Confirmed\": 2.663193607427707, \"Deaths\": 0.04926311045129727, \"Recovered\": 0.017913858345926282, \"Lat\": 47.0, \"Long\": 2.0}, {\"Country/Region\": \"Germany\", \"Confirmed\": 1.7569474368355689, \"Deaths\": 0.0024117329263357162, \"Recovered\": 0.021705596337021446, \"Lat\": 51.0, \"Long\": 9.0}, {\"Country/Region\": \"Hong Kong SAR\", \"Confirmed\": 1.61052207757348, \"Deaths\": 0.040263051939337005, \"Recovered\": 0.8723661253523016, \"Lat\": 22.3, \"Long\": 114.2}, {\"Country/Region\": \"Iran (Islamic Republic of)\", \"Confirmed\": 9.831263513326588, \"Deaths\": 0.3557445514023921, \"Recovered\": 3.3386198277660917, \"Lat\": 32.0, \"Long\": 53.0}, {\"Country/Region\": \"Italy\", \"Confirmed\": 16.794281862259982, \"Deaths\": 1.0441611838689575, \"Recovered\": 1.198054987513669, \"Lat\": 43.0, \"Long\": 12.0}, {\"Country/Region\": \"Japan\", \"Confirmed\": 0.4591829073311989, \"Deaths\": 0.007903320263876057, \"Recovered\": 0.07982353466514817, \"Lat\": 36.0, \"Long\": 138.0}, {\"Country/Region\": \"Mainland China\", \"Confirmed\": 5.798467757569664, \"Deaths\": 0.2251692718617392, \"Recovered\": 4.315696509732684, \"Lat\": 33.40693612903227, \"Long\": 111.54290322580646}, {\"Country/Region\": \"Malaysia\", \"Confirmed\": 0.4091525198482584, \"Deaths\": 0.0, \"Recovered\": 0.07612139904153642, \"Lat\": 2.5, \"Long\": 112.5}, {\"Country/Region\": \"Netherlands\", \"Confirmed\": 2.216932407413909, \"Deaths\": 0.02321395191009329, \"Recovered\": 0.0, \"Lat\": 52.1326, \"Long\": 5.2913}, {\"Country/Region\": \"Norway\", \"Confirmed\": 7.526810498997428, \"Deaths\": 0.0, \"Recovered\": 0.018817026247493568, \"Lat\": 60.472, \"Long\": 8.4689}, {\"Country/Region\": \"Republic of Korea\", \"Confirmed\": 14.550136054326911, \"Deaths\": 0.10457970809711876, \"Recovered\": 0.4783553314812655, \"Lat\": 36.0, \"Long\": 128.0}, {\"Country/Region\": \"Singapore\", \"Confirmed\": 2.837545551473431, \"Deaths\": 0.0, \"Recovered\": 1.3833034563432978, \"Lat\": 1.2833, \"Long\": 103.8333}, {\"Country/Region\": \"Spain\", \"Confirmed\": 3.6277054737195855, \"Deaths\": 0.07490837261367876, \"Recovered\": 0.06848765496107773, \"Lat\": 40.0, \"Long\": -4.0}, {\"Country/Region\": \"Sweden\", \"Confirmed\": 3.4861425832316537, \"Deaths\": 0.0, \"Recovered\": 0.009820119952765223, \"Lat\": 63.0, \"Long\": 16.0}, {\"Country/Region\": \"Switzerland\", \"Confirmed\": 5.7652500550986465, \"Deaths\": 0.035225560418118015, \"Recovered\": 0.035225560418118015, \"Lat\": 46.8182, \"Long\": 8.2275}, {\"Country/Region\": \"UK\", \"Confirmed\": 0.5745312032182892, \"Deaths\": 0.009024050312329149, \"Recovered\": 0.027072150936987446, \"Lat\": 55.0, \"Long\": -3.0}, {\"Country/Region\": \"US\", \"Confirmed\": 0.5104420019995022, \"Deaths\": 0.017116618031121033, \"Recovered\": 0.004584808401193134, \"Lat\": 38.77302746113991, \"Long\": -93.61047823834195}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 15,
+ "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",
+ ")\n",
+ "\n",
+ "text = bars.mark_text(\n",
+ " align='left',\n",
+ " 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",
+ ")\n",
+ "\n",
+ "(bars + text).properties(height=900)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.6"
+ },
+ "papermill": {
+ "duration": 2.520956,
+ "end_time": "2020-03-13T17:04:16.371464",
+ "environment_variables": {},
+ "exception": null,
+ "input_path": "notebooks/Dashboard.ipynb",
+ "output_path": "runs/Dashboard.run.ipynb",
+ "parameters": {
+ "PAPERMILL_INPUT_PATH": "notebooks/Dashboard.ipynb",
+ "PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
+ "rates_folder": "./data/covid-19_rates/",
+ "ts_folder": "./data/covid-19_jhu-csse/"
+ },
+ "start_time": "2020-03-13T17:04:13.850508",
+ "version": "1.1.0"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
\ No newline at end of file