From e30ded375020e02f15dafcbf70514b118b48bc59 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Sun, 15 Mar 2020 19:37:36 +0100
Subject: [PATCH] renku update --with-siblings
---
.../c5ee81c0a49441369e109730c6d900cf.cwl | 132 ++++++
.../ts_rates_19-covid-confirmed.csv | 3 +
.../ts_rates_19-covid-deaths.csv | 3 +
.../ts_rates_19-covid-recovered.csv | 3 +
runs/Dashboard.run.ipynb | 433 +++++++++---------
runs/ToRates.run.ipynb | 162 +++----
6 files changed, 439 insertions(+), 297 deletions(-)
create mode 100644 .renku/workflow/c5ee81c0a49441369e109730c6d900cf.cwl
create mode 100644 data/covid-19_rates/ts_rates_19-covid-confirmed.csv
create mode 100644 data/covid-19_rates/ts_rates_19-covid-deaths.csv
create mode 100644 data/covid-19_rates/ts_rates_19-covid-recovered.csv
diff --git a/.renku/workflow/c5ee81c0a49441369e109730c6d900cf.cwl b/.renku/workflow/c5ee81c0a49441369e109730c6d900cf.cwl
new file mode 100644
index 00000000..00eaeeea
--- /dev/null
+++ b/.renku/workflow/c5ee81c0a49441369e109730c6d900cf.cwl
@@ -0,0 +1,132 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ streamable: false
+ type: string
+ input_10:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_11:
+ default: wb_path
+ streamable: false
+ type: string
+ input_12:
+ default:
+ class: File
+ path: ../../data/worldbank/SP.POP.TOTL.zip
+ streamable: false
+ type: File
+ input_13:
+ default: geodata_path
+ streamable: false
+ type: string
+ input_14:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ streamable: false
+ type: File
+ input_15:
+ default: out_folder
+ streamable: false
+ type: string
+ input_16:
+ default: data/covid-19_rates
+ streamable: false
+ type: string
+ input_17:
+ default:
+ class: File
+ path: ../../notebooks/ToRates.ipynb
+ streamable: false
+ type: File
+ input_2:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_3:
+ default: rates_folder
+ streamable: false
+ type: string
+ input_4:
+ default: geodata_path
+ streamable: false
+ type: string
+ input_5:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ streamable: false
+ type: File
+ input_6:
+ default:
+ class: File
+ path: ../../notebooks/Dashboard.ipynb
+ streamable: false
+ type: File
+ input_7:
+ default: runs/Dashboard.run.ipynb
+ streamable: false
+ type: string
+ input_8:
+ default: ts_folder
+ streamable: false
+ type: string
+ input_9:
+ default: runs/ToRates.run.ipynb
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_1:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: step_2/output_1
+ input_5: input_4
+ input_6: input_5
+ input_7: input_6
+ input_8: input_7
+ out:
+ - output_0
+ run: 4cc7ffe9d5a045efb048ef2222a40ffa_papermill.cwl
+ step_2:
+ in:
+ input_1: input_8
+ input_10: input_9
+ input_2: input_10
+ input_3: input_11
+ input_4: input_12
+ input_5: input_13
+ input_6: input_14
+ input_7: input_15
+ input_8: input_16
+ input_9: input_17
+ out:
+ - output_0
+ - output_1
+ run: 2c413376f8aa4ba1a325212655d423e5_papermill.cwl
diff --git a/data/covid-19_rates/ts_rates_19-covid-confirmed.csv b/data/covid-19_rates/ts_rates_19-covid-confirmed.csv
new file mode 100644
index 00000000..56d95691
--- /dev/null
+++ b/data/covid-19_rates/ts_rates_19-covid-confirmed.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eaf597680f5c0173a9df77b542cbd0b135b864014570eb8e246f2e227bf17109
+size 69756
diff --git a/data/covid-19_rates/ts_rates_19-covid-deaths.csv b/data/covid-19_rates/ts_rates_19-covid-deaths.csv
new file mode 100644
index 00000000..1be0fd31
--- /dev/null
+++ b/data/covid-19_rates/ts_rates_19-covid-deaths.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1add0765faacbf0777043b63e5f52884dbcc58b0e744fc602fe9d07009905fca
+size 39014
diff --git a/data/covid-19_rates/ts_rates_19-covid-recovered.csv b/data/covid-19_rates/ts_rates_19-covid-recovered.csv
new file mode 100644
index 00000000..eb1ebf6c
--- /dev/null
+++ b/data/covid-19_rates/ts_rates_19-covid-recovered.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:261c4036d5485dc919439f403b3f743142e9953117796e53afd2ee1175f3579e
+size 49919
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
index 892ce26f..cc8928fe 100644
--- a/runs/Dashboard.run.ipynb
+++ b/runs/Dashboard.run.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.293932,
- "end_time": "2020-03-15T16:43:45.973942",
+ "duration": 0.459578,
+ "end_time": "2020-03-15T18:37:34.869556",
"exception": false,
- "start_time": "2020-03-15T16:43:45.680010",
+ "start_time": "2020-03-15T18:37:34.409978",
"status": "completed"
},
"tags": []
@@ -17,7 +17,8 @@
"source": [
"import pandas as pd\n",
"import os\n",
- "from IPython.display import display, HTML, Markdown"
+ "from IPython.display import display, HTML, Markdown\n",
+ "import covid_19_dashboard as helper"
]
},
{
@@ -25,10 +26,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021561,
- "end_time": "2020-03-15T16:43:46.016060",
+ "duration": 0.021643,
+ "end_time": "2020-03-15T18:37:34.909914",
"exception": false,
- "start_time": "2020-03-15T16:43:45.994499",
+ "start_time": "2020-03-15T18:37:34.888271",
"status": "completed"
},
"tags": [
@@ -49,10 +50,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021241,
- "end_time": "2020-03-15T16:43:46.046986",
+ "duration": 0.020476,
+ "end_time": "2020-03-15T18:37:34.939191",
"exception": false,
- "start_time": "2020-03-15T16:43:46.025745",
+ "start_time": "2020-03-15T18:37:34.918715",
"status": "completed"
},
"tags": [
@@ -62,11 +63,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/e5179t23/notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/fer34kve/notebooks/Dashboard.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
- "ts_folder = \"/tmp/e5179t23/data/covid-19_jhu-csse\"\n",
- "rates_folder = \"/tmp/e5179t23/data/covid-19_rates\"\n",
- "geodata_path = \"/tmp/e5179t23/data/geodata/geo_data.csv\"\n"
+ "ts_folder = \"/tmp/fer34kve/data/covid-19_jhu-csse\"\n",
+ "rates_folder = \"/tmp/fer34kve/data/covid-19_rates\"\n",
+ "geodata_path = \"/tmp/fer34kve/data/geodata/geo_data.csv\"\n"
]
},
{
@@ -74,10 +75,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.018914,
- "end_time": "2020-03-15T16:43:46.075312",
+ "duration": 0.019696,
+ "end_time": "2020-03-15T18:37:34.967260",
"exception": false,
- "start_time": "2020-03-15T16:43:46.056398",
+ "start_time": "2020-03-15T18:37:34.947564",
"status": "completed"
},
"tags": []
@@ -92,114 +93,32 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.083927,
- "end_time": "2020-03-15T16:43:46.168567",
+ "duration": 0.11357,
+ "end_time": "2020-03-15T18:37:35.089592",
"exception": false,
- "start_time": "2020-03-15T16:43:46.084640",
+ "start_time": "2020-03-15T18:37:34.976022",
"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",
+ "jhu_frames_map = helper.read_jhu_frames_map(ts_folder)\n",
+ "rates_frames_map = helper.read_rates_frames_map(rates_folder)\n",
+ "geodata_df = helper.read_geodata(geodata_path)\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": 0.05099,
- "end_time": "2020-03-15T16:43:46.238223",
- "exception": false,
- "start_time": "2020-03-15T16:43:46.187233",
- "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": 0.035159,
- "end_time": "2020-03-15T16:43:46.292298",
- "exception": false,
- "start_time": "2020-03-15T16:43:46.257139",
- "status": "completed"
- },
- "tags": []
- },
- "outputs": [],
- "source": [
- "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')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 8,
- "metadata": {
- "papermill": {
- "duration": 0.03375,
- "end_time": "2020-03-15T16:43:46.338662",
- "exception": false,
- "start_time": "2020-03-15T16:43:46.304912",
- "status": "completed"
- },
- "tags": []
- },
- "outputs": [],
- "source": [
"# Identify countries with 100 or more cases\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"
+ "countries_over_thresh = helper.countries_with_number_of_cases(jhu_frames_map, 'confirmed', 100)"
]
},
{
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008732,
- "end_time": "2020-03-15T16:43:46.360234",
+ "duration": 0.010515,
+ "end_time": "2020-03-15T18:37:35.119478",
"exception": false,
- "start_time": "2020-03-15T16:43:46.351502",
+ "start_time": "2020-03-15T18:37:35.108963",
"status": "completed"
},
"tags": []
@@ -214,13 +133,13 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.039299,
- "end_time": "2020-03-15T16:43:46.406504",
+ "duration": 0.043214,
+ "end_time": "2020-03-15T18:37:35.170249",
"exception": false,
- "start_time": "2020-03-15T16:43:46.367205",
+ "start_time": "2020-03-15T18:37:35.127035",
"status": "completed"
},
"tags": []
@@ -248,10 +167,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009517,
- "end_time": "2020-03-15T16:43:46.431623",
+ "duration": 0.008951,
+ "end_time": "2020-03-15T18:37:35.196228",
"exception": false,
- "start_time": "2020-03-15T16:43:46.422106",
+ "start_time": "2020-03-15T18:37:35.187277",
"status": "completed"
},
"tags": []
@@ -262,114 +181,49 @@
},
{
"cell_type": "code",
- "execution_count": 10,
- "metadata": {
- "papermill": {
- "duration": 0.19163,
- "end_time": "2020-03-15T16:43:46.630939",
- "exception": false,
- "start_time": "2020-03-15T16:43:46.439309",
- "status": "completed"
- },
- "tags": []
- },
- "outputs": [],
- "source": [
- "import altair as alt\n",
- "from vega_datasets import data"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 11,
+ "execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.048909,
- "end_time": "2020-03-15T16:43:46.699290",
+ "duration": 0.019124,
+ "end_time": "2020-03-15T18:37:35.222813",
"exception": false,
- "start_time": "2020-03-15T16:43:46.650381",
+ "start_time": "2020-03-15T18:37:35.203689",
"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",
- " 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', \n",
- " 'Confirmed/100k', 'Deaths/100k', 'Recovered/100k', \n",
- " 'Confirmed', 'Deaths', 'Recovered',\n",
- " 'Long', 'Lat']"
+ "import altair as alt"
]
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.032927,
- "end_time": "2020-03-15T16:43:46.747943",
+ "duration": 0.049232,
+ "end_time": "2020-03-15T18:37:35.282648",
"exception": false,
- "start_time": "2020-03-15T16:43:46.715016",
+ "start_time": "2020-03-15T18:37:35.233416",
"status": "completed"
},
"tags": []
},
"outputs": [],
"source": [
- "def map_of_variable(map_df, variable, title):\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\", \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\"{title} cases per 100k inhabitants\"\n",
- " ).configure_view(stroke=None)\n",
- " return p"
+ "map_df = helper.compute_map_df(rates_frames_map, jhu_frames_map, geodata_df, countries_over_thresh)"
]
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.118918,
- "end_time": "2020-03-15T16:43:46.881935",
+ "duration": 0.126646,
+ "end_time": "2020-03-15T18:37:35.429936",
"exception": false,
- "start_time": "2020-03-15T16:43:46.763017",
+ "start_time": "2020-03-15T18:37:35.303290",
"status": "completed"
},
"tags": []
@@ -379,10 +233,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-88d3169c31ab4a01b36f275f24a4faa8\"></div>\n",
+ "<div id=\"altair-viz-e60bad1540b84172a14811370b16a4b1\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-88d3169c31ab4a01b36f275f24a4faa8\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-e60bad1540b84172a14811370b16a4b1\");\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",
@@ -452,7 +306,7 @@
}
],
"source": [
- "display(map_of_variable(map_df, 'Confirmed/100k', 'Confirmed'))\n",
+ "display(helper.map_of_variable(map_df, 'Confirmed/100k', 'Confirmed'))\n",
"display(HTML('''\n",
"<p style=\"font-size: smaller\">Data Sources: \n",
" <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
@@ -463,13 +317,13 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.091709,
- "end_time": "2020-03-15T16:43:46.992648",
+ "duration": 0.097247,
+ "end_time": "2020-03-15T18:37:35.544984",
"exception": false,
- "start_time": "2020-03-15T16:43:46.900939",
+ "start_time": "2020-03-15T18:37:35.447737",
"status": "completed"
},
"tags": []
@@ -479,10 +333,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-1547c49492144563b9afc56050315808\"></div>\n",
+ "<div id=\"altair-viz-59f2d4843002481eb23decfa32046c7c\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-1547c49492144563b9afc56050315808\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-59f2d4843002481eb23decfa32046c7c\");\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",
@@ -523,16 +377,32 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
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\"Deaths\": 0.0, \"Recovered\": 5.0, \"Long\": 47.58700459, \"Lat\": 29.33431262}, {\"Country/Region\": \"Malaysia\", \"Confirmed/100k\": 0.7548705404952363, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.11101037360224064, \"Confirmed\": 238.0, \"Deaths\": 0.0, \"Recovered\": 35.0, \"Long\": 109.69762284, \"Lat\": 3.78986846}, {\"Country/Region\": \"Netherlands\", \"Confirmed/100k\": 5.565544970444868, \"Deaths/100k\": 0.06964185573027988, \"Recovered/100k\": 0.011606975955046644, \"Confirmed\": 959.0, \"Deaths\": 12.0, \"Recovered\": 2.0, \"Long\": 5.28144793, \"Lat\": 52.1007899}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 20.510558609767997, \"Deaths/100k\": 0.056451078742480724, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 1090.0, \"Deaths\": 3.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572}, {\"Country/Region\": \"Philippines\", \"Confirmed/100k\": 0.10407688667814162, \"Deaths/100k\": 0.007501036877703902, \"Recovered/100k\": 0.0018752592194259754, \"Confirmed\": 111.0, \"Deaths\": 8.0, \"Recovered\": 2.0, \"Long\": 122.88393253, \"Lat\": 11.77536778}, {\"Country/Region\": \"Poland\", \"Confirmed/100k\": 0.2712057343529827, \"Deaths/100k\": 0.007899196146203378, \"Recovered/100k\": 0.0, \"Confirmed\": 103.0, \"Deaths\": 3.0, \"Recovered\": 0.0, \"Long\": 19.39012835, \"Lat\": 52.12759564}, {\"Country/Region\": \"Portugal\", \"Confirmed/100k\": 1.6436871423399997, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.01945191884426035, \"Confirmed\": 169.0, \"Deaths\": 0.0, \"Recovered\": 2.0, \"Long\": -8.50104361, \"Lat\": 39.59550671}, {\"Country/Region\": \"Qatar\", \"Confirmed/100k\": 12.114993940705553, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.14379814766416085, \"Confirmed\": 337.0, \"Deaths\": 0.0, \"Recovered\": 4.0, \"Long\": 51.18479632, \"Lat\": 25.30601188}, {\"Country/Region\": \"Romania\", \"Confirmed/100k\": 0.6316134550303544, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.046215618660757636, \"Confirmed\": 123.0, \"Deaths\": 0.0, \"Recovered\": 9.0, \"Long\": 24.97293039, \"Lat\": 45.85243127}, {\"Country/Region\": \"Saudi Arabia\", \"Confirmed/100k\": 0.30563846287354696, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0029673637172189025, \"Confirmed\": 103.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 44.53686271, \"Lat\": 24.12245841}, {\"Country/Region\": \"Singapore\", \"Confirmed/100k\": 3.7597478557022965, \"Deaths/100k\": 0.0, \"Recovered/100k\": 1.8621392681544395, \"Confirmed\": 212.0, \"Deaths\": 0.0, \"Recovered\": 105.0, \"Long\": 103.81725592, \"Lat\": 1.35876087}, {\"Country/Region\": \"Slovenia\", \"Confirmed/100k\": 8.755076493248433, \"Deaths/100k\": 0.04837058836048858, \"Recovered/100k\": 0.0, \"Confirmed\": 181.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 14.80444238, \"Lat\": 46.11554772}, {\"Country/Region\": \"Spain\", \"Confirmed/100k\": 13.678268839257742, \"Deaths/100k\": 0.4173466474190673, \"Recovered/100k\": 1.1065036754649118, \"Confirmed\": 6391.0, \"Deaths\": 195.0, \"Recovered\": 517.0, \"Long\": -3.64755047, \"Lat\": 40.24448698}, {\"Country/Region\": \"Sweden\", \"Confirmed/100k\": 9.437135274607376, \"Deaths/100k\": 0.019640239905530446, \"Recovered/100k\": 0.009820119952765223, \"Confirmed\": 961.0, \"Deaths\": 2.0, \"Recovered\": 1.0, \"Long\": 16.74558049, \"Lat\": 62.77966519}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 15.957178869407455, \"Deaths/100k\": 0.15264409514517804, \"Recovered/100k\": 0.04696741389082401, \"Confirmed\": 1359.0, \"Deaths\": 13.0, \"Recovered\": 4.0, \"Long\": 8.20867471, \"Lat\": 46.79785878}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 0.8335181673369116, \"Deaths/100k\": 0.01650531024429528, \"Recovered/100k\": 0.0036678467209545055, \"Confirmed\": 2727.0, \"Deaths\": 54.0, \"Recovered\": 12.0, \"Long\": -112.4616737, \"Lat\": 45.6795472}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 1.719081584498703, \"Deaths/100k\": 0.031584176093152026, \"Recovered/100k\": 0.028576159322375637, \"Confirmed\": 1143.0, \"Deaths\": 21.0, \"Recovered\": 19.0, \"Long\": -2.86563164, \"Lat\": 54.12387156}]}}, {\"mode\": \"vega-lite\"});\n",
"</script>"
],
"text/plain": [
"alt.LayerChart(...)"
]
},
- "execution_count": 14,
"metadata": {},
- "output_type": "execute_result"
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\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": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
}
],
"source": [
@@ -552,7 +422,138 @@
" text=alt.Text('Confirmed/100k:Q', format=\".3\")\n",
")\n",
"\n",
- "(bars + text).properties(height=900)"
+ "chart = (bars + text).properties(height=900, title=f\"Confirmed cases per 100k inhabitants\")\n",
+ "display(chart)\n",
+ "display(HTML('''\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": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.010252,
+ "end_time": "2020-03-15T18:37:35.572988",
+ "exception": false,
+ "start_time": "2020-03-15T18:37:35.562736",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## How have cases been growing?"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "papermill": {
+ "duration": 0.070855,
+ "end_time": "2020-03-15T18:37:35.653535",
+ "exception": false,
+ "start_time": "2020-03-15T18:37:35.582680",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "confirmed_rate_df = helper.growth_df(rates_frames_map, geodata_df, 'confirmed', countries_over_thresh)\n",
+ "latest_confirmed_ser = confirmed_rate_df.set_index(\n",
+ " ['Country/Region', 'Geo Region', 'Date']).drop(\n",
+ " ['Longitude', 'Latitude'], axis=1).unstack().iloc[:,-1]\n",
+ "sort_order = latest_confirmed_ser.groupby('Geo Region').mean().sort_values(ascending=False).index.tolist()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "papermill": {
+ "duration": 0.123355,
+ "end_time": "2020-03-15T18:37:35.799231",
+ "exception": false,
+ "start_time": "2020-03-15T18:37:35.675876",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-07cbea5bc0ce418e826951bb4e106548\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-07cbea5bc0ce418e826951bb4e106548\");\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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\"Geo Region\": \"Europe\", \"Date\": \"2020-02-19T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-20T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-21T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-22T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-23T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-24T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-25T00:00:00\", \"Confirmed/100k\": 0.02260643874327642}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-26T00:00:00\", \"Confirmed/100k\": 0.02260643874327642}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-27T00:00:00\", \"Confirmed/100k\": 0.03390965811491463}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-28T00:00:00\", \"Confirmed/100k\": 0.03390965811491463}, {\"Country/Region\": \"Austria\", \"Longitude\": 14.1264761, \"Latitude\": 47.58549439, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-29T00:00:00\", \"Confirmed/100k\": 0.1017289743447439}, {\"Country/Region\": \"Austria\", \"Longitude\": 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\"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-11T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-12T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-13T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-14T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-15T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-16T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-17T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-18T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-19T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-20T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-21T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-22T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-23T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-24T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-25T00:00:00\", \"Confirmed/100k\": 0.011741853472706005}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-26T00:00:00\", \"Confirmed/100k\": 0.011741853472706005}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-27T00:00:00\", \"Confirmed/100k\": 0.09393482778164802}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-28T00:00:00\", \"Confirmed/100k\": 0.09393482778164802}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-29T00:00:00\", \"Confirmed/100k\": 0.21135336250870806}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-01T00:00:00\", \"Confirmed/100k\": 0.3170300437630621}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-02T00:00:00\", \"Confirmed/100k\": 0.4931578458536522}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-03T00:00:00\", \"Confirmed/100k\": 0.6575437944715362}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-04T00:00:00\", \"Confirmed/100k\": 1.0567668125435403}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-05T00:00:00\", \"Confirmed/100k\": 1.3385712958884843}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-06T00:00:00\", \"Confirmed/100k\": 2.5127566431590846}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-07T00:00:00\", \"Confirmed/100k\": 3.1468167306852086}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-08T00:00:00\", \"Confirmed/100k\": 3.957004620301923}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-09T00:00:00\", \"Confirmed/100k\": 4.391453198792045}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-10T00:00:00\", \"Confirmed/100k\": 5.7652500550986465}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-11T00:00:00\", \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-12T00:00:00\", \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-13T00:00:00\", \"Confirmed/100k\": 13.373971105412135}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-14T00:00:00\", \"Confirmed/100k\": 15.957178869407455}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.Chart(...)"
+ ]
+ },
+ "execution_count": 12,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "base = alt.Chart(confirmed_rate_df).properties(width=300, height=200, title=\"Countries with 2 or more cases per 100k\")\n",
+ "line = base.mark_line().encode(\n",
+ " x='Date',\n",
+ " y='Confirmed/100k',\n",
+ " color='Country/Region',\n",
+ " facet=alt.Facet('Geo Region:N', columns=1, sort=alt.SortArray(sort_order), title='Geographic Region'),\n",
+ " tooltip=[\"Country/Region:N\", \"Date:T\", \"Confirmed/100k:Q\"]\n",
+ ")\n",
+ "line"
]
}
],
@@ -575,20 +576,20 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 2.488601,
- "end_time": "2020-03-15T16:43:47.325947",
+ "duration": 2.560957,
+ "end_time": "2020-03-15T18:37:36.125203",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/e5179t23/notebooks/Dashboard.ipynb",
+ "input_path": "/tmp/fer34kve/notebooks/Dashboard.ipynb",
"output_path": "runs/Dashboard.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/e5179t23/notebooks/Dashboard.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/fer34kve/notebooks/Dashboard.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
- "geodata_path": "/tmp/e5179t23/data/geodata/geo_data.csv",
- "rates_folder": "/tmp/e5179t23/data/covid-19_rates",
- "ts_folder": "/tmp/e5179t23/data/covid-19_jhu-csse"
+ "geodata_path": "/tmp/fer34kve/data/geodata/geo_data.csv",
+ "rates_folder": "/tmp/fer34kve/data/covid-19_rates",
+ "ts_folder": "/tmp/fer34kve/data/covid-19_jhu-csse"
},
- "start_time": "2020-03-15T16:43:44.837346",
+ "start_time": "2020-03-15T18:37:33.564246",
"version": "1.1.0"
}
},
diff --git a/runs/ToRates.run.ipynb b/runs/ToRates.run.ipynb
index 34d9fda6..0a30ca67 100644
--- a/runs/ToRates.run.ipynb
+++ b/runs/ToRates.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.026762,
- "end_time": "2020-03-15T16:43:42.228951",
+ "duration": 0.024961,
+ "end_time": "2020-03-15T18:37:31.040525",
"exception": false,
- "start_time": "2020-03-15T16:43:42.202189",
+ "start_time": "2020-03-15T18:37:31.015564",
"status": "completed"
},
"tags": []
@@ -21,10 +21,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.308159,
- "end_time": "2020-03-15T16:43:42.549233",
+ "duration": 0.301514,
+ "end_time": "2020-03-15T18:37:31.355857",
"exception": false,
- "start_time": "2020-03-15T16:43:42.241074",
+ "start_time": "2020-03-15T18:37:31.054343",
"status": "completed"
},
"tags": []
@@ -40,10 +40,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024464,
- "end_time": "2020-03-15T16:43:42.596678",
+ "duration": 0.024072,
+ "end_time": "2020-03-15T18:37:31.401335",
"exception": false,
- "start_time": "2020-03-15T16:43:42.572214",
+ "start_time": "2020-03-15T18:37:31.377263",
"status": "completed"
},
"tags": [
@@ -64,10 +64,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.023161,
- "end_time": "2020-03-15T16:43:42.632795",
+ "duration": 0.024999,
+ "end_time": "2020-03-15T18:37:31.439386",
"exception": false,
- "start_time": "2020-03-15T16:43:42.609634",
+ "start_time": "2020-03-15T18:37:31.414387",
"status": "completed"
},
"tags": [
@@ -77,11 +77,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/sj0uwmdy/notebooks/ToRates.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/fsb4wn_r/notebooks/ToRates.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/ToRates.run.ipynb\"\n",
- "ts_folder = \"/tmp/sj0uwmdy/data/covid-19_jhu-csse\"\n",
- "wb_path = \"/tmp/sj0uwmdy/data/worldbank/SP.POP.TOTL.zip\"\n",
- "geodata_path = \"/tmp/sj0uwmdy/data/geodata/geo_data.csv\"\n",
+ "ts_folder = \"/tmp/fsb4wn_r/data/covid-19_jhu-csse\"\n",
+ "wb_path = \"/tmp/fsb4wn_r/data/worldbank/SP.POP.TOTL.zip\"\n",
+ "geodata_path = \"/tmp/fsb4wn_r/data/geodata/geo_data.csv\"\n",
"out_folder = \"data/covid-19_rates\"\n"
]
},
@@ -89,10 +89,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008873,
- "end_time": "2020-03-15T16:43:42.653860",
+ "duration": 0.010544,
+ "end_time": "2020-03-15T18:37:31.463234",
"exception": false,
- "start_time": "2020-03-15T16:43:42.644987",
+ "start_time": "2020-03-15T18:37:31.452690",
"status": "completed"
},
"tags": [
@@ -110,10 +110,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.027857,
- "end_time": "2020-03-15T16:43:42.690591",
+ "duration": 0.030699,
+ "end_time": "2020-03-15T18:37:31.504252",
"exception": false,
- "start_time": "2020-03-15T16:43:42.662734",
+ "start_time": "2020-03-15T18:37:31.473553",
"status": "completed"
},
"tags": []
@@ -135,10 +135,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.132113,
- "end_time": "2020-03-15T16:43:42.839054",
+ "duration": 0.130448,
+ "end_time": "2020-03-15T18:37:31.650988",
"exception": false,
- "start_time": "2020-03-15T16:43:42.706941",
+ "start_time": "2020-03-15T18:37:31.520540",
"status": "completed"
},
"tags": []
@@ -156,10 +156,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.01131,
- "end_time": "2020-03-15T16:43:42.871122",
+ "duration": 0.022829,
+ "end_time": "2020-03-15T18:37:31.697981",
"exception": false,
- "start_time": "2020-03-15T16:43:42.859812",
+ "start_time": "2020-03-15T18:37:31.675152",
"status": "completed"
},
"tags": []
@@ -173,10 +173,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.042676,
- "end_time": "2020-03-15T16:43:42.923258",
+ "duration": 0.047034,
+ "end_time": "2020-03-15T18:37:31.756497",
"exception": false,
- "start_time": "2020-03-15T16:43:42.880582",
+ "start_time": "2020-03-15T18:37:31.709463",
"status": "completed"
},
"tags": []
@@ -192,10 +192,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011135,
- "end_time": "2020-03-15T16:43:42.955397",
+ "duration": 0.011097,
+ "end_time": "2020-03-15T18:37:31.790107",
"exception": false,
- "start_time": "2020-03-15T16:43:42.944262",
+ "start_time": "2020-03-15T18:37:31.779010",
"status": "completed"
},
"tags": []
@@ -209,10 +209,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.063297,
- "end_time": "2020-03-15T16:43:43.027899",
+ "duration": 0.063536,
+ "end_time": "2020-03-15T18:37:31.862736",
"exception": false,
- "start_time": "2020-03-15T16:43:42.964602",
+ "start_time": "2020-03-15T18:37:31.799200",
"status": "completed"
},
"tags": []
@@ -345,10 +345,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010848,
- "end_time": "2020-03-15T16:43:43.059760",
+ "duration": 0.010344,
+ "end_time": "2020-03-15T18:37:31.891117",
"exception": false,
- "start_time": "2020-03-15T16:43:43.048912",
+ "start_time": "2020-03-15T18:37:31.880773",
"status": "completed"
},
"tags": []
@@ -362,10 +362,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.041061,
- "end_time": "2020-03-15T16:43:43.110716",
+ "duration": 0.027744,
+ "end_time": "2020-03-15T18:37:31.928366",
"exception": false,
- "start_time": "2020-03-15T16:43:43.069655",
+ "start_time": "2020-03-15T18:37:31.900622",
"status": "completed"
},
"tags": []
@@ -394,10 +394,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.034436,
- "end_time": "2020-03-15T16:43:43.163584",
+ "duration": 0.020322,
+ "end_time": "2020-03-15T18:37:31.963446",
"exception": false,
- "start_time": "2020-03-15T16:43:43.129148",
+ "start_time": "2020-03-15T18:37:31.943124",
"status": "completed"
},
"tags": []
@@ -412,10 +412,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012003,
- "end_time": "2020-03-15T16:43:43.199703",
+ "duration": 0.010478,
+ "end_time": "2020-03-15T18:37:31.984626",
"exception": false,
- "start_time": "2020-03-15T16:43:43.187700",
+ "start_time": "2020-03-15T18:37:31.974148",
"status": "completed"
},
"tags": []
@@ -429,10 +429,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.050802,
- "end_time": "2020-03-15T16:43:43.260325",
+ "duration": 0.047267,
+ "end_time": "2020-03-15T18:37:32.042700",
"exception": false,
- "start_time": "2020-03-15T16:43:43.209523",
+ "start_time": "2020-03-15T18:37:31.995433",
"status": "completed"
},
"tags": []
@@ -626,10 +626,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011461,
- "end_time": "2020-03-15T16:43:43.292694",
+ "duration": 0.011403,
+ "end_time": "2020-03-15T18:37:32.074357",
"exception": false,
- "start_time": "2020-03-15T16:43:43.281233",
+ "start_time": "2020-03-15T18:37:32.062954",
"status": "completed"
},
"tags": []
@@ -643,10 +643,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.037434,
- "end_time": "2020-03-15T16:43:43.340346",
+ "duration": 0.036638,
+ "end_time": "2020-03-15T18:37:32.121372",
"exception": false,
- "start_time": "2020-03-15T16:43:43.302912",
+ "start_time": "2020-03-15T18:37:32.084734",
"status": "completed"
},
"tags": []
@@ -660,10 +660,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010233,
- "end_time": "2020-03-15T16:43:43.366112",
+ "duration": 0.010241,
+ "end_time": "2020-03-15T18:37:32.149495",
"exception": false,
- "start_time": "2020-03-15T16:43:43.355879",
+ "start_time": "2020-03-15T18:37:32.139254",
"status": "completed"
},
"tags": []
@@ -677,10 +677,10 @@
"execution_count": 12,
"metadata": {
"papermill": {
- "duration": 0.062288,
- "end_time": "2020-03-15T16:43:43.438245",
+ "duration": 0.049287,
+ "end_time": "2020-03-15T18:37:32.209471",
"exception": false,
- "start_time": "2020-03-15T16:43:43.375957",
+ "start_time": "2020-03-15T18:37:32.160184",
"status": "completed"
},
"tags": []
@@ -889,10 +889,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012259,
- "end_time": "2020-03-15T16:43:43.474771",
+ "duration": 0.011342,
+ "end_time": "2020-03-15T18:37:32.242689",
"exception": false,
- "start_time": "2020-03-15T16:43:43.462512",
+ "start_time": "2020-03-15T18:37:32.231347",
"status": "completed"
},
"tags": []
@@ -906,10 +906,10 @@
"execution_count": 13,
"metadata": {
"papermill": {
- "duration": 0.080269,
- "end_time": "2020-03-15T16:43:43.565663",
+ "duration": 0.079225,
+ "end_time": "2020-03-15T18:37:32.333345",
"exception": false,
- "start_time": "2020-03-15T16:43:43.485394",
+ "start_time": "2020-03-15T18:37:32.254120",
"status": "completed"
},
"tags": []
@@ -934,10 +934,10 @@
"execution_count": 14,
"metadata": {
"papermill": {
- "duration": 0.065907,
- "end_time": "2020-03-15T16:43:43.656507",
+ "duration": 0.05118,
+ "end_time": "2020-03-15T18:37:32.407865",
"exception": false,
- "start_time": "2020-03-15T16:43:43.590600",
+ "start_time": "2020-03-15T18:37:32.356685",
"status": "completed"
},
"tags": []
@@ -970,21 +970,21 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 2.541462,
- "end_time": "2020-03-15T16:43:43.994344",
+ "duration": 2.574464,
+ "end_time": "2020-03-15T18:37:32.738690",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/sj0uwmdy/notebooks/ToRates.ipynb",
+ "input_path": "/tmp/fsb4wn_r/notebooks/ToRates.ipynb",
"output_path": "runs/ToRates.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/sj0uwmdy/notebooks/ToRates.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/fsb4wn_r/notebooks/ToRates.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/ToRates.run.ipynb",
- "geodata_path": "/tmp/sj0uwmdy/data/geodata/geo_data.csv",
+ "geodata_path": "/tmp/fsb4wn_r/data/geodata/geo_data.csv",
"out_folder": "data/covid-19_rates",
- "ts_folder": "/tmp/sj0uwmdy/data/covid-19_jhu-csse",
- "wb_path": "/tmp/sj0uwmdy/data/worldbank/SP.POP.TOTL.zip"
+ "ts_folder": "/tmp/fsb4wn_r/data/covid-19_jhu-csse",
+ "wb_path": "/tmp/fsb4wn_r/data/worldbank/SP.POP.TOTL.zip"
},
- "start_time": "2020-03-15T16:43:41.452882",
+ "start_time": "2020-03-15T18:37:30.164226",
"version": "1.1.0"
}
},
--
GitLab