From 20a27ffe957c4241c06d3f421afd90cc3beb5305 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Thu, 26 Mar 2020 13:22:52 +0000
Subject: [PATCH] renku update --with-siblings
---
.../69ffb70aa73345e6876d1d23497af960.cwl | 191 ++++++++++++
.../ts_rates_19-covid-confirmed.csv | 4 +-
.../ts_rates_19-covid-deaths.csv | 4 +-
runs/CompileGeoData.run.ipynb | 168 +++++------
runs/Dashboard.run.ipynb | 182 ++++++------
runs/ToRates.run.ipynb | 271 ++++++++++--------
6 files changed, 515 insertions(+), 305 deletions(-)
create mode 100644 .renku/workflow/69ffb70aa73345e6876d1d23497af960.cwl
diff --git a/.renku/workflow/69ffb70aa73345e6876d1d23497af960.cwl b/.renku/workflow/69ffb70aa73345e6876d1d23497af960.cwl
new file mode 100644
index 00000000..98b2bd6c
--- /dev/null
+++ b/.renku/workflow/69ffb70aa73345e6876d1d23497af960.cwl
@@ -0,0 +1,191 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ streamable: false
+ type: string
+ input_10:
+ default:
+ class: File
+ path: ../../notebooks/process/ToRates.ipynb
+ streamable: false
+ type: File
+ input_11:
+ default: ts_folder
+ streamable: false
+ type: string
+ input_12:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_13:
+ default: rates_folder
+ streamable: false
+ type: string
+ input_14:
+ default: geodata_path
+ streamable: false
+ type: string
+ input_15:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ streamable: false
+ type: File
+ input_16:
+ default:
+ class: File
+ path: ../../notebooks/Dashboard.ipynb
+ streamable: false
+ type: File
+ input_17:
+ default: runs/Dashboard.run.ipynb
+ streamable: false
+ type: string
+ input_18:
+ default: ts_folder
+ streamable: false
+ type: string
+ input_19:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_2:
+ default: runs/ToRates.run.ipynb
+ streamable: false
+ type: string
+ input_20:
+ default: worldmap_path
+ streamable: false
+ type: string
+ input_21:
+ default:
+ class: File
+ path: ../../data/worldmap/country_centroids.csv
+ streamable: false
+ type: File
+ input_22:
+ default: out_folder
+ streamable: false
+ type: string
+ input_23:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/geodata
+ streamable: false
+ type: Directory
+ input_24:
+ default:
+ class: File
+ path: ../../notebooks/process/CompileGeoData.ipynb
+ streamable: false
+ type: File
+ input_25:
+ default: runs/CompileGeoData.run.ipynb
+ streamable: false
+ type: string
+ input_3:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_4:
+ default: wb_path
+ streamable: false
+ type: string
+ input_5:
+ default:
+ class: File
+ path: ../../data/worldbank/SP.POP.TOTL.zip
+ streamable: false
+ type: File
+ input_6:
+ default: geodata_path
+ streamable: false
+ type: string
+ input_7:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ streamable: false
+ type: File
+ input_8:
+ default: out_folder
+ streamable: false
+ type: string
+ input_9:
+ default: data/covid-19_rates
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+ output_1:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_10: input_2
+ input_2: input_3
+ input_3: input_4
+ input_4: input_5
+ input_5: input_6
+ input_6: input_7
+ input_7: input_8
+ input_8: input_9
+ input_9: input_10
+ out:
+ - output_0
+ - output_1
+ run: 6f3ea2ea2542427d8ac95d26349080ed_papermill.cwl
+ step_2:
+ in:
+ input_2: input_11
+ input_3: input_12
+ input_4: input_13
+ input_5: step_1/output_1
+ input_6: input_14
+ input_7: input_15
+ input_8: input_16
+ input_9: input_17
+ out:
+ - output_0
+ run: f2fb09baacb048be928c7b7bd9a47b6b_papermill.cwl
+ step_3:
+ in:
+ input_1: input_18
+ input_2: input_19
+ input_3: input_20
+ input_4: input_21
+ input_5: input_22
+ input_6: input_23
+ input_7: input_24
+ input_8: input_25
+ out:
+ - output_0
+ run: 9f96a8bde4314c539e6fde022b289b63_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
index a8c6f48b..14294f6a 100644
--- a/data/covid-19_rates/ts_rates_19-covid-confirmed.csv
+++ b/data/covid-19_rates/ts_rates_19-covid-confirmed.csv
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:c021fbd9b0623ca6fda3386b6b82d2973749d434a384704e1eb5afbc81be0932
-size 105565
+oid sha256:b7a9660553d445e163c0760ed46b95da52d28c821850e09bd2cfd12a5d890858
+size 110145
diff --git a/data/covid-19_rates/ts_rates_19-covid-deaths.csv b/data/covid-19_rates/ts_rates_19-covid-deaths.csv
index bb293e55..df5b6d67 100644
--- a/data/covid-19_rates/ts_rates_19-covid-deaths.csv
+++ b/data/covid-19_rates/ts_rates_19-covid-deaths.csv
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:cf36cf8457f0e1625144bd3bb75592635eebd906624bc677ecc373acf8d7a532
-size 63060
+oid sha256:8480095f36095407d80eee773be9ca4a91209d663ad87c4ae6af1863384e73f1
+size 66337
diff --git a/runs/CompileGeoData.run.ipynb b/runs/CompileGeoData.run.ipynb
index b634743e..42ced54c 100644
--- a/runs/CompileGeoData.run.ipynb
+++ b/runs/CompileGeoData.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.022012,
- "end_time": "2020-03-25T23:06:29.412987",
+ "duration": 0.022323,
+ "end_time": "2020-03-26T13:22:44.646598",
"exception": false,
- "start_time": "2020-03-25T23:06:29.390975",
+ "start_time": "2020-03-26T13:22:44.624275",
"status": "completed"
},
"tags": []
@@ -23,10 +23,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.31006,
- "end_time": "2020-03-25T23:06:29.733704",
+ "duration": 0.337871,
+ "end_time": "2020-03-26T13:22:44.995055",
"exception": false,
- "start_time": "2020-03-25T23:06:29.423644",
+ "start_time": "2020-03-26T13:22:44.657184",
"status": "completed"
},
"tags": []
@@ -42,10 +42,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.032622,
- "end_time": "2020-03-25T23:06:29.791939",
+ "duration": 0.024696,
+ "end_time": "2020-03-26T13:22:45.036188",
"exception": false,
- "start_time": "2020-03-25T23:06:29.759317",
+ "start_time": "2020-03-26T13:22:45.011492",
"status": "completed"
},
"tags": []
@@ -62,10 +62,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010303,
- "end_time": "2020-03-25T23:06:29.819422",
+ "duration": 0.008821,
+ "end_time": "2020-03-26T13:22:45.057062",
"exception": false,
- "start_time": "2020-03-25T23:06:29.809119",
+ "start_time": "2020-03-26T13:22:45.048241",
"status": "completed"
},
"tags": [
@@ -81,10 +81,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.02561,
- "end_time": "2020-03-25T23:06:29.853366",
+ "duration": 0.024941,
+ "end_time": "2020-03-26T13:22:45.090116",
"exception": false,
- "start_time": "2020-03-25T23:06:29.827756",
+ "start_time": "2020-03-26T13:22:45.065175",
"status": "completed"
},
"tags": [
@@ -94,11 +94,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"notebooks/process/CompileGeoData.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/g3lga9o8/notebooks/process/CompileGeoData.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/CompileGeoData.run.ipynb\"\n",
- "ts_folder = \"./data/covid-19_jhu-csse/\"\n",
- "worldmap_path = \"./data/worldmap/country_centroids.csv\"\n",
- "out_folder = \"./data/geodata/\"\n"
+ "ts_folder = \"/tmp/g3lga9o8/data/covid-19_jhu-csse\"\n",
+ "worldmap_path = \"/tmp/g3lga9o8/data/worldmap/country_centroids.csv\"\n",
+ "out_folder = \"/tmp/g3lga9o8/data/geodata\"\n"
]
},
{
@@ -106,10 +106,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.030257,
- "end_time": "2020-03-25T23:06:29.896762",
+ "duration": 0.025233,
+ "end_time": "2020-03-26T13:22:45.135369",
"exception": false,
- "start_time": "2020-03-25T23:06:29.866505",
+ "start_time": "2020-03-26T13:22:45.110136",
"status": "completed"
},
"tags": []
@@ -130,10 +130,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.043726,
- "end_time": "2020-03-25T23:06:29.950112",
+ "duration": 0.054123,
+ "end_time": "2020-03-26T13:22:45.202307",
"exception": false,
- "start_time": "2020-03-25T23:06:29.906386",
+ "start_time": "2020-03-26T13:22:45.148184",
"status": "completed"
},
"tags": []
@@ -147,10 +147,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010675,
- "end_time": "2020-03-25T23:06:29.969305",
+ "duration": 0.007699,
+ "end_time": "2020-03-26T13:22:45.217884",
"exception": false,
- "start_time": "2020-03-25T23:06:29.958630",
+ "start_time": "2020-03-26T13:22:45.210185",
"status": "completed"
},
"tags": []
@@ -164,10 +164,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.03387,
- "end_time": "2020-03-25T23:06:30.011734",
+ "duration": 0.031588,
+ "end_time": "2020-03-26T13:22:45.257211",
"exception": false,
- "start_time": "2020-03-25T23:06:29.977864",
+ "start_time": "2020-03-26T13:22:45.225623",
"status": "completed"
},
"tags": []
@@ -184,10 +184,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.024666,
- "end_time": "2020-03-25T23:06:30.044629",
+ "duration": 0.037705,
+ "end_time": "2020-03-26T13:22:45.303604",
"exception": false,
- "start_time": "2020-03-25T23:06:30.019963",
+ "start_time": "2020-03-26T13:22:45.265899",
"status": "completed"
},
"tags": []
@@ -214,10 +214,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008554,
- "end_time": "2020-03-25T23:06:30.061787",
+ "duration": 0.009762,
+ "end_time": "2020-03-26T13:22:45.332521",
"exception": false,
- "start_time": "2020-03-25T23:06:30.053233",
+ "start_time": "2020-03-26T13:22:45.322759",
"status": "completed"
},
"tags": []
@@ -231,10 +231,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.021791,
- "end_time": "2020-03-25T23:06:30.092630",
+ "duration": 0.030831,
+ "end_time": "2020-03-26T13:22:45.371494",
"exception": false,
- "start_time": "2020-03-25T23:06:30.070839",
+ "start_time": "2020-03-26T13:22:45.340663",
"status": "completed"
},
"tags": []
@@ -260,10 +260,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.016177,
- "end_time": "2020-03-25T23:06:30.118527",
+ "duration": 0.026196,
+ "end_time": "2020-03-26T13:22:45.411424",
"exception": false,
- "start_time": "2020-03-25T23:06:30.102350",
+ "start_time": "2020-03-26T13:22:45.385228",
"status": "completed"
},
"tags": []
@@ -278,10 +278,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008023,
- "end_time": "2020-03-25T23:06:30.135845",
+ "duration": 0.009748,
+ "end_time": "2020-03-26T13:22:45.435849",
"exception": false,
- "start_time": "2020-03-25T23:06:30.127822",
+ "start_time": "2020-03-26T13:22:45.426101",
"status": "completed"
},
"tags": []
@@ -295,10 +295,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.024846,
- "end_time": "2020-03-25T23:06:30.169128",
+ "duration": 0.04638,
+ "end_time": "2020-03-26T13:22:45.491053",
"exception": false,
- "start_time": "2020-03-25T23:06:30.144282",
+ "start_time": "2020-03-26T13:22:45.444673",
"status": "completed"
},
"tags": []
@@ -325,8 +325,8 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>2020-03-23</th>\n",
" <th>2020-03-24</th>\n",
+ " <th>2020-03-25</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Country/Region</th>\n",
@@ -338,7 +338,7 @@
" <tr>\n",
" <th>Cabo Verde</th>\n",
" <td>3</td>\n",
- " <td>3</td>\n",
+ " <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Congo (Brazzaville)</th>\n",
@@ -347,8 +347,8 @@
" </tr>\n",
" <tr>\n",
" <th>Congo (Kinshasa)</th>\n",
- " <td>36</td>\n",
" <td>45</td>\n",
+ " <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Diamond Princess</th>\n",
@@ -362,46 +362,46 @@
" </tr>\n",
" <tr>\n",
" <th>Gambia</th>\n",
- " <td>2</td>\n",
+ " <td>3</td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Holy See</th>\n",
- " <td>1</td>\n",
+ " <td>4</td>\n",
" <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Laos</th>\n",
- " <td>0</td>\n",
" <td>2</td>\n",
+ " <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>North Macedonia</th>\n",
- " <td>136</td>\n",
" <td>148</td>\n",
+ " <td>177</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>The West Bank and Gaza</th>\n",
- " <td>59</td>\n",
+ " <th>West Bank and Gaza</th>\n",
" <td>59</td>\n",
+ " <td>-1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
- " 2020-03-23 2020-03-24\n",
- "Country/Region \n",
- "Cabo Verde 3 3\n",
- "Congo (Brazzaville) 4 4\n",
- "Congo (Kinshasa) 36 45\n",
- "Diamond Princess 712 712\n",
- "Eswatini 4 4\n",
- "Gambia 2 3\n",
- "Holy See 1 4\n",
- "Laos 0 2\n",
- "North Macedonia 136 148\n",
- "The West Bank and Gaza 59 59"
+ " 2020-03-24 2020-03-25\n",
+ "Country/Region \n",
+ "Cabo Verde 3 4\n",
+ "Congo (Brazzaville) 4 4\n",
+ "Congo (Kinshasa) 45 48\n",
+ "Diamond Princess 712 712\n",
+ "Eswatini 4 4\n",
+ "Gambia 3 3\n",
+ "Holy See 4 4\n",
+ "Laos 2 3\n",
+ "North Macedonia 148 177\n",
+ "West Bank and Gaza 59 -1"
]
},
"execution_count": 10,
@@ -419,10 +419,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008814,
- "end_time": "2020-03-25T23:06:30.186744",
+ "duration": 0.009932,
+ "end_time": "2020-03-26T13:22:45.518476",
"exception": false,
- "start_time": "2020-03-25T23:06:30.177930",
+ "start_time": "2020-03-26T13:22:45.508544",
"status": "completed"
},
"tags": []
@@ -436,10 +436,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.02285,
- "end_time": "2020-03-25T23:06:30.218131",
+ "duration": 0.037962,
+ "end_time": "2020-03-26T13:22:45.565000",
"exception": false,
- "start_time": "2020-03-25T23:06:30.195281",
+ "start_time": "2020-03-26T13:22:45.527038",
"status": "completed"
},
"tags": []
@@ -471,20 +471,20 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 2.077387,
- "end_time": "2020-03-25T23:06:30.537956",
+ "duration": 2.257336,
+ "end_time": "2020-03-26T13:22:46.017593",
"environment_variables": {},
"exception": null,
- "input_path": "notebooks/process/CompileGeoData.ipynb",
+ "input_path": "/tmp/g3lga9o8/notebooks/process/CompileGeoData.ipynb",
"output_path": "runs/CompileGeoData.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "notebooks/process/CompileGeoData.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/g3lga9o8/notebooks/process/CompileGeoData.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/CompileGeoData.run.ipynb",
- "out_folder": "./data/geodata/",
- "ts_folder": "./data/covid-19_jhu-csse/",
- "worldmap_path": "./data/worldmap/country_centroids.csv"
+ "out_folder": "/tmp/g3lga9o8/data/geodata",
+ "ts_folder": "/tmp/g3lga9o8/data/covid-19_jhu-csse",
+ "worldmap_path": "/tmp/g3lga9o8/data/worldmap/country_centroids.csv"
},
- "start_time": "2020-03-25T23:06:28.460569",
+ "start_time": "2020-03-26T13:22:43.760257",
"version": "1.1.0"
}
},
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
index a1fefb04..ebb70ea6 100644
--- a/runs/Dashboard.run.ipynb
+++ b/runs/Dashboard.run.ipynb
@@ -8,10 +8,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.512393,
- "end_time": "2020-03-25T23:22:57.054825",
+ "duration": 0.484766,
+ "end_time": "2020-03-26T13:22:48.268772",
"exception": false,
- "start_time": "2020-03-25T23:22:56.542432",
+ "start_time": "2020-03-26T13:22:47.784006",
"status": "completed"
},
"tags": []
@@ -33,10 +33,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.023158,
- "end_time": "2020-03-25T23:22:57.098925",
+ "duration": 0.028053,
+ "end_time": "2020-03-26T13:22:48.317261",
"exception": false,
- "start_time": "2020-03-25T23:22:57.075767",
+ "start_time": "2020-03-26T13:22:48.289208",
"status": "completed"
},
"tags": [
@@ -60,10 +60,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.032132,
- "end_time": "2020-03-25T23:22:57.145898",
+ "duration": 0.026441,
+ "end_time": "2020-03-26T13:22:48.356577",
"exception": false,
- "start_time": "2020-03-25T23:22:57.113766",
+ "start_time": "2020-03-26T13:22:48.330136",
"status": "completed"
},
"tags": [
@@ -73,11 +73,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/rh_o282i/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",
- "geodata_path = \"./data/geodata/geo_data.csv\"\n"
+ "ts_folder = \"/tmp/rh_o282i/data/covid-19_jhu-csse\"\n",
+ "rates_folder = \"/tmp/rh_o282i/data/covid-19_rates\"\n",
+ "geodata_path = \"/tmp/rh_o282i/data/geodata/geo_data.csv\"\n"
]
},
{
@@ -88,10 +88,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.022307,
- "end_time": "2020-03-25T23:22:57.181692",
+ "duration": 0.024714,
+ "end_time": "2020-03-26T13:22:48.394385",
"exception": false,
- "start_time": "2020-03-25T23:22:57.159385",
+ "start_time": "2020-03-26T13:22:48.369671",
"status": "completed"
},
"tags": []
@@ -109,10 +109,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.10598,
- "end_time": "2020-03-25T23:22:57.300114",
+ "duration": 0.094078,
+ "end_time": "2020-03-26T13:22:48.502200",
"exception": false,
- "start_time": "2020-03-25T23:22:57.194134",
+ "start_time": "2020-03-26T13:22:48.408122",
"status": "completed"
},
"tags": []
@@ -133,10 +133,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011489,
- "end_time": "2020-03-25T23:22:57.336706",
+ "duration": 0.011094,
+ "end_time": "2020-03-26T13:22:48.537154",
"exception": false,
- "start_time": "2020-03-25T23:22:57.325217",
+ "start_time": "2020-03-26T13:22:48.526060",
"status": "completed"
},
"tags": []
@@ -157,10 +157,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.040462,
- "end_time": "2020-03-25T23:22:57.386860",
+ "duration": 0.046529,
+ "end_time": "2020-03-26T13:22:48.594490",
"exception": false,
- "start_time": "2020-03-25T23:22:57.346398",
+ "start_time": "2020-03-26T13:22:48.547961",
"status": "completed"
},
"tags": []
@@ -169,7 +169,7 @@
{
"data": {
"text/html": [
- "<em>Data up to Mar 24 2020; countries with 100 or more confirmed cases.</em>"
+ "<em>Data up to Mar 25 2020; countries with 100 or more confirmed cases.</em>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
@@ -188,10 +188,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010368,
- "end_time": "2020-03-25T23:22:57.413993",
+ "duration": 0.012004,
+ "end_time": "2020-03-26T13:22:48.625059",
"exception": false,
- "start_time": "2020-03-25T23:22:57.403625",
+ "start_time": "2020-03-26T13:22:48.613055",
"status": "completed"
},
"tags": []
@@ -208,10 +208,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.02346,
- "end_time": "2020-03-25T23:22:57.447533",
+ "duration": 0.026189,
+ "end_time": "2020-03-26T13:22:48.663014",
"exception": false,
- "start_time": "2020-03-25T23:22:57.424073",
+ "start_time": "2020-03-26T13:22:48.636825",
"status": "completed"
},
"tags": []
@@ -229,10 +229,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.049505,
- "end_time": "2020-03-25T23:22:57.509484",
+ "duration": 0.054551,
+ "end_time": "2020-03-26T13:22:48.733684",
"exception": false,
- "start_time": "2020-03-25T23:22:57.459979",
+ "start_time": "2020-03-26T13:22:48.679133",
"status": "completed"
},
"tags": []
@@ -250,10 +250,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.103145,
- "end_time": "2020-03-25T23:22:57.629115",
+ "duration": 0.111374,
+ "end_time": "2020-03-26T13:22:48.864878",
"exception": false,
- "start_time": "2020-03-25T23:22:57.525970",
+ "start_time": "2020-03-26T13:22:48.753504",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-c9c93ab3d04346e19c70ff509bde07a4\"></div>\n",
+ "<div id=\"altair-viz-ed9c522d189f4cefa7cce0642fcb352f\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-c9c93ab3d04346e19c70ff509bde07a4\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-ed9c522d189f4cefa7cce0642fcb352f\");\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",
@@ -307,7 +307,7 @@
" .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-b91a61172d8dd61402e38a5635335c32\"}, \"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\", \"field\": \"Country/Region\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, {\"type\": \"quantitative\", \"field\": \"Deaths\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, {\"type\": \"quantitative\", \"field\": \"Deaths/100k\"}]}}], \"height\": 400, \"projection\": {\"type\": \"naturalEarth1\"}, \"title\": \"Confirmed cases per 100k inhabitants\", \"width\": 600, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-b91a61172d8dd61402e38a5635335c32\": [{\"Country/Region\": \"Albania\", \"Confirmed/100k\": 4.291132775323265, \"Deaths/100k\": 0.17443629167980754, \"Confirmed\": 123.0, \"Deaths\": 5.0, \"Long\": 20.04983396, \"Lat\": 41.14244989}, {\"Country/Region\": \"Algeria\", \"Confirmed/100k\": 0.6251712560749063, \"Deaths/100k\": 0.044993385853875835, \"Confirmed\": 264.0, \"Deaths\": 19.0, \"Long\": 2.61732301, \"Lat\": 28.15893849}, {\"Country/Region\": \"Argentina\", \"Confirmed/100k\": 0.8697703819676417, 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0.020251590572580816, \"Confirmed\": 114.0, \"Deaths\": 4.0, \"Long\": -1.75456601, \"Lat\": 12.26953846}, {\"Country/Region\": \"Canada\", \"Confirmed/100k\": 7.528564832114624, \"Deaths/100k\": 0.07015866868637284, \"Confirmed\": 2790.0, \"Deaths\": 26.0, \"Long\": -98.30777028, \"Lat\": 61.36206324}, {\"Country/Region\": \"Chile\", \"Confirmed/100k\": 4.922804866849341, \"Deaths/100k\": 0.010678535502926986, \"Confirmed\": 922.0, \"Deaths\": 2.0, \"Long\": -71.38256213, \"Lat\": -37.73070989}, {\"Country/Region\": \"China\", \"Confirmed/100k\": 5.858350146833915, \"Deaths/100k\": 0.2355804786283056, \"Confirmed\": 81591.0, \"Deaths\": 3281.0, \"Long\": 103.81907349, \"Lat\": 36.56176546}, {\"Country/Region\": \"Colombia\", \"Confirmed/100k\": 0.7613494697795118, \"Deaths/100k\": 0.006042456109361205, \"Confirmed\": 378.0, \"Deaths\": 3.0, \"Long\": -73.08114582, \"Lat\": 3.91383431}, {\"Country/Region\": \"Costa Rica\", \"Confirmed/100k\": 3.5403958162522566, \"Deaths/100k\": 0.0400044725000255, \"Confirmed\": 177.0, \"Deaths\": 2.0, \"Long\": -84.19208768, \"Lat\": 9.97634464}, {\"Country/Region\": \"Croatia\", \"Confirmed/100k\": 9.341223651391402, \"Deaths/100k\": 0.02445346505599844, \"Confirmed\": 382.0, \"Deaths\": 1.0, \"Long\": 16.40412899, \"Lat\": 45.08047631}, {\"Country/Region\": \"Cyprus\", \"Confirmed/100k\": 10.426608031010751, \"Deaths/100k\": 0.2522566459115504, \"Confirmed\": 124.0, \"Deaths\": 3.0, \"Long\": 33.0060022, \"Lat\": 34.91667211}, {\"Country/Region\": \"Czechia\", \"Confirmed/100k\": 13.119141853779919, \"Deaths/100k\": 0.028233447318034257, \"Confirmed\": 1394.0, \"Deaths\": 3.0, \"Long\": 15.31240163, \"Lat\": 49.73341233}, {\"Country/Region\": \"Denmark\", \"Confirmed/100k\": 29.633738718739252, \"Deaths/100k\": 0.5519671938298347, \"Confirmed\": 1718.0, \"Deaths\": 32.0, \"Long\": 10.02800992, \"Lat\": 55.98125296}, {\"Country/Region\": \"Dominican Republic\", \"Confirmed/100k\": 2.9358723610671333, \"Deaths/100k\": 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35.92149632}, {\"Country/Region\": \"Mexico\", \"Confirmed/100k\": 0.29082947005608684, \"Deaths/100k\": 0.0031698034883497197, \"Confirmed\": 367.0, \"Deaths\": 4.0, \"Long\": -102.52345169, \"Lat\": 23.94753724}, {\"Country/Region\": \"Moldova\", \"Confirmed/100k\": 3.525215016964745, \"Deaths/100k\": 0.028201720135717964, \"Confirmed\": 125.0, \"Deaths\": 1.0, \"Long\": 28.45673372, \"Lat\": 47.19498804}, {\"Country/Region\": \"Morocco\", \"Confirmed/100k\": 0.4718403199099573, \"Deaths/100k\": 0.01387765646793992, \"Confirmed\": 170.0, \"Deaths\": 5.0, \"Long\": -8.45615795, \"Lat\": 29.83762955}, {\"Country/Region\": \"Netherlands\", \"Confirmed/100k\": 32.38346291458014, \"Deaths/100k\": 1.6075661697739605, \"Confirmed\": 5580.0, \"Deaths\": 277.0, \"Long\": 5.28144793, \"Lat\": 52.1007899}, {\"Country/Region\": \"New Zealand\", \"Confirmed/100k\": 3.1726537713642413, \"Deaths/100k\": 0.0, \"Confirmed\": 155.0, \"Deaths\": 0.0, \"Long\": 171.48492347, \"Lat\": -41.81113557}, 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\"Confirmed/100k\": 1.99348435041134}, {\"Country/Region\": \"Sweden\", \"Days\": 3, \"Confirmed\": 147, \"Confirmed/100k\": 2.435389748285776}, {\"Country/Region\": \"Sweden\", \"Days\": 4, \"Confirmed\": 254, \"Confirmed/100k\": 3.4861425832316537}, {\"Country/Region\": \"Sweden\", \"Days\": 5, \"Confirmed\": 399, \"Confirmed/100k\": 4.9100599763826125}, {\"Country/Region\": \"Sweden\", \"Days\": 6, \"Confirmed\": 498, \"Confirmed/100k\": 5.882251851706369}, {\"Country/Region\": \"Sweden\", \"Days\": 7, \"Confirmed\": 713, \"Confirmed/100k\": 7.993577641550892}, {\"Country/Region\": \"Sweden\", \"Days\": 8, \"Confirmed\": 860, \"Confirmed/100k\": 9.437135274607376}, {\"Country/Region\": \"Sweden\", \"Days\": 9, \"Confirmed\": 921, \"Confirmed/100k\": 10.036162591726056}, {\"Country/Region\": \"Sweden\", \"Days\": 10, \"Confirmed\": 1002, \"Confirmed/100k\": 10.831592307900042}, {\"Country/Region\": \"Sweden\", \"Days\": 11, \"Confirmed\": 1089, \"Confirmed/100k\": 11.685942743790614}, {\"Country/Region\": \"Sweden\", \"Days\": 12, \"Confirmed\": 1178, \"Confirmed/100k\": 12.559933419586716}, {\"Country/Region\": \"Sweden\", \"Days\": 13, \"Confirmed\": 1338, \"Confirmed/100k\": 14.131152612029155}, {\"Country/Region\": \"Sweden\", \"Days\": 14, \"Confirmed\": 1538, \"Confirmed/100k\": 16.0951766025822}, {\"Country/Region\": \"Sweden\", \"Days\": 15, \"Confirmed\": 1662, \"Confirmed/100k\": 17.31287147672509}, {\"Country/Region\": \"Sweden\", \"Days\": 16, \"Confirmed\": 1833, \"Confirmed/100k\": 18.99211198864794}, {\"Country/Region\": \"Sweden\", \"Days\": 17, \"Confirmed\": 1945, \"Confirmed/100k\": 20.09196542335765}, {\"Country/Region\": \"Sweden\", \"Days\": 18, \"Confirmed\": 2185, \"Confirmed/100k\": 22.448794212021298}, {\"Country/Region\": \"Sweden\", \"Days\": 19, \"Confirmed\": 2425, \"Confirmed/100k\": 24.805623000684953}, {\"Country/Region\": \"Switzerland\", \"Days\": 0, \"Confirmed\": 0, \"Confirmed/100k\": 1.3385712958884843}, {\"Country/Region\": \"Switzerland\", \"Days\": 1, \"Confirmed\": 100, \"Confirmed/100k\": 2.5127566431590846}, {\"Country/Region\": \"Switzerland\", \"Days\": 2, \"Confirmed\": 154, \"Confirmed/100k\": 3.1468167306852086}, {\"Country/Region\": \"Switzerland\", \"Days\": 3, \"Confirmed\": 223, \"Confirmed/100k\": 3.957004620301923}, {\"Country/Region\": \"Switzerland\", \"Days\": 4, \"Confirmed\": 260, \"Confirmed/100k\": 4.391453198792045}, {\"Country/Region\": \"Switzerland\", \"Days\": 5, \"Confirmed\": 377, \"Confirmed/100k\": 5.7652500550986465}, {\"Country/Region\": \"Switzerland\", \"Days\": 6, \"Confirmed\": 538, \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Days\": 7, \"Confirmed\": 538, \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Days\": 8, \"Confirmed\": 1025, \"Confirmed/100k\": 13.373971105412135}, {\"Country/Region\": \"Switzerland\", \"Days\": 9, \"Confirmed\": 1245, \"Confirmed/100k\": 15.957178869407455}, {\"Country/Region\": \"Switzerland\", \"Days\": 10, \"Confirmed\": 2086, \"Confirmed/100k\": 25.8320776399532}, {\"Country/Region\": \"Switzerland\", \"Days\": 11, \"Confirmed\": 2086, \"Confirmed/100k\": 25.8320776399532}, {\"Country/Region\": \"Switzerland\", \"Days\": 12, \"Confirmed\": 2586, \"Confirmed/100k\": 31.70300437630621}, {\"Country/Region\": \"Switzerland\", \"Days\": 13, \"Confirmed\": 2914, \"Confirmed/100k\": 35.554332315353776}, {\"Country/Region\": \"Switzerland\", \"Days\": 14, \"Confirmed\": 3961, \"Confirmed/100k\": 47.84805290127696}, {\"Country/Region\": \"Switzerland\", \"Days\": 15, \"Confirmed\": 5180, \"Confirmed/100k\": 62.161372284505575}, {\"Country/Region\": \"Switzerland\", \"Days\": 16, \"Confirmed\": 6461, \"Confirmed/100k\": 77.20268658304197}, {\"Country/Region\": \"Switzerland\", \"Days\": 17, \"Confirmed\": 7360, \"Confirmed/100k\": 87.75861285500467}, {\"Country/Region\": \"Switzerland\", \"Days\": 18, \"Confirmed\": 8681, \"Confirmed/100k\": 103.26960129244931}, {\"Country/Region\": \"Switzerland\", \"Days\": 19, \"Confirmed\": 9763, \"Confirmed/100k\": 115.9742867499172}, {\"Country/Region\": \"Switzerland\", \"Days\": 20, \"Confirmed\": 10783, \"Confirmed/100k\": 127.9509772920773}, {\"Country/Region\": \"Turkey\", \"Days\": 0, \"Confirmed\": 0, \"Confirmed/100k\": 0.2332369335932176}, {\"Country/Region\": \"Turkey\", \"Days\": 1, \"Confirmed\": 167, \"Confirmed/100k\": 0.436104474791485}, {\"Country/Region\": \"Turkey\", \"Days\": 2, \"Confirmed\": 478, \"Confirmed/100k\": 0.8138997161846656}, {\"Country/Region\": \"Turkey\", \"Days\": 3, \"Confirmed\": 1044, \"Confirmed/100k\": 1.5014627600063382}, {\"Country/Region\": \"Turkey\", \"Days\": 4, \"Confirmed\": 1337, \"Confirmed/100k\": 1.8573920388751548}, {\"Country/Region\": \"Turkey\", \"Days\": 5, \"Confirmed\": 1680, \"Confirmed/100k\": 2.274060102533872}, {\"Country/Region\": \"Turkey\", \"Days\": 6, \"Confirmed\": 2241, \"Confirmed/100k\": 2.9555492678765543}, {\"Country/Region\": \"US\", \"Days\": 0, \"Confirmed\": 0, \"Confirmed/100k\": 0.03606715942271932}, {\"Country/Region\": \"US\", \"Days\": 1, \"Confirmed\": 31, \"Confirmed/100k\": 0.04554243011851846}, {\"Country/Region\": \"US\", \"Days\": 2, \"Confirmed\": 99, \"Confirmed/100k\": 0.06632689487059401}, {\"Country/Region\": \"US\", \"Days\": 3, \"Confirmed\": 144, \"Confirmed/100k\": 0.0800813200741734}, {\"Country/Region\": \"US\", \"Days\": 4, \"Confirmed\": 284, \"Confirmed/100k\": 0.122872865151976}, {\"Country/Region\": \"US\", \"Days\": 5, \"Confirmed\": 400, \"Confirmed/100k\": 0.15832871678786953}, {\"Country/Region\": \"US\", \"Days\": 6, \"Confirmed\": 465, \"Confirmed/100k\": 0.17819621985970646}, {\"Country/Region\": \"US\", \"Days\": 7, \"Confirmed\": 841, \"Confirmed/100k\": 0.2931220837829477}, {\"Country/Region\": \"US\", \"Days\": 8, \"Confirmed\": 1163, \"Confirmed/100k\": 0.3915426374618936}, {\"Country/Region\": \"US\", \"Days\": 9, \"Confirmed\": 1545, \"Confirmed/100k\": 0.508302424745612}, {\"Country/Region\": \"US\", \"Days\": 10, \"Confirmed\": 2061, \"Confirmed/100k\": 0.6660198337466559}, {\"Country/Region\": \"US\", \"Days\": 11, \"Confirmed\": 2609, \"Confirmed/100k\": 0.8335181673369116}, {\"Country/Region\": \"US\", \"Days\": 12, \"Confirmed\": 3381, \"Confirmed/100k\": 1.0694829730516515}, {\"Country/Region\": \"US\", \"Days\": 13, \"Confirmed\": 4514, \"Confirmed/100k\": 1.4157888342884395}, {\"Country/Region\": \"US\", \"Days\": 14, \"Confirmed\": 6303, \"Confirmed/100k\": 1.962603649604074}, {\"Country/Region\": \"US\", \"Days\": 15, \"Confirmed\": 7665, \"Confirmed/100k\": 2.3789042524324104}, {\"Country/Region\": \"US\", \"Days\": 16, \"Confirmed\": 13559, \"Confirmed/100k\": 4.1804283002078995}, {\"Country/Region\": \"US\", \"Days\": 17, \"Confirmed\": 18982, \"Confirmed/100k\": 5.837989364185924}, {\"Country/Region\": \"US\", \"Days\": 18, \"Confirmed\": 25371, \"Confirmed/100k\": 7.790812089200786}, {\"Country/Region\": \"US\", \"Days\": 19, \"Confirmed\": 33158, \"Confirmed/100k\": 10.170938957206848}, {\"Country/Region\": \"US\", \"Days\": 20, \"Confirmed\": 43729, \"Confirmed/100k\": 13.402006264474355}, {\"Country/Region\": \"US\", \"Days\": 21, \"Confirmed\": 53622, \"Confirmed/100k\": 16.425840232007932}, {\"Country/Region\": \"US\", \"Days\": 22, \"Confirmed\": 65660, \"Confirmed/100k\": 20.10530180091213}, {\"Country/Region\": \"United Kingdom\", \"Days\": 0, \"Confirmed\": 0, \"Confirmed/100k\": 0.17446497270503022}, {\"Country/Region\": \"United Kingdom\", \"Days\": 1, \"Confirmed\": 48, \"Confirmed/100k\": 0.2466573752036634}, {\"Country/Region\": \"United Kingdom\", \"Days\": 2, \"Confirmed\": 91, \"Confirmed/100k\": 0.3113297357753557}, {\"Country/Region\": \"United Kingdom\", \"Days\": 3, \"Confirmed\": 158, \"Confirmed/100k\": 0.4120982975963645}, {\"Country/Region\": \"United Kingdom\", \"Days\": 4, \"Confirmed\": 206, \"Confirmed/100k\": 0.4842907000949977}, {\"Country/Region\": \"United Kingdom\", \"Days\": 5, \"Confirmed\": 268, \"Confirmed/100k\": 0.5775392199890655}, {\"Country/Region\": \"United Kingdom\", \"Days\": 6, \"Confirmed\": 343, \"Confirmed/100k\": 0.6903398488931799}, {\"Country/Region\": \"United Kingdom\", \"Days\": 7, \"Confirmed\": 343, \"Confirmed/100k\": 0.6903398488931799}, {\"Country/Region\": \"United Kingdom\", \"Days\": 8, \"Confirmed\": 686, \"Confirmed/100k\": 1.2062147250813295}, {\"Country/Region\": \"United Kingdom\", \"Days\": 9, \"Confirmed\": 1028, \"Confirmed/100k\": 1.7205855928840912}, {\"Country/Region\": \"United Kingdom\", \"Days\": 10, \"Confirmed\": 1029, \"Confirmed/100k\": 1.7220896012694793}, {\"Country/Region\": \"United Kingdom\", \"Days\": 11, \"Confirmed\": 1435, \"Confirmed/100k\": 2.332717005737085}, {\"Country/Region\": \"United Kingdom\", \"Days\": 12, \"Confirmed\": 1844, \"Confirmed/100k\": 2.947856435360856}, {\"Country/Region\": \"United Kingdom\", \"Days\": 13, \"Confirmed\": 2526, \"Confirmed/100k\": 3.973590154195602}, {\"Country/Region\": \"United Kingdom\", \"Days\": 14, \"Confirmed\": 2600, \"Confirmed/100k\": 4.084886774714328}, {\"Country/Region\": \"United Kingdom\", \"Days\": 15, \"Confirmed\": 3898, \"Confirmed/100k\": 6.037089658948201}, {\"Country/Region\": \"United Kingdom\", \"Days\": 16, \"Confirmed\": 4951, \"Confirmed/100k\": 7.6208104887619665}, {\"Country/Region\": \"United Kingdom\", \"Days\": 17, \"Confirmed\": 5629, \"Confirmed/100k\": 8.640528174055161}, {\"Country/Region\": \"United Kingdom\", \"Days\": 18, \"Confirmed\": 6610, \"Confirmed/100k\": 10.115960400120976}, {\"Country/Region\": \"United Kingdom\", \"Days\": 19, \"Confirmed\": 8048, \"Confirmed/100k\": 12.278724458309195}, {\"Country/Region\": \"United Kingdom\", \"Days\": 20, \"Confirmed\": 9524, \"Confirmed/100k\": 14.498640835142163}]}}, {\"mode\": \"vega-lite\"});\n",
"</script>"
],
"text/plain": [
@@ -1074,20 +1074,20 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 4.980539,
- "end_time": "2020-03-25T23:23:00.671107",
+ "duration": 5.235334,
+ "end_time": "2020-03-26T13:22:52.157667",
"environment_variables": {},
"exception": null,
- "input_path": "notebooks/Dashboard.ipynb",
+ "input_path": "/tmp/rh_o282i/notebooks/Dashboard.ipynb",
"output_path": "runs/Dashboard.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "notebooks/Dashboard.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/rh_o282i/notebooks/Dashboard.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
- "geodata_path": "./data/geodata/geo_data.csv",
- "rates_folder": "./data/covid-19_rates/",
- "ts_folder": "./data/covid-19_jhu-csse/"
+ "geodata_path": "/tmp/rh_o282i/data/geodata/geo_data.csv",
+ "rates_folder": "/tmp/rh_o282i/data/covid-19_rates",
+ "ts_folder": "/tmp/rh_o282i/data/covid-19_jhu-csse"
},
- "start_time": "2020-03-25T23:22:55.690568",
+ "start_time": "2020-03-26T13:22:46.922333",
"version": "1.1.0"
}
},
diff --git a/runs/ToRates.run.ipynb b/runs/ToRates.run.ipynb
index ce87fd77..49f2d046 100644
--- a/runs/ToRates.run.ipynb
+++ b/runs/ToRates.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.025552,
- "end_time": "2020-03-25T23:09:00.721703",
+ "duration": 0.025823,
+ "end_time": "2020-03-26T13:22:40.981642",
"exception": false,
- "start_time": "2020-03-25T23:09:00.696151",
+ "start_time": "2020-03-26T13:22:40.955819",
"status": "completed"
},
"tags": []
@@ -21,10 +21,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.31148,
- "end_time": "2020-03-25T23:09:01.045691",
+ "duration": 0.309273,
+ "end_time": "2020-03-26T13:22:41.302953",
"exception": false,
- "start_time": "2020-03-25T23:09:00.734211",
+ "start_time": "2020-03-26T13:22:40.993680",
"status": "completed"
},
"tags": []
@@ -40,10 +40,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.026205,
- "end_time": "2020-03-25T23:09:01.091854",
+ "duration": 0.029122,
+ "end_time": "2020-03-26T13:22:41.356215",
"exception": false,
- "start_time": "2020-03-25T23:09:01.065649",
+ "start_time": "2020-03-26T13:22:41.327093",
"status": "completed"
},
"tags": [
@@ -64,10 +64,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.026742,
- "end_time": "2020-03-25T23:09:01.132065",
+ "duration": 0.025734,
+ "end_time": "2020-03-26T13:22:41.394022",
"exception": false,
- "start_time": "2020-03-25T23:09:01.105323",
+ "start_time": "2020-03-26T13:22:41.368288",
"status": "completed"
},
"tags": [
@@ -77,22 +77,22 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"notebooks/process/ToRates.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/b8zw8ggm/notebooks/process/ToRates.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/ToRates.run.ipynb\"\n",
- "ts_folder = \"./data/covid-19_jhu-csse/\"\n",
- "wb_path = \"./data/worldbank/SP.POP.TOTL.zip\"\n",
- "geodata_path = \"./data/geodata/geo_data.csv\"\n",
- "out_folder = \"./data/covid-19_rates/\"\n"
+ "ts_folder = \"/tmp/b8zw8ggm/data/covid-19_jhu-csse\"\n",
+ "wb_path = \"/tmp/b8zw8ggm/data/worldbank/SP.POP.TOTL.zip\"\n",
+ "geodata_path = \"/tmp/b8zw8ggm/data/geodata/geo_data.csv\"\n",
+ "out_folder = \"data/covid-19_rates\"\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010624,
- "end_time": "2020-03-25T23:09:01.158674",
+ "duration": 0.011285,
+ "end_time": "2020-03-26T13:22:41.417678",
"exception": false,
- "start_time": "2020-03-25T23:09:01.148050",
+ "start_time": "2020-03-26T13:22:41.406393",
"status": "completed"
},
"tags": [
@@ -110,10 +110,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.033521,
- "end_time": "2020-03-25T23:09:01.202510",
+ "duration": 0.032856,
+ "end_time": "2020-03-26T13:22:41.460771",
"exception": false,
- "start_time": "2020-03-25T23:09:01.168989",
+ "start_time": "2020-03-26T13:22:41.427915",
"status": "completed"
},
"tags": []
@@ -135,10 +135,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.113015,
- "end_time": "2020-03-25T23:09:01.331507",
+ "duration": 0.162421,
+ "end_time": "2020-03-26T13:22:41.635476",
"exception": false,
- "start_time": "2020-03-25T23:09:01.218492",
+ "start_time": "2020-03-26T13:22:41.473055",
"status": "completed"
},
"tags": []
@@ -155,10 +155,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011508,
- "end_time": "2020-03-25T23:09:01.366642",
+ "duration": 0.016634,
+ "end_time": "2020-03-26T13:22:41.669694",
"exception": false,
- "start_time": "2020-03-25T23:09:01.355134",
+ "start_time": "2020-03-26T13:22:41.653060",
"status": "completed"
},
"tags": []
@@ -172,10 +172,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.047665,
- "end_time": "2020-03-25T23:09:01.424394",
+ "duration": 0.049529,
+ "end_time": "2020-03-26T13:22:41.731131",
"exception": false,
- "start_time": "2020-03-25T23:09:01.376729",
+ "start_time": "2020-03-26T13:22:41.681602",
"status": "completed"
},
"tags": []
@@ -191,10 +191,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011664,
- "end_time": "2020-03-25T23:09:01.458401",
+ "duration": 0.01096,
+ "end_time": "2020-03-26T13:22:41.761990",
"exception": false,
- "start_time": "2020-03-25T23:09:01.446737",
+ "start_time": "2020-03-26T13:22:41.751030",
"status": "completed"
},
"tags": []
@@ -208,10 +208,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.069897,
- "end_time": "2020-03-25T23:09:01.538499",
+ "duration": 0.069116,
+ "end_time": "2020-03-26T13:22:41.841635",
"exception": false,
- "start_time": "2020-03-25T23:09:01.468602",
+ "start_time": "2020-03-26T13:22:41.772519",
"status": "completed"
},
"tags": []
@@ -344,10 +344,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.01164,
- "end_time": "2020-03-25T23:09:01.571944",
+ "duration": 0.011488,
+ "end_time": "2020-03-26T13:22:41.873495",
"exception": false,
- "start_time": "2020-03-25T23:09:01.560304",
+ "start_time": "2020-03-26T13:22:41.862007",
"status": "completed"
},
"tags": []
@@ -361,10 +361,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.041515,
- "end_time": "2020-03-25T23:09:01.624843",
+ "duration": 0.041295,
+ "end_time": "2020-03-26T13:22:41.925422",
"exception": false,
- "start_time": "2020-03-25T23:09:01.583328",
+ "start_time": "2020-03-26T13:22:41.884127",
"status": "completed"
},
"tags": []
@@ -393,10 +393,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.024827,
- "end_time": "2020-03-25T23:09:01.672486",
+ "duration": 0.025143,
+ "end_time": "2020-03-26T13:22:41.973081",
"exception": false,
- "start_time": "2020-03-25T23:09:01.647659",
+ "start_time": "2020-03-26T13:22:41.947938",
"status": "completed"
},
"tags": []
@@ -411,10 +411,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010816,
- "end_time": "2020-03-25T23:09:01.698035",
+ "duration": 0.01324,
+ "end_time": "2020-03-26T13:22:41.999080",
"exception": false,
- "start_time": "2020-03-25T23:09:01.687219",
+ "start_time": "2020-03-26T13:22:41.985840",
"status": "completed"
},
"tags": []
@@ -428,10 +428,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.051115,
- "end_time": "2020-03-25T23:09:01.759963",
+ "duration": 0.056999,
+ "end_time": "2020-03-26T13:22:42.074331",
"exception": false,
- "start_time": "2020-03-25T23:09:01.708848",
+ "start_time": "2020-03-26T13:22:42.017332",
"status": "completed"
},
"tags": []
@@ -460,8 +460,8 @@
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
- " <th>2020-03-23 00:00:00</th>\n",
" <th>2020-03-24 00:00:00</th>\n",
+ " <th>2020-03-25 00:00:00</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Country/Region</th>\n",
@@ -476,7 +476,7 @@
" <th>Bahamas</th>\n",
" <th>-77.396300</th>\n",
" <th>25.034300</th>\n",
- " <td>4</td>\n",
+ " <td>5</td>\n",
" <td>5</td>\n",
" </tr>\n",
" <tr>\n",
@@ -490,8 +490,8 @@
" <th>Congo (Kinshasa)</th>\n",
" <th>21.758700</th>\n",
" <th>-4.038300</th>\n",
- " <td>36</td>\n",
" <td>45</td>\n",
+ " <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Diamond Princess</th>\n",
@@ -504,27 +504,34 @@
" <th>Gambia</th>\n",
" <th>-15.310100</th>\n",
" <th>13.443200</th>\n",
- " <td>2</td>\n",
+ " <td>3</td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Holy See</th>\n",
" <th>12.453400</th>\n",
" <th>41.902900</th>\n",
- " <td>1</td>\n",
+ " <td>4</td>\n",
" <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Kyrgyzstan</th>\n",
" <th>74.766100</th>\n",
" <th>41.204400</th>\n",
- " <td>16</td>\n",
" <td>42</td>\n",
+ " <td>44</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Laos</th>\n",
" <th>102.495496</th>\n",
" <th>19.856270</th>\n",
+ " <td>2</td>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Saint Kitts and Nevis</th>\n",
+ " <th>-62.782998</th>\n",
+ " <th>17.357822</th>\n",
" <td>0</td>\n",
" <td>2</td>\n",
" </tr>\n",
@@ -547,67 +554,60 @@
" <th>38.996815</th>\n",
" <th>34.802075</th>\n",
" <td>1</td>\n",
- " <td>1</td>\n",
+ " <td>5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Taiwan*</th>\n",
" <th>121.000000</th>\n",
" <th>23.700000</th>\n",
- " <td>195</td>\n",
" <td>215</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>The West Bank and Gaza</th>\n",
- " <th>35.233200</th>\n",
- " <th>31.952200</th>\n",
- " <td>59</td>\n",
- " <td>59</td>\n",
+ " <td>235</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Venezuela</th>\n",
" <th>-66.589700</th>\n",
" <th>6.423800</th>\n",
- " <td>77</td>\n",
" <td>84</td>\n",
+ " <td>91</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
- " 2020-03-23 00:00:00 \\\n",
+ " 2020-03-24 00:00:00 \\\n",
"Country/Region Long Lat \n",
- "Bahamas -77.396300 25.034300 4 \n",
+ "Bahamas -77.396300 25.034300 5 \n",
"Congo (Brazzaville) 21.758700 -4.038300 4 \n",
- "Congo (Kinshasa) 21.758700 -4.038300 36 \n",
+ "Congo (Kinshasa) 21.758700 -4.038300 45 \n",
"Diamond Princess 0.000000 0.000000 712 \n",
- "Gambia -15.310100 13.443200 2 \n",
- "Holy See 12.453400 41.902900 1 \n",
- "Kyrgyzstan 74.766100 41.204400 16 \n",
- "Laos 102.495496 19.856270 0 \n",
+ "Gambia -15.310100 13.443200 3 \n",
+ "Holy See 12.453400 41.902900 4 \n",
+ "Kyrgyzstan 74.766100 41.204400 42 \n",
+ "Laos 102.495496 19.856270 2 \n",
+ "Saint Kitts and Nevis -62.782998 17.357822 0 \n",
"Saint Lucia -60.978900 13.909400 3 \n",
"Saint Vincent and the Grenadines -61.287200 12.984300 1 \n",
"Syria 38.996815 34.802075 1 \n",
- "Taiwan* 121.000000 23.700000 195 \n",
- "The West Bank and Gaza 35.233200 31.952200 59 \n",
- "Venezuela -66.589700 6.423800 77 \n",
+ "Taiwan* 121.000000 23.700000 215 \n",
+ "Venezuela -66.589700 6.423800 84 \n",
"\n",
- " 2020-03-24 00:00:00 \n",
+ " 2020-03-25 00:00:00 \n",
"Country/Region Long Lat \n",
"Bahamas -77.396300 25.034300 5 \n",
"Congo (Brazzaville) 21.758700 -4.038300 4 \n",
- "Congo (Kinshasa) 21.758700 -4.038300 45 \n",
+ "Congo (Kinshasa) 21.758700 -4.038300 48 \n",
"Diamond Princess 0.000000 0.000000 712 \n",
"Gambia -15.310100 13.443200 3 \n",
"Holy See 12.453400 41.902900 4 \n",
- "Kyrgyzstan 74.766100 41.204400 42 \n",
- "Laos 102.495496 19.856270 2 \n",
+ "Kyrgyzstan 74.766100 41.204400 44 \n",
+ "Laos 102.495496 19.856270 3 \n",
+ "Saint Kitts and Nevis -62.782998 17.357822 2 \n",
"Saint Lucia -60.978900 13.909400 3 \n",
"Saint Vincent and the Grenadines -61.287200 12.984300 1 \n",
- "Syria 38.996815 34.802075 1 \n",
- "Taiwan* 121.000000 23.700000 215 \n",
- "The West Bank and Gaza 35.233200 31.952200 59 \n",
- "Venezuela -66.589700 6.423800 84 "
+ "Syria 38.996815 34.802075 5 \n",
+ "Taiwan* 121.000000 23.700000 235 \n",
+ "Venezuela -66.589700 6.423800 91 "
]
},
"execution_count": 10,
@@ -625,10 +625,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012299,
- "end_time": "2020-03-25T23:09:01.794347",
+ "duration": 0.02353,
+ "end_time": "2020-03-26T13:22:42.115274",
"exception": false,
- "start_time": "2020-03-25T23:09:01.782048",
+ "start_time": "2020-03-26T13:22:42.091744",
"status": "completed"
},
"tags": []
@@ -642,10 +642,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.039545,
- "end_time": "2020-03-25T23:09:01.845375",
+ "duration": 0.047169,
+ "end_time": "2020-03-26T13:22:42.176310",
"exception": false,
- "start_time": "2020-03-25T23:09:01.805830",
+ "start_time": "2020-03-26T13:22:42.129141",
"status": "completed"
},
"tags": []
@@ -659,10 +659,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.0115,
- "end_time": "2020-03-25T23:09:01.878845",
+ "duration": 0.012405,
+ "end_time": "2020-03-26T13:22:42.212063",
"exception": false,
- "start_time": "2020-03-25T23:09:01.867345",
+ "start_time": "2020-03-26T13:22:42.199658",
"status": "completed"
},
"tags": []
@@ -676,10 +676,10 @@
"execution_count": 12,
"metadata": {
"papermill": {
- "duration": 0.068348,
- "end_time": "2020-03-25T23:09:01.958498",
+ "duration": 0.064872,
+ "end_time": "2020-03-26T13:22:42.289568",
"exception": false,
- "start_time": "2020-03-25T23:09:01.890150",
+ "start_time": "2020-03-26T13:22:42.224696",
"status": "completed"
},
"tags": []
@@ -759,6 +759,19 @@
" <td>41.462219</td>\n",
" </tr>\n",
" <tr>\n",
+ " <th>Saint Kitts and Nevis</th>\n",
+ " <td>St. Kitts and Nevis</td>\n",
+ " <td>Saint Kitts and Nevis</td>\n",
+ " <td>Americas</td>\n",
+ " <td>Caribbean</td>\n",
+ " <td>Latin America & Caribbean</td>\n",
+ " <td>40131</td>\n",
+ " <td>777.7</td>\n",
+ " <td>2. High income: nonOECD</td>\n",
+ " <td>-62.687553</td>\n",
+ " <td>17.264599</td>\n",
+ " </tr>\n",
+ " <tr>\n",
" <th>Saint Lucia</th>\n",
" <td>Saint Lucia</td>\n",
" <td>Saint Lucia</td>\n",
@@ -828,20 +841,22 @@
"</div>"
],
"text/plain": [
- " name \\\n",
- "name_jhu \n",
- "Bahamas Bahamas \n",
- "Kyrgyzstan Kyrgyzstan \n",
- "Saint Lucia Saint Lucia \n",
- "Syria Syria \n",
- "Taiwan* Taiwan \n",
- "Saint Vincent and the Grenadines St. Vin. and Gren. \n",
- "Venezuela Venezuela \n",
+ " name \\\n",
+ "name_jhu \n",
+ "Bahamas Bahamas \n",
+ "Kyrgyzstan Kyrgyzstan \n",
+ "Saint Kitts and Nevis St. Kitts and Nevis \n",
+ "Saint Lucia Saint Lucia \n",
+ "Syria Syria \n",
+ "Taiwan* Taiwan \n",
+ "Saint Vincent and the Grenadines St. Vin. and Gren. \n",
+ "Venezuela Venezuela \n",
"\n",
" name_long region_un \\\n",
"name_jhu \n",
"Bahamas Bahamas Americas \n",
"Kyrgyzstan Kyrgyzstan Asia \n",
+ "Saint Kitts and Nevis Saint Kitts and Nevis Americas \n",
"Saint Lucia Saint Lucia Americas \n",
"Syria Syria Asia \n",
"Taiwan* Taiwan Asia \n",
@@ -852,6 +867,7 @@
"name_jhu \n",
"Bahamas Caribbean Latin America & Caribbean \n",
"Kyrgyzstan Central Asia Europe & Central Asia \n",
+ "Saint Kitts and Nevis Caribbean Latin America & Caribbean \n",
"Saint Lucia Caribbean Latin America & Caribbean \n",
"Syria Western Asia Middle East & North Africa \n",
"Taiwan* Eastern Asia East Asia & Pacific \n",
@@ -862,6 +878,7 @@
"name_jhu \n",
"Bahamas 309156 9093.0 \n",
"Kyrgyzstan 5431747 11610.0 \n",
+ "Saint Kitts and Nevis 40131 777.7 \n",
"Saint Lucia 160267 1778.0 \n",
"Syria 20178485 98830.0 \n",
"Taiwan* 22974347 712000.0 \n",
@@ -872,6 +889,7 @@
"name_jhu \n",
"Bahamas 2. High income: nonOECD -76.628430 \n",
"Kyrgyzstan 5. Low income 74.541655 \n",
+ "Saint Kitts and Nevis 2. High income: nonOECD -62.687553 \n",
"Saint Lucia 3. Upper middle income -60.969699 \n",
"Syria 4. Lower middle income 38.507882 \n",
"Taiwan* 2. High income: nonOECD 120.954273 \n",
@@ -882,6 +900,7 @@
"name_jhu \n",
"Bahamas 24.290367 \n",
"Kyrgyzstan 41.462219 \n",
+ "Saint Kitts and Nevis 17.264599 \n",
"Saint Lucia 13.894795 \n",
"Syria 35.025474 \n",
"Taiwan* 23.753993 \n",
@@ -907,10 +926,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012118,
- "end_time": "2020-03-25T23:09:01.988062",
+ "duration": 0.01249,
+ "end_time": "2020-03-26T13:22:42.324941",
"exception": false,
- "start_time": "2020-03-25T23:09:01.975944",
+ "start_time": "2020-03-26T13:22:42.312451",
"status": "completed"
},
"tags": []
@@ -924,10 +943,10 @@
"execution_count": 13,
"metadata": {
"papermill": {
- "duration": 0.053488,
- "end_time": "2020-03-25T23:09:02.053219",
+ "duration": 0.049891,
+ "end_time": "2020-03-26T13:22:42.386852",
"exception": false,
- "start_time": "2020-03-25T23:09:01.999731",
+ "start_time": "2020-03-26T13:22:42.336961",
"status": "completed"
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"tags": []
@@ -952,10 +971,10 @@
"execution_count": 14,
"metadata": {
"papermill": {
- "duration": 0.069275,
- "end_time": "2020-03-25T23:09:02.144625",
+ "duration": 0.07352,
+ "end_time": "2020-03-26T13:22:42.482178",
"exception": false,
- "start_time": "2020-03-25T23:09:02.075350",
+ "start_time": "2020-03-26T13:22:42.408658",
"status": "completed"
},
"tags": []
@@ -988,21 +1007,21 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 2.640022,
- "end_time": "2020-03-25T23:09:02.478791",
+ "duration": 2.639475,
+ "end_time": "2020-03-26T13:22:42.821535",
"environment_variables": {},
"exception": null,
- "input_path": "notebooks/process/ToRates.ipynb",
+ "input_path": "/tmp/b8zw8ggm/notebooks/process/ToRates.ipynb",
"output_path": "runs/ToRates.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "notebooks/process/ToRates.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/b8zw8ggm/notebooks/process/ToRates.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/ToRates.run.ipynb",
- "geodata_path": "./data/geodata/geo_data.csv",
- "out_folder": "./data/covid-19_rates/",
- "ts_folder": "./data/covid-19_jhu-csse/",
- "wb_path": "./data/worldbank/SP.POP.TOTL.zip"
+ "geodata_path": "/tmp/b8zw8ggm/data/geodata/geo_data.csv",
+ "out_folder": "data/covid-19_rates",
+ "ts_folder": "/tmp/b8zw8ggm/data/covid-19_jhu-csse",
+ "wb_path": "/tmp/b8zw8ggm/data/worldbank/SP.POP.TOTL.zip"
},
- "start_time": "2020-03-25T23:08:59.838769",
+ "start_time": "2020-03-26T13:22:40.182060",
"version": "1.1.0"
}
},
--
GitLab