From 046d7de01c83fe87e712610dc4c76cffedd95a3f Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Wed, 25 Mar 2020 23:09:02 +0000
Subject: [PATCH] renku run papermill -p ts_folder ./data/covid-19_jhu-csse/ -p
wb_path ./data/worldbank/SP.POP.TOTL.zip -p geodata_path
./data/geodata/geo_data.csv -p out_folder ./data/covid-19_rates/
--inject-paths notebooks/process/ToRates.ipynb runs/ToRates.run.ipynb
---
...a2ea2542427d8ac95d26349080ed_papermill.cwl | 137 +++++
.../ts_rates_19-covid-confirmed.csv | 4 +-
.../ts_rates_19-covid-deaths.csv | 4 +-
runs/ToRates.run.ipynb | 512 +++++++-----------
4 files changed, 332 insertions(+), 325 deletions(-)
create mode 100644 .renku/workflow/6f3ea2ea2542427d8ac95d26349080ed_papermill.cwl
diff --git a/.renku/workflow/6f3ea2ea2542427d8ac95d26349080ed_papermill.cwl b/.renku/workflow/6f3ea2ea2542427d8ac95d26349080ed_papermill.cwl
new file mode 100644
index 00000000..988afcd8
--- /dev/null
+++ b/.renku/workflow/6f3ea2ea2542427d8ac95d26349080ed_papermill.cwl
@@ -0,0 +1,137 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ inputBinding:
+ position: 1
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_10:
+ default: runs/ToRates.run.ipynb
+ inputBinding:
+ position: 10
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_2:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ inputBinding:
+ position: 2
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_3:
+ default: wb_path
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: File
+ path: ../../data/worldbank/SP.POP.TOTL.zip
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_5:
+ default: geodata_path
+ inputBinding:
+ position: 5
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_6:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ inputBinding:
+ position: 6
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_7:
+ default: out_folder
+ inputBinding:
+ position: 7
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_8:
+ default: data/covid-19_rates
+ inputBinding:
+ position: 8
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_9:
+ default:
+ class: File
+ path: ../../notebooks/process/ToRates.ipynb
+ inputBinding:
+ position: 9
+ prefix: --inject-paths
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_10)
+ streamable: false
+ type: File
+ output_1:
+ outputBinding:
+ glob: $(inputs.input_8)
+ streamable: false
+ type: Directory
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: data/covid-19_rates
+ writable: true
+ - entry: $(inputs.input_2)
+ entryname: data/covid-19_jhu-csse
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/worldbank/SP.POP.TOTL.zip
+ writable: false
+ - entry: $(inputs.input_6)
+ entryname: data/geodata/geo_data.csv
+ writable: false
+ - entry: $(inputs.input_9)
+ entryname: notebooks/process/ToRates.ipynb
+ writable: false
+successCodes: []
+temporaryFailCodes: []
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 d5f82309..a8c6f48b 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 sha256:9ae1fd02112a3f7f1f74c314625a7042c89de2f6df105dc4c13f53b3d00e8cd6
-size 104570
+oid sha256:c021fbd9b0623ca6fda3386b6b82d2973749d434a384704e1eb5afbc81be0932
+size 105565
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 be053acd..bb293e55 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 sha256:905ade4dbd24d54b75fcef4b21b2642b71cac902a4fc314d180880e7a5ebd499
-size 62770
+oid sha256:cf36cf8457f0e1625144bd3bb75592635eebd906624bc677ecc373acf8d7a532
+size 63060
diff --git a/runs/ToRates.run.ipynb b/runs/ToRates.run.ipynb
index 60c0a454..ce87fd77 100644
--- a/runs/ToRates.run.ipynb
+++ b/runs/ToRates.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.032494,
- "end_time": "2020-03-25T13:55:04.106838",
+ "duration": 0.025552,
+ "end_time": "2020-03-25T23:09:00.721703",
"exception": false,
- "start_time": "2020-03-25T13:55:04.074344",
+ "start_time": "2020-03-25T23:09:00.696151",
"status": "completed"
},
"tags": []
@@ -21,10 +21,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.307799,
- "end_time": "2020-03-25T13:55:04.426890",
+ "duration": 0.31148,
+ "end_time": "2020-03-25T23:09:01.045691",
"exception": false,
- "start_time": "2020-03-25T13:55:04.119091",
+ "start_time": "2020-03-25T23:09:00.734211",
"status": "completed"
},
"tags": []
@@ -40,10 +40,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024997,
- "end_time": "2020-03-25T13:55:04.473087",
+ "duration": 0.026205,
+ "end_time": "2020-03-25T23:09:01.091854",
"exception": false,
- "start_time": "2020-03-25T13:55:04.448090",
+ "start_time": "2020-03-25T23:09:01.065649",
"status": "completed"
},
"tags": [
@@ -52,9 +52,9 @@
},
"outputs": [],
"source": [
- "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",
+ "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 = None\n",
"PAPERMILL_OUTPUT_PATH = None"
]
@@ -64,10 +64,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.022661,
- "end_time": "2020-03-25T13:55:04.509511",
+ "duration": 0.026742,
+ "end_time": "2020-03-25T23:09:01.132065",
"exception": false,
- "start_time": "2020-03-25T13:55:04.486850",
+ "start_time": "2020-03-25T23:09:01.105323",
"status": "completed"
},
"tags": [
@@ -89,10 +89,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010324,
- "end_time": "2020-03-25T13:55:04.532118",
+ "duration": 0.010624,
+ "end_time": "2020-03-25T23:09:01.158674",
"exception": false,
- "start_time": "2020-03-25T13:55:04.521794",
+ "start_time": "2020-03-25T23:09:01.148050",
"status": "completed"
},
"tags": [
@@ -110,10 +110,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.029616,
- "end_time": "2020-03-25T13:55:04.571972",
+ "duration": 0.033521,
+ "end_time": "2020-03-25T23:09:01.202510",
"exception": false,
- "start_time": "2020-03-25T13:55:04.542356",
+ "start_time": "2020-03-25T23:09:01.168989",
"status": "completed"
},
"tags": []
@@ -121,7 +121,7 @@
"outputs": [],
"source": [
"def read_jhu_covid_region_df(name):\n",
- " filename = os.path.join(ts_folder, f\"time_series_19-covid-{name}.csv\")\n",
+ " filename = os.path.join(ts_folder, f\"time_series_covid19_{name}_global.csv\")\n",
" df = pd.read_csv(filename)\n",
" df = df.set_index(['Country/Region', 'Province/State', 'Lat', 'Long'])\n",
" df.columns = pd.to_datetime(df.columns)\n",
@@ -135,10 +135,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.139315,
- "end_time": "2020-03-25T13:55:04.724324",
+ "duration": 0.113015,
+ "end_time": "2020-03-25T23:09:01.331507",
"exception": false,
- "start_time": "2020-03-25T13:55:04.585009",
+ "start_time": "2020-03-25T23:09:01.218492",
"status": "completed"
},
"tags": []
@@ -146,9 +146,8 @@
"outputs": [],
"source": [
"frames_map = {\n",
- " \"confirmed\": read_jhu_covid_region_df(\"Confirmed\"),\n",
- " \"deaths\": read_jhu_covid_region_df(\"Deaths\"),\n",
- " \"recovered\": read_jhu_covid_region_df(\"Recovered\")\n",
+ " \"confirmed\": read_jhu_covid_region_df(\"confirmed\"),\n",
+ " \"deaths\": read_jhu_covid_region_df(\"deaths\"),\n",
"}"
]
},
@@ -156,10 +155,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011298,
- "end_time": "2020-03-25T13:55:04.758899",
+ "duration": 0.011508,
+ "end_time": "2020-03-25T23:09:01.366642",
"exception": false,
- "start_time": "2020-03-25T13:55:04.747601",
+ "start_time": "2020-03-25T23:09:01.355134",
"status": "completed"
},
"tags": []
@@ -173,10 +172,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.046291,
- "end_time": "2020-03-25T13:55:04.814885",
+ "duration": 0.047665,
+ "end_time": "2020-03-25T23:09:01.424394",
"exception": false,
- "start_time": "2020-03-25T13:55:04.768594",
+ "start_time": "2020-03-25T23:09:01.376729",
"status": "completed"
},
"tags": []
@@ -192,10 +191,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011042,
- "end_time": "2020-03-25T13:55:04.848202",
+ "duration": 0.011664,
+ "end_time": "2020-03-25T23:09:01.458401",
"exception": false,
- "start_time": "2020-03-25T13:55:04.837160",
+ "start_time": "2020-03-25T23:09:01.446737",
"status": "completed"
},
"tags": []
@@ -209,10 +208,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.070582,
- "end_time": "2020-03-25T13:55:04.929280",
+ "duration": 0.069897,
+ "end_time": "2020-03-25T23:09:01.538499",
"exception": false,
- "start_time": "2020-03-25T13:55:04.858698",
+ "start_time": "2020-03-25T23:09:01.468602",
"status": "completed"
},
"tags": []
@@ -345,10 +344,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011058,
- "end_time": "2020-03-25T13:55:04.961018",
+ "duration": 0.01164,
+ "end_time": "2020-03-25T23:09:01.571944",
"exception": false,
- "start_time": "2020-03-25T13:55:04.949960",
+ "start_time": "2020-03-25T23:09:01.560304",
"status": "completed"
},
"tags": []
@@ -362,10 +361,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.045924,
- "end_time": "2020-03-25T13:55:05.017994",
+ "duration": 0.041515,
+ "end_time": "2020-03-25T23:09:01.624843",
"exception": false,
- "start_time": "2020-03-25T13:55:04.972070",
+ "start_time": "2020-03-25T23:09:01.583328",
"status": "completed"
},
"tags": []
@@ -394,10 +393,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.024519,
- "end_time": "2020-03-25T13:55:05.063028",
+ "duration": 0.024827,
+ "end_time": "2020-03-25T23:09:01.672486",
"exception": false,
- "start_time": "2020-03-25T13:55:05.038509",
+ "start_time": "2020-03-25T23:09:01.647659",
"status": "completed"
},
"tags": []
@@ -412,10 +411,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.013202,
- "end_time": "2020-03-25T13:55:05.094653",
+ "duration": 0.010816,
+ "end_time": "2020-03-25T23:09:01.698035",
"exception": false,
- "start_time": "2020-03-25T13:55:05.081451",
+ "start_time": "2020-03-25T23:09:01.687219",
"status": "completed"
},
"tags": []
@@ -429,10 +428,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.057047,
- "end_time": "2020-03-25T13:55:05.164566",
+ "duration": 0.051115,
+ "end_time": "2020-03-25T23:09:01.759963",
"exception": false,
- "start_time": "2020-03-25T13:55:05.107519",
+ "start_time": "2020-03-25T23:09:01.708848",
"status": "completed"
},
"tags": []
@@ -461,8 +460,8 @@
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
- " <th>2020-03-22 00:00:00</th>\n",
" <th>2020-03-23 00:00:00</th>\n",
+ " <th>2020-03-24 00:00:00</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Country/Region</th>\n",
@@ -474,213 +473,141 @@
" </thead>\n",
" <tbody>\n",
" <tr>\n",
- " <th>Cape Verde</th>\n",
- " <th>-23.6167</th>\n",
- " <th>15.1111</th>\n",
- " <td>1</td>\n",
- " <td>0.0</td>\n",
+ " <th>Bahamas</th>\n",
+ " <th>-77.396300</th>\n",
+ " <th>25.034300</th>\n",
+ " <td>4</td>\n",
+ " <td>5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Congo (Brazzaville)</th>\n",
- " <th>21.7587</th>\n",
- " <th>-4.0383</th>\n",
- " <td>3</td>\n",
- " <td>3.0</td>\n",
+ " <th>21.758700</th>\n",
+ " <th>-4.038300</th>\n",
+ " <td>4</td>\n",
+ " <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Congo (Kinshasa)</th>\n",
- " <th>21.7587</th>\n",
- " <th>-4.0383</th>\n",
- " <td>30</td>\n",
- " <td>30.0</td>\n",
+ " <th>21.758700</th>\n",
+ " <th>-4.038300</th>\n",
+ " <td>36</td>\n",
+ " <td>45</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>Cruise Ship</th>\n",
- " <th>139.6380</th>\n",
- " <th>35.4437</th>\n",
+ " <th>Diamond Princess</th>\n",
+ " <th>0.000000</th>\n",
+ " <th>0.000000</th>\n",
+ " <td>712</td>\n",
" <td>712</td>\n",
- " <td>712.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>East Timor</th>\n",
- " <th>125.5600</th>\n",
- " <th>-8.5500</th>\n",
- " <td>1</td>\n",
- " <td>0.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>French Guiana</th>\n",
- " <th>-53.1258</th>\n",
- " <th>3.9339</th>\n",
- " <td>0</td>\n",
- " <td>18.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Guadeloupe</th>\n",
- " <th>-61.5510</th>\n",
- " <th>16.2650</th>\n",
- " <td>0</td>\n",
- " <td>56.0</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>Guernsey</th>\n",
- " <th>-2.5800</th>\n",
- " <th>49.4500</th>\n",
- " <td>0</td>\n",
- " <td>0.0</td>\n",
+ " <th>Gambia</th>\n",
+ " <th>-15.310100</th>\n",
+ " <th>13.443200</th>\n",
+ " <td>2</td>\n",
+ " <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Holy See</th>\n",
- " <th>12.4534</th>\n",
- " <th>41.9029</th>\n",
+ " <th>12.453400</th>\n",
+ " <th>41.902900</th>\n",
" <td>1</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Jersey</th>\n",
- " <th>-2.1100</th>\n",
- " <th>49.1900</th>\n",
- " <td>0</td>\n",
- " <td>0.0</td>\n",
+ " <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Kyrgyzstan</th>\n",
- " <th>74.7661</th>\n",
- " <th>41.2044</th>\n",
- " <td>14</td>\n",
- " <td>14.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Martinique</th>\n",
- " <th>-61.0242</th>\n",
- " <th>14.6415</th>\n",
- " <td>37</td>\n",
- " <td>37.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Mayotte</th>\n",
- " <th>45.1662</th>\n",
- " <th>-12.8275</th>\n",
- " <td>0</td>\n",
- " <td>11.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Republic of the Congo</th>\n",
- " <th>15.5560</th>\n",
- " <th>-1.4400</th>\n",
- " <td>0</td>\n",
- " <td>0.0</td>\n",
+ " <th>74.766100</th>\n",
+ " <th>41.204400</th>\n",
+ " <td>16</td>\n",
+ " <td>42</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>Reunion</th>\n",
- " <th>55.5364</th>\n",
- " <th>-21.1151</th>\n",
+ " <th>Laos</th>\n",
+ " <th>102.495496</th>\n",
+ " <th>19.856270</th>\n",
" <td>0</td>\n",
- " <td>47.0</td>\n",
+ " <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Saint Lucia</th>\n",
- " <th>-60.9789</th>\n",
- " <th>13.9094</th>\n",
- " <td>2</td>\n",
- " <td>2.0</td>\n",
+ " <th>-60.978900</th>\n",
+ " <th>13.909400</th>\n",
+ " <td>3</td>\n",
+ " <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Saint Vincent and the Grenadines</th>\n",
- " <th>-61.2872</th>\n",
- " <th>12.9843</th>\n",
+ " <th>-61.287200</th>\n",
+ " <th>12.984300</th>\n",
+ " <td>1</td>\n",
" <td>1</td>\n",
- " <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Syria</th>\n",
- " <th>38.9968</th>\n",
- " <th>34.8021</th>\n",
+ " <th>38.996815</th>\n",
+ " <th>34.802075</th>\n",
+ " <td>1</td>\n",
" <td>1</td>\n",
- " <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Taiwan*</th>\n",
- " <th>121.0000</th>\n",
- " <th>23.7000</th>\n",
- " <td>169</td>\n",
- " <td>169.0</td>\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 Bahamas</th>\n",
- " <th>-76.0000</th>\n",
- " <th>24.2500</th>\n",
- " <td>0</td>\n",
- " <td>0.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>The Gambia</th>\n",
- " <th>-16.6000</th>\n",
- " <th>13.4667</th>\n",
- " <td>0</td>\n",
- " <td>0.0</td>\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",
" </tr>\n",
" <tr>\n",
" <th>Venezuela</th>\n",
- " <th>-66.5897</th>\n",
- " <th>6.4238</th>\n",
- " <td>70</td>\n",
- " <td>70.0</td>\n",
+ " <th>-66.589700</th>\n",
+ " <th>6.423800</th>\n",
+ " <td>77</td>\n",
+ " <td>84</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
- " 2020-03-22 00:00:00 \\\n",
- "Country/Region Long Lat \n",
- "Cape Verde -23.6167 15.1111 1 \n",
- "Congo (Brazzaville) 21.7587 -4.0383 3 \n",
- "Congo (Kinshasa) 21.7587 -4.0383 30 \n",
- "Cruise Ship 139.6380 35.4437 712 \n",
- "East Timor 125.5600 -8.5500 1 \n",
- "French Guiana -53.1258 3.9339 0 \n",
- "Guadeloupe -61.5510 16.2650 0 \n",
- "Guernsey -2.5800 49.4500 0 \n",
- "Holy See 12.4534 41.9029 1 \n",
- "Jersey -2.1100 49.1900 0 \n",
- "Kyrgyzstan 74.7661 41.2044 14 \n",
- "Martinique -61.0242 14.6415 37 \n",
- "Mayotte 45.1662 -12.8275 0 \n",
- "Republic of the Congo 15.5560 -1.4400 0 \n",
- "Reunion 55.5364 -21.1151 0 \n",
- "Saint Lucia -60.9789 13.9094 2 \n",
- "Saint Vincent and the Grenadines -61.2872 12.9843 1 \n",
- "Syria 38.9968 34.8021 1 \n",
- "Taiwan* 121.0000 23.7000 169 \n",
- "The Bahamas -76.0000 24.2500 0 \n",
- "The Gambia -16.6000 13.4667 0 \n",
- "Venezuela -66.5897 6.4238 70 \n",
+ " 2020-03-23 00:00:00 \\\n",
+ "Country/Region Long Lat \n",
+ "Bahamas -77.396300 25.034300 4 \n",
+ "Congo (Brazzaville) 21.758700 -4.038300 4 \n",
+ "Congo (Kinshasa) 21.758700 -4.038300 36 \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",
+ "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",
"\n",
- " 2020-03-23 00:00:00 \n",
- "Country/Region Long Lat \n",
- "Cape Verde -23.6167 15.1111 0.0 \n",
- "Congo (Brazzaville) 21.7587 -4.0383 3.0 \n",
- "Congo (Kinshasa) 21.7587 -4.0383 30.0 \n",
- "Cruise Ship 139.6380 35.4437 712.0 \n",
- "East Timor 125.5600 -8.5500 0.0 \n",
- "French Guiana -53.1258 3.9339 18.0 \n",
- "Guadeloupe -61.5510 16.2650 56.0 \n",
- "Guernsey -2.5800 49.4500 0.0 \n",
- "Holy See 12.4534 41.9029 1.0 \n",
- "Jersey -2.1100 49.1900 0.0 \n",
- "Kyrgyzstan 74.7661 41.2044 14.0 \n",
- "Martinique -61.0242 14.6415 37.0 \n",
- "Mayotte 45.1662 -12.8275 11.0 \n",
- "Republic of the Congo 15.5560 -1.4400 0.0 \n",
- "Reunion 55.5364 -21.1151 47.0 \n",
- "Saint Lucia -60.9789 13.9094 2.0 \n",
- "Saint Vincent and the Grenadines -61.2872 12.9843 1.0 \n",
- "Syria 38.9968 34.8021 1.0 \n",
- "Taiwan* 121.0000 23.7000 169.0 \n",
- "The Bahamas -76.0000 24.2500 0.0 \n",
- "The Gambia -16.6000 13.4667 0.0 \n",
- "Venezuela -66.5897 6.4238 70.0 "
+ " 2020-03-24 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",
+ "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",
+ "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 "
]
},
"execution_count": 10,
@@ -698,10 +625,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012705,
- "end_time": "2020-03-25T13:55:05.196368",
+ "duration": 0.012299,
+ "end_time": "2020-03-25T23:09:01.794347",
"exception": false,
- "start_time": "2020-03-25T13:55:05.183663",
+ "start_time": "2020-03-25T23:09:01.782048",
"status": "completed"
},
"tags": []
@@ -715,10 +642,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.041453,
- "end_time": "2020-03-25T13:55:05.249421",
+ "duration": 0.039545,
+ "end_time": "2020-03-25T23:09:01.845375",
"exception": false,
- "start_time": "2020-03-25T13:55:05.207968",
+ "start_time": "2020-03-25T23:09:01.805830",
"status": "completed"
},
"tags": []
@@ -732,10 +659,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012499,
- "end_time": "2020-03-25T13:55:05.286397",
+ "duration": 0.0115,
+ "end_time": "2020-03-25T23:09:01.878845",
"exception": false,
- "start_time": "2020-03-25T13:55:05.273898",
+ "start_time": "2020-03-25T23:09:01.867345",
"status": "completed"
},
"tags": []
@@ -749,10 +676,10 @@
"execution_count": 12,
"metadata": {
"papermill": {
- "duration": 0.067215,
- "end_time": "2020-03-25T13:55:05.366227",
+ "duration": 0.068348,
+ "end_time": "2020-03-25T23:09:01.958498",
"exception": false,
- "start_time": "2020-03-25T13:55:05.299012",
+ "start_time": "2020-03-25T23:09:01.890150",
"status": "completed"
},
"tags": []
@@ -806,56 +733,17 @@
" </thead>\n",
" <tbody>\n",
" <tr>\n",
- " <th>Cape Verde</th>\n",
- " <td>Cape Verde</td>\n",
- " <td>Cape Verde</td>\n",
- " <td>Africa</td>\n",
- " <td>Western Africa</td>\n",
- " <td>Sub-Saharan Africa</td>\n",
- " <td>429474</td>\n",
- " <td>1626.0</td>\n",
- " <td>4. Lower middle income</td>\n",
- " <td>-23.959888</td>\n",
- " <td>15.955233</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Guernsey</th>\n",
- " <td>Guernsey</td>\n",
- " <td>Guernsey</td>\n",
- " <td>Europe</td>\n",
- " <td>Northern Europe</td>\n",
- " <td>Europe & Central Asia</td>\n",
- " <td>68633</td>\n",
- " <td>2742.0</td>\n",
- " <td>2. High income: nonOECD</td>\n",
- " <td>-2.572391</td>\n",
- " <td>49.468098</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>The Gambia</th>\n",
- " <td>Gambia</td>\n",
- " <td>The Gambia</td>\n",
- " <td>Africa</td>\n",
- " <td>Western Africa</td>\n",
- " <td>Sub-Saharan Africa</td>\n",
- " <td>1782893</td>\n",
- " <td>2272.0</td>\n",
- " <td>5. Low income</td>\n",
- " <td>-15.396013</td>\n",
- " <td>13.449652</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Jersey</th>\n",
- " <td>Jersey</td>\n",
- " <td>Jersey</td>\n",
- " <td>Europe</td>\n",
- " <td>Northern Europe</td>\n",
- " <td>Europe & Central Asia</td>\n",
- " <td>91626</td>\n",
- " <td>5100.0</td>\n",
+ " <th>Bahamas</th>\n",
+ " <td>Bahamas</td>\n",
+ " <td>Bahamas</td>\n",
+ " <td>Americas</td>\n",
+ " <td>Caribbean</td>\n",
+ " <td>Latin America & Caribbean</td>\n",
+ " <td>309156</td>\n",
+ " <td>9093.0</td>\n",
" <td>2. High income: nonOECD</td>\n",
- " <td>-2.126899</td>\n",
- " <td>49.218374</td>\n",
+ " <td>-76.628430</td>\n",
+ " <td>24.290367</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Kyrgyzstan</th>\n",
@@ -942,10 +830,7 @@
"text/plain": [
" name \\\n",
"name_jhu \n",
- "Cape Verde Cape Verde \n",
- "Guernsey Guernsey \n",
- "The Gambia Gambia \n",
- "Jersey Jersey \n",
+ "Bahamas Bahamas \n",
"Kyrgyzstan Kyrgyzstan \n",
"Saint Lucia Saint Lucia \n",
"Syria Syria \n",
@@ -955,10 +840,7 @@
"\n",
" name_long region_un \\\n",
"name_jhu \n",
- "Cape Verde Cape Verde Africa \n",
- "Guernsey Guernsey Europe \n",
- "The Gambia The Gambia Africa \n",
- "Jersey Jersey Europe \n",
+ "Bahamas Bahamas Americas \n",
"Kyrgyzstan Kyrgyzstan Asia \n",
"Saint Lucia Saint Lucia Americas \n",
"Syria Syria Asia \n",
@@ -966,25 +848,19 @@
"Saint Vincent and the Grenadines Saint Vincent and the Grenadines Americas \n",
"Venezuela Venezuela Americas \n",
"\n",
- " subregion region_wb \\\n",
- "name_jhu \n",
- "Cape Verde Western Africa Sub-Saharan Africa \n",
- "Guernsey Northern Europe Europe & Central Asia \n",
- "The Gambia Western Africa Sub-Saharan Africa \n",
- "Jersey Northern Europe Europe & Central Asia \n",
- "Kyrgyzstan Central Asia Europe & Central Asia \n",
- "Saint Lucia Caribbean Latin America & Caribbean \n",
- "Syria Western Asia Middle East & North Africa \n",
- "Taiwan* Eastern Asia East Asia & Pacific \n",
- "Saint Vincent and the Grenadines Caribbean Latin America & Caribbean \n",
- "Venezuela South America Latin America & Caribbean \n",
+ " subregion region_wb \\\n",
+ "name_jhu \n",
+ "Bahamas Caribbean Latin America & Caribbean \n",
+ "Kyrgyzstan Central Asia Europe & Central Asia \n",
+ "Saint Lucia Caribbean Latin America & Caribbean \n",
+ "Syria Western Asia Middle East & North Africa \n",
+ "Taiwan* Eastern Asia East Asia & Pacific \n",
+ "Saint Vincent and the Grenadines Caribbean Latin America & Caribbean \n",
+ "Venezuela South America Latin America & Caribbean \n",
"\n",
" pop_est gdp_md_est \\\n",
"name_jhu \n",
- "Cape Verde 429474 1626.0 \n",
- "Guernsey 68633 2742.0 \n",
- "The Gambia 1782893 2272.0 \n",
- "Jersey 91626 5100.0 \n",
+ "Bahamas 309156 9093.0 \n",
"Kyrgyzstan 5431747 11610.0 \n",
"Saint Lucia 160267 1778.0 \n",
"Syria 20178485 98830.0 \n",
@@ -994,10 +870,7 @@
"\n",
" income_grp Longitude \\\n",
"name_jhu \n",
- "Cape Verde 4. Lower middle income -23.959888 \n",
- "Guernsey 2. High income: nonOECD -2.572391 \n",
- "The Gambia 5. Low income -15.396013 \n",
- "Jersey 2. High income: nonOECD -2.126899 \n",
+ "Bahamas 2. High income: nonOECD -76.628430 \n",
"Kyrgyzstan 5. Low income 74.541655 \n",
"Saint Lucia 3. Upper middle income -60.969699 \n",
"Syria 4. Lower middle income 38.507882 \n",
@@ -1007,10 +880,7 @@
"\n",
" Latitude \n",
"name_jhu \n",
- "Cape Verde 15.955233 \n",
- "Guernsey 49.468098 \n",
- "The Gambia 13.449652 \n",
- "Jersey 49.218374 \n",
+ "Bahamas 24.290367 \n",
"Kyrgyzstan 41.462219 \n",
"Saint Lucia 13.894795 \n",
"Syria 35.025474 \n",
@@ -1037,10 +907,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012964,
- "end_time": "2020-03-25T13:55:05.402092",
+ "duration": 0.012118,
+ "end_time": "2020-03-25T23:09:01.988062",
"exception": false,
- "start_time": "2020-03-25T13:55:05.389128",
+ "start_time": "2020-03-25T23:09:01.975944",
"status": "completed"
},
"tags": []
@@ -1054,10 +924,10 @@
"execution_count": 13,
"metadata": {
"papermill": {
- "duration": 0.172521,
- "end_time": "2020-03-25T13:55:05.587275",
+ "duration": 0.053488,
+ "end_time": "2020-03-25T23:09:02.053219",
"exception": false,
- "start_time": "2020-03-25T13:55:05.414754",
+ "start_time": "2020-03-25T23:09:01.999731",
"status": "completed"
},
"tags": []
@@ -1082,10 +952,10 @@
"execution_count": 14,
"metadata": {
"papermill": {
- "duration": 0.078266,
- "end_time": "2020-03-25T13:55:05.678115",
+ "duration": 0.069275,
+ "end_time": "2020-03-25T23:09:02.144625",
"exception": false,
- "start_time": "2020-03-25T13:55:05.599849",
+ "start_time": "2020-03-25T23:09:02.075350",
"status": "completed"
},
"tags": []
@@ -1118,8 +988,8 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 2.775622,
- "end_time": "2020-03-25T13:55:06.012085",
+ "duration": 2.640022,
+ "end_time": "2020-03-25T23:09:02.478791",
"environment_variables": {},
"exception": null,
"input_path": "notebooks/process/ToRates.ipynb",
@@ -1132,7 +1002,7 @@
"ts_folder": "./data/covid-19_jhu-csse/",
"wb_path": "./data/worldbank/SP.POP.TOTL.zip"
},
- "start_time": "2020-03-25T13:55:03.236463",
+ "start_time": "2020-03-25T23:08:59.838769",
"version": "1.1.0"
}
},
--
GitLab