From 5ccfa488f9e5d0c388c44e48bb0a5a08f71807fd Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Thu, 9 Apr 2020 10:40:10 +0000
Subject: [PATCH] fix: make the path to the atlas a papermill argument
---
notebooks/Dashboard.ipynb | 33 ++++++++++-----------------------
1 file changed, 10 insertions(+), 23 deletions(-)
diff --git a/notebooks/Dashboard.ipynb b/notebooks/Dashboard.ipynb
index 6c8183f6c..a077f842b 100644
--- a/notebooks/Dashboard.ipynb
+++ b/notebooks/Dashboard.ipynb
@@ -37,6 +37,7 @@
"ts_folder = \"../data/covid-19_jhu-csse/\"\n",
"rates_folder = \"../data/covid-19_rates/\"\n",
"geodata_path = \"../data/geodata/geo_data.csv\"\n",
+ "atlas_path = \"../data/atlas\"\n",
"out_folder = None\n",
"PAPERMILL_OUTPUT_PATH = None"
]
@@ -49,7 +50,7 @@
"source": [
"# Read in and transform the case data\n",
"from covid_19_utils.converters import CaseConverter\n",
- "converter = CaseConverter('../data/atlas')\n",
+ "converter = CaseConverter(atlas_path)\n",
"jhu_df = converter.read_convert(ts_folder)\n",
"\n",
"# Read in geographical data\n",
@@ -89,9 +90,7 @@
"Understanding the spread, distribution, and deadliness of COVID-19 is difficult, despite the data available about it. Differences in rates of testing, quality of data, demographics, etc. make it difficult to compare data between countries. \n",
"\n",
"All this needs to be considered when looking at the plots below. But despite those caveats, I found it helpful to plot the raw data, even though direct comparisons between countries might not be inaccurate."
- ],
- "execution_count": null,
- "outputs": []
+ ]
},
{
"cell_type": "code",
@@ -108,9 +107,7 @@
"metadata": {},
"source": [
"## How are cases per 100,000 distributed geographically?"
- ],
- "execution_count": null,
- "outputs": []
+ ]
},
{
"cell_type": "code",
@@ -127,8 +124,7 @@
"metadata": {},
"outputs": [],
"source": [
- "map_df = latest_df[latest_df.country_label.isin(countries_over_thresh)]\n",
- ""
+ "map_df = latest_df[latest_df.country_label.isin(countries_over_thresh)]\n"
]
},
{
@@ -183,9 +179,7 @@
"metadata": {},
"source": [
"## How have cases been growing?"
- ],
- "execution_count": null,
- "outputs": []
+ ]
},
{
"cell_type": "code",
@@ -295,21 +289,14 @@
" <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
"</p>'''))"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
"hide_input": true,
"kernelspec": {
- "display_name": "Python 3.7.7 64-bit ('.venv': venv)",
+ "display_name": "Python 3",
"language": "python",
- "name": "python37764bitvenvvenv814492364d964019a25eb1cf3dc3e99c"
+ "name": "python3"
},
"language_info": {
"codemirror_mode": {
@@ -321,9 +308,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.7.7-final"
+ "version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 4
-}
\ No newline at end of file
+}
--
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