281 Scaling of commuter migration/mobility data

cpp/simulations/paper_202011.cpp

@@ -515,7 +515,7 @@ mio::IOResult<void> set_edges(const fs::path& data_dir,
 {
     //migration between nodes
     BOOST_OUTCOME_TRY(migration_data_commuter,
-                      mio::read_mobility_plain((data_dir / "mobility" / "commuter_migration_scaled.txt").string()));
+                      mio::read_mobility_plain((data_dir / "mobility" / "commuter_mobility_scaled.txt").string()));
     BOOST_OUTCOME_TRY(migration_data_twitter,
                       mio::read_mobility_plain((data_dir / "mobility" / "twitter_scaled_1252.txt").string()));
     if (size_t(migration_data_commuter.rows()) != params_graph.nodes().size() ||

pycode/memilio-epidata/memilio/epidata/transformMobilityData.py

@@ -132,11 +132,11 @@ def main():
 
     # Merge Eisenach and Wartbugkreis in Input Data if need be
     updateMobility2022(directory, mobility_file='twitter_scaled_1252')
-    updateMobility2022(directory, mobility_file='commuter_migration_scaled')
+    updateMobility2022(directory, mobility_file='commuter_mobility_scaled')
     # create federal states mobility matrix (not used in simulation for now)
     createFederalStatesMobility(directory, mobility_file='twitter_scaled_1252')
     createFederalStatesMobility(
-        directory, mobility_file='commuter_migration_scaled')
+        directory, mobility_file='commuter_mobility_scaled')
 
 
 if __name__ == "__main__":

pycode/memilio-epidata/memilio/epidata_test/test_epidata_getCommuterMobility.py

@@ -24,6 +24,7 @@
 import pandas as pd
 import os
 import collections
+from os.path import dirname as up
 from memilio.epidata import getCommuterMobility as gcm
 from memilio.epidata import geoModificationGermany as geoger
 from memilio.epidata import getDataIntoPandasDataFrame as gD
@@ -63,6 +64,10 @@ class TestCommuterMigration(fake_filesystem_unittest.TestCase):
         ['05512', '05513', '05515', '05554', '05558', '05562', '05566',
          '05570'],
         ['05711', '05754', '05758', '05762', '05766', '05770', '05774'])
+
+    memilio_path = up(up(up(up(up(__file__)))))
+    center_coordinates = pd.read_json(os.path.join(
+        memilio_path, 'data', 'mobility' , 'county_centers_dim400.json'))
 
     def setUp(self):
         self.setUpPyfakefs()
@@ -317,14 +322,20 @@ def test_some_errors(self, mock_print):
         self.assertEqual(len(os.listdir(self.path)), 17)
 
     def test_commuter_data(self):
-        """! Tests migration data by some randomly chosen tests.
+        """! Tests mobility data by some randomly chosen tests.
         """
 
-        df_commuter_migration = gcm.get_commuter_data(out_folder=self.path)
+        df_commuter_mobility_no_scale = gcm.get_commuter_data(
+            out_folder=self.path)
+        df_commuter_mobility_scaled = gcm.get_commuter_data(
+            out_folder=self.path, center_coordinates=self.center_coordinates)
         # the first column and first row are just the county IDs
-        # mat_commuter_migration is the real Data that should be tested
-        mat_commuter_migration = df_commuter_migration.iloc[:, 0:]
-        mat_commuter_migration = mat_commuter_migration.iloc[0:, :]
+        # mat_commuter_mobility is the real Data that should be tested
+        mat_commuter_mobility_scaled = df_commuter_mobility_scaled.iloc[:, 0:]
+        mat_commuter_mobility_scaled = mat_commuter_mobility_scaled.iloc[0:, :]
+
+        mat_commuter_mobility_no_scale = df_commuter_mobility_no_scale.iloc[:, 0:]
+        mat_commuter_mobility_no_scale = mat_commuter_mobility_no_scale.iloc[0:, :]
 
         countykey2numlist = collections.OrderedDict(
             zip(self.countykey_list, list(range(0, len(self.countykey_list)))))
@@ -334,32 +345,37 @@ def test_commuter_data(self):
         self.write_commuter_all_federal_states(self.path)
         self.assertEqual(len(os.listdir(self.path)), 18)
 
-        # just do some tests on randomly chosen migrations
+        # just do some tests on randomly chosen mobility
 
-        # check migration from Leverkusen (averaged from NRW, 05) to Hildburghausen
+        # check mobility from Leverkusen (averaged from NRW, 05) to Hildburghausen
         city_from = countykey2numlist['05316']
         city_to = countykey2numlist['16069']
         population = gpd.get_population_data(
             out_folder=self.path, merge_eisenach=False)
         countypop_list = list(population[dd.EngEng['population']])
         self.assertEqual(countypop_list[city_from], 163905)
         self.assertAlmostEqual(
-            mat_commuter_migration.iat[city_from, city_to], 1.526, 2)
+            mat_commuter_mobility_scaled.iat[city_from, city_to], 0.305, 2)
+        self.assertAlmostEqual(
+            mat_commuter_mobility_no_scale.iat[city_from, city_to], 1.526, 2)
 
-        # check migration from Duisburg to Oberspreewald-Lausitz
+        # check mobility from Duisburg to Oberspreewald-Lausitz
         city_from = countykey2numlist['05112']
         city_to = countykey2numlist['12066']
-        self.assertEqual(mat_commuter_migration.iat[city_from, city_to], 11)
+        self.assertEqual(mat_commuter_mobility_scaled.iat[city_from, city_to], 2.2)
+        self.assertEqual(mat_commuter_mobility_no_scale.iat[city_from, city_to], 11)
 
-        # check migration from Lahn-Dill-Kreis to Hamburg
+        # check mobility from Lahn-Dill-Kreis to Hamburg
         city_from = countykey2numlist['06532']
         city_to = countykey2numlist['02000']
-        self.assertEqual(mat_commuter_migration.iat[city_from, city_to], 96)
+        self.assertAlmostEqual(mat_commuter_mobility_scaled.iat[city_from, city_to], 19.2, 2)
+        self.assertEqual(mat_commuter_mobility_no_scale.iat[city_from, city_to], 96, 2)
 
-        # check migration from Herzogtum Lauenburg to Flensburg, Stadt
+        # check mobility from Herzogtum Lauenburg to Flensburg, Stadt
         city_from = countykey2numlist['01001']
         city_to = countykey2numlist['01053']
-        self.assertEqual(mat_commuter_migration.iat[city_from, city_to], 14)
+        self.assertEqual(mat_commuter_mobility_scaled.iat[city_from, city_to], 7)
+        self.assertEqual(mat_commuter_mobility_no_scale.iat[city_from, city_to], 14)
 
     @patch('builtins.print')
     def test_get_neighbors_mobility(self, mock_print):
@@ -369,30 +385,33 @@ def test_get_neighbors_mobility(self, mock_print):
         #direction = both
         (countykey_list, commuter_all) = gcm.get_neighbors_mobility(
             tci, direction='both', abs_tol=0, rel_tol=0,
-            tol_comb='or', merge_eisenach=True, out_folder=self.path)
+            tol_comb='or', merge_eisenach=True, out_folder=self.path, 
+            center_coordinates=self.center_coordinates)
         self.assertEqual(len(countykey_list), 398)
         self.assertAlmostEqual(228, commuter_all[0], 2)
         self.assertAlmostEqual(2146, commuter_all[9], 2)
-        self.assertAlmostEqual(293, commuter_all[11], 2)
-        self.assertAlmostEqual(1, commuter_all[397], 2)
+        self.assertAlmostEqual(146.5, commuter_all[11], 2)
+        self.assertAlmostEqual(.2, commuter_all[397], 2)
 
         # direction = in
         (countykey_list, commuter_all) = gcm.get_neighbors_mobility(
             tci, direction='in', abs_tol=0, rel_tol=0,
-            tol_comb='or', merge_eisenach=True, out_folder=self.path)
+            tol_comb='or', merge_eisenach=True, out_folder=self.path,
+            center_coordinates=self.center_coordinates)
         self.assertEqual(len(countykey_list), 393)
         self.assertAlmostEqual(48, commuter_all[0], 2)
         self.assertAlmostEqual(842, commuter_all[9], 2)
-        self.assertAlmostEqual(92, commuter_all[11], 2)
+        self.assertAlmostEqual(46, commuter_all[11], 2)
 
         # direction = out
         (countykey_list, commuter_all) = gcm.get_neighbors_mobility(
             tci, direction='out', abs_tol=0, rel_tol=0,
-            tol_comb='or', merge_eisenach=True, out_folder=self.path)
+            tol_comb='or', merge_eisenach=True, out_folder=self.path,
+            center_coordinates=self.center_coordinates)
         self.assertEqual(len(countykey_list), 375)
         self.assertAlmostEqual(180, commuter_all[0], 2)
         self.assertAlmostEqual(1304, commuter_all[9], 2)
-        self.assertAlmostEqual(201, commuter_all[11], 2)
+        self.assertAlmostEqual(100.5, commuter_all[11], 2)
 
 
 if __name__ == '__main__':

pycode/memilio-epidata/setup.py

@@ -78,7 +78,9 @@ def run(self):
         'xlrd',
         'requests',
 	    'pyxlsb',
-        'wget'
+        'wget',
+        'geojson',
+        'shapely'
     ],
     extras_require={
         'dev': [