diff --git a/src/add_rki_to_map.py b/src/add_rki_to_map.py new file mode 100644 index 0000000000000000000000000000000000000000..25af46418ce10bc516d8ddb73f0a1019c5d34465 --- /dev/null +++ b/src/add_rki_to_map.py @@ -0,0 +1,27 @@ +import os +import pickle as pkl +import pandas as pd + +data = pd.read_csv('../data/diseases/covid19.csv', sep=',', encoding='iso-8859-1', index_col=0) +data.index = [pd.Timestamp(date) for date in data.index] + +with open('../data/counties/counties.pkl', 'rb') as f: + counties = pkl.load(f) + +shared_assets = '/p/project/covid19dynstat/shared_assets/' +figures = os.path.join(shared_assets, 'figures/') +dates = next(os.walk(figures))[1] + +# errors if the RKI based csv is out of date with the available folders +for date in dates: + map_csv_path = os.path.join(figures, date, 'map.csv') + + map_rki = data.loc[date.replace('_', '-')].values.astype('float64') + for (i, (key, _)) in enumerate(counties.items()): + n_people = counties[key]['demographics'][('total', 2018)] + map_rki[i] = map_rki[i] / n_people * 100000 + + map_data = pd.read_csv(map_csv_path, index_col=0) + map_data["newInf100k_RKI"] = list(map_rki) + + map_data.to_csv(map_csv_path) diff --git a/src/plot_window_germany.py b/src/plot_window_germany.py index b4c4037f8b346c1a5fd3f3cd817210a6f4218104..e99e125339082c39c75e12db27ca80e7c595a382 100644 --- a/src/plot_window_germany.py +++ b/src/plot_window_germany.py @@ -121,17 +121,20 @@ def curves(start, n_weeks=3, model_i=35,save_plot=False): # relativize prediction mean. map_vals = prediction_mean.iloc[-10] + map_rki = data.iloc[-1].values.astype('float64') map_keys = [] - ik= 0 - for key, _ in counties.items(): + # ik= 0 + for (ik, (key, _)) in enumerate(counties.items()): n_people = counties[key]['demographics'][('total',2018)] map_vals[ik] = (map_vals[ik] / n_people) * 100000 - ik = ik+1 + map_rki[ik] = (map_rki[ik] / n_people) * 100000 + # ik = ik+1 map_keys.append(key) map_df = pd.DataFrame(index=None) map_df["countyID"] = map_keys map_df["newInf100k"] = list(map_vals) + map_df["newInf100k_RKI"] = list(map_rki) # plot the chloropleth map plot_counties(map_ax,