Merge branch 'main' into 211-python-dependencies

Author: annette-lutz

.github/actions/test-py/action.yml

@@ -47,7 +47,7 @@ runs:
         fi
         
         if [[ "${{ inputs.package }}" == "epidata" ]]; then
-          getrkidata --help
+          getcasedata --help
           getpopuldata --help
           getjhdata --help
           getdividata --help

.github/workflows/main.yml

@@ -227,7 +227,7 @@ jobs:
       - name: Dowload Data
         run: |
           mkdir -p data_dl
-          getrkidata -o data_dl
+          getcasedata -o data_dl
           getpopuldata -o data_dl
           getjhdata -o data_dl
           getdividata -o data_dl

cpp/models/secir/secir_parameters_io.h

@@ -344,7 +344,7 @@ IOResult<void> extrapolate_rki_results(std::vector<Model>& model, const std::str
         std::vector<double> num_icu(model.size(), 0.0);
 
         BOOST_OUTCOME_TRY(details::read_rki_data(
-            path_join(data_dir, "all_county_age_ma_rki.json"), id_name, region, date, num_exp, num_car, num_inf, num_hosp,
+            path_join(data_dir, "cases_all_county_age_ma7.json"), id_name, region, date, num_exp, num_car, num_inf, num_hosp,
             dummy_icu, num_death, num_rec, t_car_to_rec, t_car_to_inf, t_exp_to_car, t_inf_to_rec, t_inf_to_hosp,
             t_hosp_to_rec, t_hosp_to_icu, t_icu_to_dead, mu_C_R, mu_I_H, mu_H_U, scaling_factor_inf));
         BOOST_OUTCOME_TRY(details::read_divi_data(path_join(data_dir, "county_divi.json"), id_name, region, date, num_icu));
@@ -406,7 +406,7 @@ IOResult<void> read_population_data_germany(std::vector<Model>& model, Date date
         log_warning("No DIVI data available for this date");
     }
     BOOST_OUTCOME_TRY(
-        details::set_rki_data(model, path_join(dir, "all_age_ma_rki.json"), id_name, {0}, date, scaling_factor_inf));
+        details::set_rki_data(model, path_join(dir, "cases_all_age_ma7.json"), id_name, {0}, date, scaling_factor_inf));
     BOOST_OUTCOME_TRY(
         details::set_population_data(model, path_join(dir, "county_current_population.json"), "ID_County", {0}));
     return success();
@@ -435,7 +435,7 @@ IOResult<void> read_population_data_state(std::vector<Model>& model, Date date,
         log_warning("No DIVI data available for this date");
     }
 
-    BOOST_OUTCOME_TRY(details::set_rki_data(model, path_join(dir, "all_state_age_ma_rki.json"), id_name, state, date,
+    BOOST_OUTCOME_TRY(details::set_rki_data(model, path_join(dir, "cases_all_state_age_ma7.json"), id_name, state, date,
                                             scaling_factor_inf));
     BOOST_OUTCOME_TRY(
         details::set_population_data(model, path_join(dir, "county_current_population.json"), "ID_County", state));
@@ -465,7 +465,7 @@ IOResult<void> read_population_data_county(std::vector<Model>& model, Date date,
     else {
         log_warning("No DIVI data available for this date");
     }
-    BOOST_OUTCOME_TRY(details::set_rki_data(model, path_join(dir, "all_county_age_ma_rki.json"), id_name, county, date,
+    BOOST_OUTCOME_TRY(details::set_rki_data(model, path_join(dir, "cases_all_county_age_ma7.json"), id_name, county, date,
                                             scaling_factor_inf));
     BOOST_OUTCOME_TRY(
         details::set_population_data(model, path_join(dir, "county_current_population.json"), "ID_County", county));

cpp/tests/data/all_age_ma_rki.json renamed to cpp/tests/data/cases_all_age_ma7.json

@@ -17,12 +17,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #############################################################################
+"""@PlotGermanData.py
+WARNING: This file is currently not tested and maintained.
+"""
 import pandas as pd
 import numpy as np
 import matplotlib.pyplot as plt
 from datetime import datetime
 
-df = pd.read_json('all_age_rki.json')
+df = pd.read_json('cases_all_age.json')
 
 for i in range(len(df)):
     df.Date[i] = df.Date[i].date()
@@ -54,7 +57,7 @@
 ax[2].set_xticks(tick_range)
 ax[2].set_xticklabels(datelist[tick_range],rotation=45)
 fig.tight_layout()
-fig.savefig('RKI_Groups.pdf')
+fig.savefig('Cases_Groups.pdf')
 
 
 all_data = np.sum(group_data, axis=1)
@@ -72,5 +75,5 @@
 ax[3].set_xticks(tick_range)
 ax[3].set_xticklabels(datelist[tick_range],rotation=45)
 fig.tight_layout()
-fig.savefig('RKI_All.pdf')
+fig.savefig('Cases_All.pdf')
 plt.show()

cpp/tests/data/all_county_age_ma_rki.json renamed to cpp/tests/data/cases_all_county_age_ma7.json

@@ -32,17 +32,17 @@ Getting data from different sources and convert them to usable data using the py
 
 Our sources are:
 
-- Robert Koch institute (RKI) For German data:
+- Robert Koch Institute (RKI) for case data in Germany:
 
-  RKI Dashboard: https://experience.arcgis.com/experience/478220a4c454480e823b17327b2bf1d4/page/page_1/
+  Robert Koch-Institut (2021): SARS-CoV-2 Infektionen in Deutschland, Berlin: Zenodo. DOI:10.5281/zenodo.4681153.
 
-  You can find the data also on:
+  Data is downloaded from github: https://github.com/robert-koch-institut/SARS-CoV-2_Infektionen_in_Deutschland
 
-  https://npgeo-corona-npgeo-de.hub.arcgis.com/datasets/dd4580c810204019a7b8eb3e0b329dd6_0
+  If the data on github is not available, downloading case data is tried from
+  https://npgeo-corona-npgeo-de.hub.arcgis.com/datasets/66876b81065340a4a48710b062319336/about
+  In this case the provided data is either geojson or csv.
 
-  The provided data is either geojson or csv.
-
-- Population data (P) like "Einwoherzahl" for Bundesländer and Landkreise:
+- Population data (P) like "Einwohnerzahl" for Bundesländer and Landkreise:
 
   https://opendata.arcgis.com/datasets/abad92e8eead46a4b0d252ee9438eb53_1.csv
 
@@ -132,15 +132,15 @@ optional arguments working for some are:
 |                                             | where new cases have been reported.                       |
 |                                             |  Note that this option will have a negative impact        |
 |                                             |  on performance as well as on the storage space needed.   |
-|                                             |  [rki]                                                    |
+|                                             |  [cases]                                                    |
 +---------------------------------------------+-----------------------------------------------------------+
-| -ma, --moving-average                       | The 7 day moving average is computed for the data.        |
-|                                             |  Note that the --fill_dates option will be implicitly     |
+| -m N, --moving-average N                       | The central N days moving average is computed for the data.        |
+|                                             |  Note that the --impute_dates option will be implicitly     |
 |                                             |  turned on, as computing the moving average requires all  |
-|                                             |  dates to be available. [rki]                             |
+|                                             |  dates to be available. [cases]                             |
 +---------------------------------------------+-----------------------------------------------------------+
 | -sb, --split-berlin                         | Berlin data is split into different counties              |
-|                                             |  , instead of having only one county for Berlin. [rki]    |
+|                                             |  , instead of having only one county for Berlin. [cases]    |
 +---------------------------------------------+-----------------------------------------------------------+
 | -u, -- update-data                          | Just chronological missing data is added,                 |
 |                                             | **after** the existing ones [divi]                        |
@@ -159,31 +159,31 @@ When speaking about infected, means always infected inclusive the already recove
 ============== ==========  ================================== =================
 Source         Folder      Files                              Data description
 ============== ==========  ================================== =================
-RKI            Germany     infected_rki                       Numbers of infected over time for whole Germany
-RKI            Germany     deaths_rki                         Numbers of deaths over time for whole Germany
-RKI            Germany     all_germany_rki                    infected, deaths, recovered over time for whole Germany
-RKI            Germany     infected_state_rki                 infected over time for different states (Bundesländer)
-RKI            Germany     all_state_rki                      infected, deaths, recovered over time for different states (Bundesländer)
-RKI            Germany     infected_county_rki                infected over time for different counties (Landkreise)
-RKI            Germany     all_county_rki                     infected, deaths, recovered over time for different counties (Landkreise)
-RKI            Germany     all_gender_rki                     infected, deaths, recovered over time for different gender
-RKI            Germany     all_age_rki                        infected, deaths, recovered over time for different age ranges
-RKI            Germany     all_state_age_rki                  infected, deaths, recovered over time for different age ranges and states
-RKI            Germany     all_state_gender_rki               infected, deaths, recovered over time for different genders and states
-RKI            Germany     all_county_age_rki                 infected, deaths, recovered over time for different age ranges and counties
-RKI            Germany     all_county_gender_rki              infected, deaths, recovered over time for different genders counties
-
-RKI            Germany     vaccine_data_[DATE]                administered vaccines, first shot, full vaccination, vaccination ratio, vacc ratio young, vacc ratio old
-
-RKI-Estimation Germany     all_germany_rki_estimated          infected, deaths, recovered, recovered_estimated, deaths_estimated over time for whole Germany
-RKI-Estimation Germany     all_state_rki_estimated            infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different states (Bundesländer)
-RKI-Estimation Germany     all_county_rki_estimated           infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different counties (Landkreise)
-RKI-Estimation Germany     all_gender_rki_estimated           infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different gender
-RKI-Estimation Germany     all_age_rki_estimated              infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different age ranges
-RKI-Estimation Germany     all_state_age_rki_estimated        infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different age ranges and states
-RKI-Estimation Germany     all_state_gender_rki_estimated     infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different genders and states
-RKI-Estimation Germany     all_county_age_rki_estimated       infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different age ranges and counties
-RKI-Estimation Germany     all_county_gender_rki_estimated    infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different genders counties
+RKI            Germany     cases_infected                     Numbers of infected over time for whole Germany
+RKI            Germany     cases_deaths                       Numbers of deaths over time for whole Germany
+RKI            Germany     cases_all_germany                  infected, deaths, recovered over time for whole Germany
+RKI            Germany     cases_infected_state               infected over time for different states (Bundesländer)
+RKI            Germany     cases_all_state                    infected, deaths, recovered over time for different states (Bundesländer)
+RKI            Germany     cases_infected_county              infected over time for different counties (Landkreise)
+RKI            Germany     cases_all_county                   infected, deaths, recovered over time for different counties (Landkreise)
+RKI            Germany     cases_all_gender                   infected, deaths, recovered over time for different gender
+RKI            Germany     cases_all_age                      infected, deaths, recovered over time for different age ranges
+RKI            Germany     cases_all_state_age                infected, deaths, recovered over time for different age ranges and states
+RKI            Germany     cases_all_state_gender             infected, deaths, recovered over time for different genders and states
+RKI            Germany     cases_all_county_age               infected, deaths, recovered over time for different age ranges and counties
+RKI            Germany     cases_all_county_gender            infected, deaths, recovered over time for different genders counties
+
+RKI            Germany     vaccine_data_[DATE]       administered vaccines, first shot, full vaccination, vaccination ratio, vacc ratio young, vacc ratio old
+
+RKI-Estimation Germany     cases_all_germany_estimated        infected, deaths, recovered, recovered_estimated, deaths_estimated over time for whole Germany
+RKI-Estimation Germany     cases_all_state_estimated          infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different states (Bundesländer)
+RKI-Estimation Germany     cases_all_county_estimated         infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different counties (Landkreise)
+RKI-Estimation Germany     cases_all_gender_estimated         infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different gender
+RKI-Estimation Germany     cases_all_age_estimated            infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different age ranges
+RKI-Estimation Germany     cases_all_state_age_estimated      infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different age ranges and states
+RKI-Estimation Germany     cases_all_state_gender_estimated   infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different genders and states
+RKI-Estimation Germany     cases_all_county_age_estimated     infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different age ranges and counties
+RKI-Estimation Germany     cases_all_county_gender_estimated  infected, deaths, recovered, recovered_estimated, deaths_estimated over time for different genders counties
 
 P              Germany     county_current_population          Einwohnerzahl for different age groups from the 2011 census, extrapolated to the current level
 P              Germany     migration                          Unchanged migration data