From c405ebb37dfd95bd35021ec5c9b2fdce88f2ca5c Mon Sep 17 00:00:00 2001 From: MaxBetz <104758467+MaxBetzDLR@users.noreply.github.com> Date: Thu, 28 Aug 2025 09:10:41 +0000 Subject: [PATCH 1/3] adjust getVaccinationData.py --- .../memilio/epidata/getVaccinationData.py | 39 +++++++++++++++++-- 1 file changed, 36 insertions(+), 3 deletions(-) diff --git a/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py b/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py index 2341ea8c44..f55670711b 100644 --- a/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py +++ b/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py @@ -971,6 +971,11 @@ def write_vaccination_data(dict_data: dict, dd.EngEng['idState'], dd.EngEng['ageRKI']]).agg( {column: "sum" for column in vacc_column_names}).reset_index() + + df_data_agevacc_ger_cs = df_data_agevacc_county_cs.groupby( + [dd.EngEng['date'], + dd.EngEng['ageRKI']]).agg( + {column: "sum" for column in vacc_column_names}).reset_index() # make plot of absolute numbers original age resolution if conf_obj.plot: @@ -1019,6 +1024,10 @@ def write_vaccination_data(dict_data: dict, [dd.EngEng['date'], dd.EngEng['idState']]).agg( {column: "sum" for column in vacc_column_names}).reset_index() + + df_data_ger_cs = df_data_county_cs.groupby( + [dd.EngEng['date']]).agg( + {column: "sum" for column in vacc_column_names}).reset_index() ####### age resolved with extrapolation to other age groups ####### # write data frame resolved per county and age (with age classes as @@ -1039,6 +1048,11 @@ def write_vaccination_data(dict_data: dict, dd.EngEng['idState'], dd.EngEng['ageRKI']]).agg( {column: "sum" for column in vacc_column_names}).reset_index() + + df_data_ageinf_ger_cs = df_data_ageinf_county_cs.groupby( + [dd.EngEng['date'], + dd.EngEng['ageRKI']]).agg( + {column: "sum" for column in vacc_column_names}).reset_index() # make plot of relative numbers of original and extrapolated age resolution if conf_obj.plot: @@ -1140,6 +1154,12 @@ def write_vaccination_data(dict_data: dict, filename = gd.append_filename(filename, impute_dates, moving_average) gd.write_dataframe(df_data_agevacc_state_cs, directory, filename, file_format) + + # store data for germany + filename = 'vacc_germany_agevacc' + filename = gd.append_filename(filename, impute_dates, moving_average) + gd.write_dataframe(df_data_agevacc_ger_cs, + directory, filename, file_format) # store data for all counties filename = 'vacc_county' @@ -1152,6 +1172,12 @@ def write_vaccination_data(dict_data: dict, filename = gd.append_filename(filename, impute_dates, moving_average) gd.write_dataframe(df_data_state_cs, directory, filename, file_format) + # store data for germany + filename = 'vacc_germany' + filename = gd.append_filename(filename, impute_dates, moving_average) + gd.write_dataframe(df_data_ger_cs, + directory, filename, file_format) + ####### age resolved with extrapolation to other age groups ####### # write data frame resolved per county and age (with age classes as # provided in RKI infection tables: 0-4, 5-14, 15-34, 35-59, 60-79, 80+) @@ -1168,11 +1194,18 @@ def write_vaccination_data(dict_data: dict, filename = gd.append_filename(filename, impute_dates, moving_average) gd.write_dataframe(df_data_ageinf_state_cs, directory, filename, file_format) + + # store data for germany + filename = 'vacc_germany_ageinf' + filename = gd.append_filename(filename, impute_dates, moving_average) + gd.write_dataframe(df_data_ageinf_ger_cs, + directory, filename, file_format) + return None else: - return (df_data_agevacc_county_cs, df_data_agevacc_state_cs, - df_data_county_cs, df_data_state_cs, - df_data_ageinf_county_cs, df_data_ageinf_state_cs) + return (df_data_agevacc_county_cs, df_data_agevacc_state_cs, df_data_agevacc_ger_cs, + df_data_county_cs, df_data_state_cs, df_data_ger_cs, + df_data_ageinf_county_cs, df_data_ageinf_state_cs, df_data_ageinf_ger_cs) def get_vaccination_data( From ad862fce45cf080ba00eaf88df75dd138e8669d2 Mon Sep 17 00:00:00 2001 From: MaxBetz <104758467+MaxBetzDLR@users.noreply.github.com> Date: Thu, 28 Aug 2025 09:17:38 +0000 Subject: [PATCH 2/3] fix formating --- .../memilio/epidata/getVaccinationData.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py b/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py index f55670711b..caa04a583e 100644 --- a/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py +++ b/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py @@ -971,7 +971,7 @@ def write_vaccination_data(dict_data: dict, dd.EngEng['idState'], dd.EngEng['ageRKI']]).agg( {column: "sum" for column in vacc_column_names}).reset_index() - + df_data_agevacc_ger_cs = df_data_agevacc_county_cs.groupby( [dd.EngEng['date'], dd.EngEng['ageRKI']]).agg( @@ -1024,7 +1024,7 @@ def write_vaccination_data(dict_data: dict, [dd.EngEng['date'], dd.EngEng['idState']]).agg( {column: "sum" for column in vacc_column_names}).reset_index() - + df_data_ger_cs = df_data_county_cs.groupby( [dd.EngEng['date']]).agg( {column: "sum" for column in vacc_column_names}).reset_index() @@ -1048,7 +1048,7 @@ def write_vaccination_data(dict_data: dict, dd.EngEng['idState'], dd.EngEng['ageRKI']]).agg( {column: "sum" for column in vacc_column_names}).reset_index() - + df_data_ageinf_ger_cs = df_data_ageinf_county_cs.groupby( [dd.EngEng['date'], dd.EngEng['ageRKI']]).agg( @@ -1154,7 +1154,7 @@ def write_vaccination_data(dict_data: dict, filename = gd.append_filename(filename, impute_dates, moving_average) gd.write_dataframe(df_data_agevacc_state_cs, directory, filename, file_format) - + # store data for germany filename = 'vacc_germany_agevacc' filename = gd.append_filename(filename, impute_dates, moving_average) @@ -1177,7 +1177,7 @@ def write_vaccination_data(dict_data: dict, filename = gd.append_filename(filename, impute_dates, moving_average) gd.write_dataframe(df_data_ger_cs, directory, filename, file_format) - + ####### age resolved with extrapolation to other age groups ####### # write data frame resolved per county and age (with age classes as # provided in RKI infection tables: 0-4, 5-14, 15-34, 35-59, 60-79, 80+) @@ -1194,7 +1194,7 @@ def write_vaccination_data(dict_data: dict, filename = gd.append_filename(filename, impute_dates, moving_average) gd.write_dataframe(df_data_ageinf_state_cs, directory, filename, file_format) - + # store data for germany filename = 'vacc_germany_ageinf' filename = gd.append_filename(filename, impute_dates, moving_average) From 332df9902f892ccf930247adc25c75b54d1c82ea Mon Sep 17 00:00:00 2001 From: MaxBetz <104758467+MaxBetzDLR@users.noreply.github.com> Date: Thu, 28 Aug 2025 09:29:47 +0000 Subject: [PATCH 3/3] fix format --- pycode/memilio-epidata/memilio/epidata/getVaccinationData.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py b/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py index caa04a583e..7d3d32d41e 100644 --- a/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py +++ b/pycode/memilio-epidata/memilio/epidata/getVaccinationData.py @@ -1200,7 +1200,7 @@ def write_vaccination_data(dict_data: dict, filename = gd.append_filename(filename, impute_dates, moving_average) gd.write_dataframe(df_data_ageinf_ger_cs, directory, filename, file_format) - + return None else: return (df_data_agevacc_county_cs, df_data_agevacc_state_cs, df_data_agevacc_ger_cs,