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Program.csv
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Program.csv
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PROGRAM;FOLDER_VAR;FILE;TYPE;FORMAT;OBJECT;KEY;PROCESSES;FUNCTIONS
Step_01_CreatePersons;path_dir;PERSONS;INPUT;CDM;PERSONS;;INPUTE birth and death date;IMPORT_PATTERN
Step_01_CreatePersons;tmp;PERSONS;OUTPUT;rds;PERSONS;person_id;;
Step_01_CreatePersons;tmp;INPUTED;OUTPUT;rds;INPUTED;;;
Step_02_CreateSpells;path_dir;OBSERVATION_PERIODS;INPUT;CDM;OBSERVATION_PERIODS;;Correct op_start_date and op_end_date;IMPORT_PATTERN, CreateSpells
Step_02_CreateSpells;tmp;PERSONS;INPUT;rds;PERSONS;;;
Step_02_CreateSpells;tmp;OBS_SPELLS;OUTPUT;rds;OBSERVATION_PERIODS1;person_id,num_spell;;
Step_02_CreateSpells;tmp;FlowChartCreateSpells;OUTPUT;rds;FlowChartCreateSpells;;;
Step_03_GetVaccins;path_dir;VACCINES;INPUT;CDM;VACCINES;;Select codes (exact or start with) and store;IMPORT_PATTERN, CreateConceptDatasets
Step_03_GetVaccins;meta_dir;VAC4EU PASS CovidVaccineMonitoringVariables-3;INPUT;xlsx;FILE;;;
Step_03_GetVaccins;vaccins_dir;CoV;OUTPUT;rds;TEMP1;person_id, Date ;;
Step_03_GetVaccins;vaccins_dir;INF;OUTPUT;rds;TEMP1;person_id, Date ;;
Step_04_CreateVariablesCovidVaccins;vaccins_dir;CoV;INPUT;rds;VAC;;Create Covid vaccin variables (1st,2nd,3th);CleanOutcomes
Step_04_CreateVariablesCovidVaccins;tmp;PERSONS;INPUT;rds;PERSONS;;;
Step_04_CreateVariablesCovidVaccins;vaccins_dir;CoV2;OUTPUT;rds;VAC2;person_id, Date ;;
Step_04_CreateVariablesCovidVaccins;tmp;PERSONS1;OUTPUT;rds;PERSONS;person_id;;
Step_04b_CreateStudyPopulation;tmp;PERSONS1;INPUT;rds;TEMP;;Exclude cases by expressions formulated in 00_SetParameters;Flowchart
Step_04b_CreateStudyPopulation;tmp;OBS_SPELLS;INPUT;rds;TEMP2;;;
Step_04b_CreateStudyPopulation;tmp;PERSONS2;OUTPUT;rds;PERSONS;person_id;;
Step_04b_CreateStudyPopulation;tmp;OBS_SPELLS1;OUTPUT;rds;TEMP2;person_id,num_spell;;
Step_04b_CreateStudyPopulation;tmp;FlowChart;OUTPUT;rds;Flow ;;;
Step_05_GetCovid;path_dir;EVENTS;INPUT;CDM;SQLite;;Select codes and append in temporary sqlite db;IMPORT_PATTERN, CreateConceptDatasets
Step_05_GetCovid;meta_dir;Pfizer_full_codelist;INPUT;csv;FILE;;;
Step_05_GetCovid;path_dir;MEDICAL_OBSERVATIONS;INPUT;CDM;;;;
Step_05_GetCovid;path_dir;SURVEY_OBSERVATIONS;INPUT;CDM;;;;
Step_05_GetCovid;meta_dir;Pfizer_additional_MO_SO;INPUT;csv;;;;
Step_05_GetCovid;concepts_dir;COVID19DX;OUTPUT;rds;TEMP1;person_id, start_date_record;;
Step_06_CreateVariableCovidInfection;tmp;PERSONS2;INPUT;rds;PERSONS;;Select first covid infection;
Step_06_CreateVariableCovidInfection;concepts_dir;COVID19DX;INPUT;rds;COVID;;;
Step_06_CreateVariableCovidInfection;tmp;PERSONS3;OUTPUT;rds;PERSONS;person_id;;
Step_07_CreateMonthlyStatus;vaccins_dir;INF;INPUT;rds;INF;;Procuce a table by month used with loopwise matching;CountHistorical
Step_07_CreateMonthlyStatus;path_dir;MEDICAL_OBSERVATIONS;INPUT;CDM;REGION;;;
Step_07_CreateMonthlyStatus;populations_dir;MATCHING;OUTPUT;FOLDER;TEMP4;person_id;;
Step_07_CreateMonthlyStatus;populations_dir;REGION;OUTPUT;rds;REGION;person_id, mo_date;Long table in case using sql join for matching;
Step_08_PrepareExposedControls;tmp;PERSONS3;INPUT;rds;PERSONS;;;
Step_08_PrepareExposedControls;tmp;OBS_SPELLS1;INPUT;rds;SPELLS;;;
Step_08_PrepareExposedControls;populations_dir;MATCHING;INPUT;FOLDER;HIST;;;
Step_08_PrepareExposedControls;tmp;EXPOSED;OUTPUT;rds;FILE_EXPOSED;person_id;;
Step_08_PrepareExposedControls;tmp;CONTROL;OUTPUT;rds;FILE_CONTROL;person_id;;
Step_09_MatchingProcedure;tmp;EXPOSED;INPUT;rds;FILE_EXPOSED;;Matching;
Step_09_MatchingProcedure;tmp;CONTROL;INPUT;rds;FILE_CONTROL;;;
Step_09_MatchingProcedure;tmp;OBS_SPELLS1;INPUT;rds;SPELLS;;;
Step_09_MatchingProcedure;populations_dir;MATCHING;INPUT;FOLDER;;;;
Step_09_MatchingProcedure;populations_dir;MATCH_PAIRS;OUTPUT;rds;MATCHED;person_id,id;;
Step_10_CombineExposedControl;populations_dir;MATCH_PAIRS;INPUT;rds;MATCHES;;Make a long format table;
Step_10_CombineExposedControl;tmp;PERSONS3;INPUT;rds;PERSONS;;;
Step_10_CombineExposedControl;tmp;OBS_SPELLS;INPUT;rds;SPELLS;;;
Step_10_CombineExposedControl;populations_dir;M_Studycohort;OUTPUT;rds;M_Studycohort;person_id,id;;
Step_11_PutConceptsInDatabase;populations_dir;MATCH_PAIRS;INPUT;rds;MATCHES;;Per file append per concept in sqliet database;
Step_11_PutConceptsInDatabase;meta_dir;Pfizer_full_codelist;INPUT;csv;FILE;;;
Step_11_PutConceptsInDatabase;path_dir;EVENTS;INPUT;CDM;TEMP;;;
Step_11_PutConceptsInDatabase;tmp;Concept name;OUTPUT;db;TEMP;person_id, Date ;;
Step_12_AddCoVariates;populations_dir;M_Studycohort;INPUT;rds;temp;;Extract dates covariates from sqlite database;
Step_12_AddCoVariates;meta_dir;Pfizer_full_codelist;INPUT;csv;FILE;;;
Step_12_AddCoVariates;tmp;Concept name;INPUT;db;temp;;;
Step_12_AddCoVariates;populations_dir;M_Studycohort2;OUTPUT;rds;M_Studycohort;person_id,id;;
Step_13_AddAESI;populations_dir;M_Studycohort2;INPUT;rds;M_Studycohort;;Extract dates AESI's from sqlite database;
Step_13_AddAESI;meta_dir;Pfizer_full_codelist;INPUT;csv;FILE;;;
Step_13_AddAESI;tmp;Concept name;INPUT;db;temp1;;;
Step_13_AddAESI;populations_dir;M_Studycohort3;OUTPUT;rds;M_Studycohort;person_id,id;;