INFO  [2023-10-15 18:27:25] 
========================================================================================
Log Path: C:/Users/marja/Desktop/BY-COVID_WP5_T5.2_baseline-use-case/vaccine_effectiveness_analytical_pipeline/logs/logfile.txt
Working Directory: C:/Users/marja/Desktop/BY-COVID_WP5_T5.2_baseline-use-case/vaccine_effectiveness_analytical_pipeline/scripts
R version: R version 4.3.1 (2023-06-16 ucrt)
Machine: DESKTOP-MHKJDLH x86-64
Operating System: Windows 11 x64 (build 22000)
Base Packages Attached: parallel stats graphics grDevices utils datasets methods base
Other Packages Attached: dbplyr_2.3.4 finalfit_1.0.6 xlsx_0.6.5 log4r_0.4.3 survRM2_1.0-4 gtsummary_1.7.2 forestmodel_0.6.2 tab_5.1.1 knitr_1.41 table1_1.4.3 survival_3.5-0 logger_0.2.2 MatchIt_4.5.0 consort_1.2.1 shiny_1.7.4 tidyr_1.3.0 mice_3.15.0 visdat_0.6.0 here_1.0.1 duckdb_0.6.2 DBI_1.1.3 naniar_0.6.1 formattable_0.2.1 scales_1.2.1 plotly_4.10.2 quarto_1.2 survminer_0.4.9 ggpubr_0.5.0 ggplot2_3.4.0 dlookr_0.6.1 purrr_1.0.1 DT_0.27 DataExplorer_0.8.2 validate_1.1.3 arrow_10.0.1 dplyr_1.1.2
Packages loaded via a namespace (and not attached): dbplyr_2.3.4 finalfit_1.0.6 xlsx_0.6.5 log4r_0.4.3 survRM2_1.0-4 gtsummary_1.7.2 forestmodel_0.6.2 tab_5.1.1 knitr_1.41 table1_1.4.3 survival_3.5-0 logger_0.2.2 MatchIt_4.5.0 consort_1.2.1 shiny_1.7.4 tidyr_1.3.0 mice_3.15.0 visdat_0.6.0 here_1.0.1 duckdb_0.6.2 DBI_1.1.3 naniar_0.6.1 formattable_0.2.1 scales_1.2.1 plotly_4.10.2 quarto_1.2 survminer_0.4.9 ggpubr_0.5.0 ggplot2_3.4.0 dlookr_0.6.1 purrr_1.0.1 DT_0.27 DataExplorer_0.8.2 validate_1.1.3 arrow_10.0.1 dplyr_1.1.2
========================================================================================
     
INFO  [2023-10-15 18:27:25] 
========================================================================================
0_global.R
========================================================================================
    
INFO  - CREATING NECESSARY AUXILIARY TABLES...
INFO  - Database path: C:/Users/marja/Desktop/BY-COVID_WP5_T5.2_baseline-use-case/vaccine_effectiveness_analytical_pipeline/input/BY-COVID-WP5-BaselineUseCase-VE.duckdb
INFO  - Database tables: cohort_data
INFO  - Table cohort_data created
INFO  - INSERT DATA INTO 'COHORT_DATA' TABLE...
INFO  - Number of rows in table cohort_data before: 0
INFO  - Number of rows in table cohort_data after: 10000
                                    
INFO  [2023-10-15 18:27:40] 
========================================================================================
1_DQA.QMD
========================================================================================
 
INFO  - LOADING THE DATA INTO MEMORY...
INFO  - OBTAINING BASIC INFORMATION ABOUT THE COHORT_DATA...
INFO  - CREATING TABLE WITH OVERALL DATASET STATISTICS...
INFO  - CREATING TABLE WITH BASIC COLUMN INFORMATION...
INFO  - CREATING TABLE WITH INFORMATION ON VARIABLE CLASSES...
INFO  - CREATING TABLE WITH MISSING DATA PROFILE...
INFO  - CREATING PLOT WITH MISSING DATA PROFILE...
INFO  - CREATING TABLE WITH ALERTS...
INFO  - CREATING TABLE WITH INFORMATION ON DUPLICATES...
INFO  - ITERATING OVER INDIVIDUAL VARIABLES...
     
INFO  [2023-10-15 18:28:22] 
========================================================================================
2_validation.QMD
========================================================================================
 
INFO  - LOADING THE DATA INTO MEMORY...
INFO  - CHECKING DATA AGAINST A SET OF VALIDATION RULES...
INFO  - CREATE TABLE WITH SUMMARY OF VALIDATION RESULTS...
INFO  - CREATE VALIDATION PLOT...
INFO  - SELECTING PATIENT IDS OF RECORDS VIOLATING AT LEAST ONE OF THE VALIDATION RULES...
INFO  - SET FLAG_VIOLATING_VAL TO TRUE WHEN AT LEAST ONE OF THE RULES IS VIOLATED...
INFO  - COUNT PATIENTS WITH FLAG_VIOLATING_VAL TRUE VERSUS FALSE...
     
INFO  [2023-10-15 18:28:44] 
========================================================================================
3_imputation.QDM
========================================================================================
 
INFO  - LOADING THE DATA INTO MEMORY...
INFO  - CREATING MISSING VALUES MAP...
INFO  - CREATING MISSING DATA MATRIX...
INFO  - CREATING A TABLE WITH VARIABLE CHARACTERISTICS...
INFO  - CREATING A TABLE WITH VARIABLE CHARACTERISTICS (ADD IMPUTATION METHOD)...
INFO  - SAVE TABLE WITH VARIABLE CHARACTERISTICS...
INFO  - LISTWISE DELETION...
INFO  - IMPUTING MISSING VALUES...
INFO  - CREATE DATABASE TABLE WITH IMPUTED DATA ONLY...
INFO  - CREATING A TABLE WITH INFORMATION ON THE IMPUTATION PROCESS...
INFO  - PLOT THE DISTRIBUTION OF IMPUTED DATA...
INFO  - ADJUSTING FLAG VARIABLE (FLAG_LISTWISE_DEL)...
     
INFO  [2023-10-15 18:29:44] 
========================================================================================
4_matching.QDM
========================================================================================
 
INFO  - EXECUTING MATCHING...
INFO  - LOADING THE DATA INTO MEMORY...
INFO  - ASSESSING BALANCE PRIOR TO MATCHING...
INFO  - ASSESSING BALANCE AFTER MATCHING...
INFO  - ASSESSING STANDARDIZED MEAN DIFFERENCE PRIOR TO MATCHING...
INFO  - PLOTTING STANDARDIZED MEAN DIFFERENCE PRIOR TO MATCHING...
INFO  - ASSESSING STANDARDIZED MEAN DIFFERENCE AFTER MATCHING...
INFO  - PLOTTING STANDARDIZED MEAN DIFFERENCE AFTER MATCHING...
INFO  - ASSISSING PROPENSITY SCORE DISTRIBUTION PRIOR TO MATCHING...
INFO  - ASSISSING PROPENSITY SCORE DISTRIBUTION AFTER MATCHING...
     
INFO  [2023-10-15 18:35:45] 
========================================================================================
5_descriptives
========================================================================================
 
INFO  - LOADING THE DATA INTO MEMORY...
INFO  - EXTRACTING ENROLLMENT AND STUDY PERIOD...
INFO  - CREATING CONSORT GRAPH...
INFO  - GENERATING A DESCRIPTION OF THE STUDY POPULATION: POPULATION ELIGIBLE FOR MATCHING...
INFO  - GENERATING A DESCRIPTION OF THE STUDY POPULATION: MATCHED POPULATION...
INFO  - PLOTTING NUMBER OF INDIVIDUALS COMPLETING A PRIMARY VACCINATION SCHEDULE OVER TIME...
INFO  - PLOTTING NUMBER OF INDIVIDUALS COMPLETING A PRIMARY VACCINATION SCHEDULE OVER TIME...
INFO  - GENERATING TWO-BY-TWO TABLES...
INFO  - GENERATING TWO-BY-TWO TABLE: ORIGINAL INPUT DATA...
INFO  - GENERATING TWO-BY-TWO TABLE: POPULATION ELIGIBLE FOR MATCHING...
INFO  - GENERATING TWO-BY-TWO TABLE: MATCHED POPULATION...
INFO  - EXECUTING A SURVIVAL ANALYSIS IN THE UN-MATCHED POPULATION...
INFO  - EXECUTING A SURVIVAL ANALYSIS IN THE UN-MATCHED POPULATION (SIMPLE MODEL)...
INFO  - GENERATING A SUMMARY OF SURVIVAL IN THE UN-MATCHED POPULATION (SIMPLE MODEL)...
INFO  - GENERATING SURVIVAL PLOT IN THE UN-MATCHED POPULATION (SIMPLE MODEL)...
INFO  - GENERATING CUMULATIVE EVENTS PLOT IN THE UN-MATCHED POPULATION (SIMPLE MODEL)...
INFO  - GENERATING CUMULATIVE EVENTS TABLE IN THE UN-MATCHED POPULATION (SIMPLE MODEL)...
INFO  - EXECUTING A SURVIVAL ANALYSIS IN THE UN-MATCHED POPULATION (COMPLEX MODEL)...
INFO  - GENERATING A SUMMARY OF SURVIVAL IN THE UN-MATCHED POPULATION (COMPLEX MODEL)...
INFO  - PLOT THE HR'S IN THE UN-MATCHED POPULATION (COMPLEX MODEL)...
     
INFO  [2023-10-15 18:36:15] 
========================================================================================
6_survival-analysis.QMD
========================================================================================
 
INFO  - LOADING THE DATA INTO MEMORY...
INFO  - PROCUDING KAPLAN-MEIER ESTIMATES OF THE PROBABILITY OF SURVIVAL OVER TIME...
INFO  - PLOTTING THE PROBABILITY OF SURVIVAL OVER TIME...
INFO  - PLOTTING CUMULATIVE INCIDENCE OVER TIME...
INFO  - ASSESSING THE PROBABILITY OF SURVIVAL BEYOND A CERTAIN TIME (X-TIME SURVIVAL)...
INFO  - CALCULATING THE MEDIAN SURVIVAL TIME...
INFO  - BUILDING A COX PROPORTIONAL HAZARDS MODEL...
INFO  - ASSESSING THE HAZARD RATIO...
INFO  - ASSESSING THE FIT OF THE COX PROPORTIONAL HAZARD MODEL
INFO  - CALCULATING THE RMST AND RMTL...
INFO  - CREATING A TABLE WITH THE RMST AND RMTL...
INFO  - CALCULATING THE AVERAGE TREATMENT EFFECT BASED ON THE RMST AND RMTL...
INFO  - PLOTTING THE PROBABILITY OF SURVIVAL OVER TIME BY VACCINATION SCHEDULE...
INFO  - PLOTTING CUMULATIVE INCIDENCE OVER TIME BY VACCINATION SCHEDULE...
INFO  - BUILDING A COX PROPORTIONAL HAZARDS MODEL STRATIFIED BY VACCINATION SCHEDULE...
INFO  - ASSESSING THE HAZARD RATIO BY VACCINATION SCHEDULE...
INFO  - ASSESSING THE FIT OF THE COX PROPORTIONAL HAZARD MODEL STRATIFIED BY VACCINATION SCHEDULE
INFO  - CALCULATING THE RMST AND RMTL BY VACCINATION SCHEDULE...
INFO  - CREATING A TABLE WITH THE RMST AND RMTL BY VACCINATION SCHEDULE...
INFO  - CALCULATING THE AVERAGE TREATMENT EFFECT BASED ON THE RMST AND RMTL...
INFO  - PLOTTING THE PROBABILITY OF SURVIVAL OVER TIME BY RESIDENCE AREA...
INFO  - PLOTTING CUMULATIVE INCIDENCE OVER TIME BY RESIDENCE AREA...
INFO  - BUILDING A COX PROPORTIONAL HAZARDS MODEL STRATIFIED BY RESIDENCE AREA...
INFO  - ASSESSING THE HAZARD RATIO BY RESIDENCE AREA...
INFO  - ASSESSING THE FIT OF THE COX PROPORTIONAL HAZARD MODEL STRATIFIED BY RESIDENCE AREA
INFO  - CALCULATING THE RMST AND RMTL BY RESIDENCE AREA...
INFO  - CREATING A TABLE WITH THE RMST AND RMTL BY RESIDENCE AREA...
INFO  - CALCULATING THE AVERAGE TREATMENT EFFECT BASED ON THE RMST AND RMTL...
INFO  - SAVING RESULTS FOR META-ANALYSIS...
     
INFO  [2023-10-15 18:36:53] 
========================================================================================
Runtime
========================================================================================
  
INFO  - Overall runtime: 9.93 mins
INFO  - Runtime 0_global.R: 29.14 secs
INFO  - Runtime 1_DQA.QMD: 42.25 secs
INFO  - Runtime 2_validation.QMD: 19.83 secs
INFO  - Runtime 3_imputation.QMD: 1.04 mins
INFO  - Runtime 4_matching.QMD: 5.94 mins
INFO  - Runtime 5_descriptives.QMD: 33.73 secs
INFO  - Runtime 6_survival-analysis.QMD: 52.27 secs
