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Scripts to update the MBDU databases


Author: Georgia O'Callaghan


Location of repository on the server: Database/Database_Scripts_Github/


Description of scripts:

  1. Master script needed to set up environmental variables & directories + to run other scripts from: Update_databases_master_script.R
  2. Scripts to merge patient trackers into a master patient list: IRTA_Merge_Code.R Other_functions/Schedule_script_functions.R
  3. Script to create clinical, behavioural and treatment databases using information from the master patient tracker, CTDB and SDQ: Database_code.R
  4. Script to create DAWBA database & generate lists for deleting old data from server: DAWBA_database_and_deletions.R
  5. Scripts to generate weekly numbers for clinical meeting: Reports/Research_meeting_numbers.Rmd Other_functions/Referrals_summary.R Other_functions/check_referrals.R
  6. Script to generate eval and screening summaries for clinical meeting: Reports/Clinician_sheet.Rmd
  7. Scripts to generate CBT reports: CBT_scripts/Produce_CBT_final_report.Rmd CBT_scripts/Produce_CBT_final_report_provider.Rmd CBT_scripts/Produce_CBT_progress_report.Rmd
  8. Scripts to generate inpatient summary: Reports/Inpatient_summary.Rmd Reports/Inpatient_end_of_treatment_graphs.R
  9. Script to generate clinician supervision summary: Reports/All_treatment_summary.Rmd
  10. Script to generate numbers for annual continuing review (CR) for IRB: Reports/Continuing_review.Rmd
  11. COVID19 related research database generation: Reports/crisis_dataset_description.Rmd Other_functions/Crisis_distribution.R
  12. Other: Other_functions/followup_counts.R

Manual:

All procedures for running these scripts are described in the latest version of the 'database_and_report_scripts_manual' contained in the repository on the server. This has not been uploaded to GitHub as it contains account login information for our online data collection platforms.


Created in RStudio: "R version 3.6.1 (2019-07-05)"


Required R libraries (aka packages): readxl writexl tidyr dplyr summarytools rmarkdown eeptools openxlsx data.table reshape2 stringr lubridate ggplot2 rlang purrr tidyverse knitr flextable shiny kableExtra chron ggpubr