- fixed all warnings from tidyverse by changing data processing to
dtplyrback end. - improved speed and memory usage for standardization step for prof claims (read claim data once for two dataset process)
- changed some loops to
furrrmap; multi-session processing - moved out build-in constant variable selections to user input map flags (std fac_clm.r, prof_clm.r)
Folder/data files structure changes
1. Standardization
- rerun sample sections from full data, because some years have no bene data. Code was not change, the data needed updates.
- Edited import mapping to include a new fac_clm variable SS_LS_SNF_IND_CD
- Created inpatient only MedPAR facility claims. Saved inpatient Medpar claims under
fac_clm_hospfolder. These were used for readmission and re-operation redefinition - Changed standardization steps membership, professional, facility claim and professional claims to be processed and saved by year.
- added a profiling document for performance comparison before and after code changes
2. Analytic file functions
- procedure_selection: process and save by year
- bene_info: process and save by year; add option to not filter patient age
- fac_dx: process and save by year; used fac_clm and fac_clm_code data folders; used current year and next year of facility claims data to make sure to have follow up like 30 days death
- fac_dx_elix: make empty icd9 and icd10 tables if some years don't have both of them. Fix Null error. Remove row ICD diagnosis code from analytic file
- ses_info: change zip code to be character to fix zip code that start with 0
- emergent_merpar_claim_ids_all_year: a newly added function to get emergent admission claim IDs; This is used for readmission and reoperation redefinition
- reoperation: use medpar claims path to only inpatient claims; emergent claims (unplanned procedures)
- readmission: use medpar claims path to only inpatient claims; emergent readmission
- complication_flags: process by year; use current year and the next year facility claim codes to ensure 30 days follow up
- multi_surgeon_proc_assit_flags: add surgeon roles including two surgeons and surgical team
- save_file and read_fiile: newly added functions that makes read and save files by year easier
3. Analytic file
- Create primary surgeon only claim cases; added if had assistant surgeon with the primary surgeon. We exclude any claims filed by assistant surgeon or surgical team.