R: Extraction and Management of Clinical Practice Research Datalink Data

# Extraction and Management of Clinical Practice Research Datalink Data

## Documentation for package ‘rcprd’ version 0.0.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

add_to_database | Adds a single .txt file to an SQLite database on the hard disk.
combine_query | Combine a database query with a cohort.
combine_query.aurum | Combine a CPRD aurum database query with a cohort.
combine_query_boolean | Combine a database query with a cohort returning a 0/1 vector depending on whether each individual has a recorded code of interest.
combine_query_boolean.aurum | Combine a CPRD aurum database query with a cohort returning a 0/1 vector depending on whether each individual has a recorded code of interest.
connect_database | Open connection to SQLite database
cprd_extract | Adds all the .txt files in a directory, with certain file names, to an SQLite database on the hard disk.
create_directory_system | Create the appropriate directory system to be able to run functions without specifying hard filepaths
db_query | Query an RSQLite database.
delete_directory_system | Deletes directory system created by 'delete_directory_system'
extract_bmi | Extract most recent BMI score relative to an index date.
extract_cholhdl_ratio | Extract most recent total cholesterol/high-density lipoprotein ratio score relative to an index date.
extract_cohort | Create cohort from patient files
extract_diabetes | Extract diabetes status prior to an index date.
extract_ho | Extract a 'history of' type variable
extract_practices | Combine practice files
extract_smoking | Extract smoking status prior to index date.
extract_test_data | Extract test data.
extract_test_data_var | Extract standard deviation of all test data values over a specified time period relative to an index date.
extract_test_recent | Extract test data.
extract_time_until | Extract a 'time until' type variable
extract_txt_char | Read in txt file with all colClasses = "character"
extract_txt_cons | Read in raw .txt consultation file
extract_txt_death | Read in raw ONS death data file
extract_txt_drug | Read in raw .txt drugissue file
extract_txt_hes_primary | Read in raw HES primary diagnoses file
extract_txt_linkage | Read in linkage eligibility file
extract_txt_obs | Read in raw .txt observation file
extract_txt_pat | Read in raw .txt patient file
extract_txt_prac | Read in raw .txt practice file
extract_txt_prob | Read in raw .txt problem file
extract_txt_ref | Read in raw .txt referral file
implement_output | Internal function to implement saving extracted variable to disk or returning into R workspace.