Extraction and Management of Clinical Practice Research Datalink Data

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Documentation for package ‘rcprd’ version 0.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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_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_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.