load_bib {parseRPDR}

Loads BiobankFile data into R.

Description

Loads Biobank file data into the R environment.

Usage

load_bib(
  file,
  merge_id = "EMPI",
  sep = ":",
  id_length = "standard",
  perc = 0.6,
  na = TRUE,
  identical = TRUE,
  nThread = parallel::detectCores() - 1,
  mrn_type = FALSE
)

Arguments

file

string, full file path to Bib.txt.

merge_id

string, column name to use to create ID_MERGE column used to merge different datasets. Defaults to EPIC_PMRN, as it is the preferred MRN in the RPDR system.

sep

string, divider between hospital ID and MRN. Defaults to :.

id_length

string, indicating whether to modify MRN length based-on required values id_length = standard, or to keep lengths as is id_length = asis. If id_length = standard then in case of MGH, BWH, MCL, EMPI and PMRN the length of the MRNs are corrected accordingly by adding zeros, or removing numeral from the beginning. In other cases the lengths are unchanged. Defaults to standard.

perc

numeric, a number between 0-1 indicating which parsed ID columns to keep. Data present in perc x 100% of patients are kept. Not used for loading mrn data.

na

boolean, whether to remove columns with only NA values. Defaults to TRUE.

identical

boolean, whether to remove columns with identical values. Defaults to TRUE.

nThread

integer, number of threads to use to load data.

mrn_type

boolean, should data in MRN_Type and MRN be parsed. Defaults to FALSE, as it is not advised to parse these for all data sources as it takes considerable time.

Value

data table, with BiobankFile data.

ID_MERGE

numeric, defined IDs by merge_id, used for merging later.

ID_bib_PMRN

string, Epic medical record number. This value is unique across Epic instances within the Partners network, corresponds to EPIC_PMRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_EMPI

string, Unique Partners-wide identifier assigned to the patient used to consolidate patient information, corresponds to Enterprise_Master_Patient_Index in RPDR. Data is formatted using pretty_mrn().

ID_bib_MGH

string, Unique Medical Record Number for Mass General Hospital, corresponds to MGH_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_BWH

string, Unique Medical Record Number for Brigham and Women's Hospital, corresponds to BWH_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_FH

string, Unique Medical Record Number for Faulkner Hospital, corresponds to FH_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_SRH

string, Unique Medical Record Number for Spaulding Rehabilitation Hospital, corresponds to SRH_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_NWH

string, Unique Medical Record Number for Newton-Wellesley Hospital, corresponds to NWH_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_NSMC

string, Unique Medical Record Number for North Shore Medical Center, corresponds to NSMC_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_MCL

string, Unique Medical Record Number for McLean Hospital, corresponds to MCL_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_MEE

string, Unique Medical Record Number for Mass Eye and Ear, corresponds to MEE_MRN in RPDR. Data is formatted using pretty_mrn().

ID_bib_DFC

string, Unique Medical Record Number for Dana Farber Cancer center, corresponds to DFC_MRN in RPDR. Data is formatted using pretty_mrn(). Legacy data.

ID_bib_WDH

string, Unique Medical Record Number for Wentworth-Douglass Hospital, corresponds to WDH_MRN in RPDR. Data is formatted using pretty_mrn(). Legacy data.

bib_subject_ID

string, Biobank unique patient identifier, corresponds to Subject_ID in RPDR. ID is not formatted.

bib_subject_ID

string, This will always default to Biobank, corresponds to Registry Name in RPDR.

Examples

## Not run: 
#Using defaults
d_bib <- load_bib(file = "test_Bib.txt")

#Use sequential processing
d_bib <- load_bib(file = "test_Bib.txt", nThread = 1)

#Use parallel processing and parse data in MRN_Type and MRN columns and keep all IDs
d_bib <- load_bib(file = "test_Bib.txt", nThread = 20, mrn_type = TRUE, perc = 1)

## End(Not run)