load_con {parseRPDR}

Loads contact information into R.

Description

Loads patient contact, insurance, and PCP information into the R environment.

Usage

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

Arguments

file

string, full file path to Con.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.

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 TURE only for Con.txt, as it is not advised to parse these for all data sources as it takes considerable time.

Value

data table, with contact information data.

ID_MERGE

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

ID_con_EMPI

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

ID_con_PMRN

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

ID_con_loc

string, if mrn_type == TRUE, then the data in MRN_Type and MRN are parsed into IDs corresponding to locations (loc). Data is formatted using pretty_mrn().

ID_con_loc_list

string, if prevalence of IDs in Patient_ID_List > perc, then they are included in the output. Data is formatted using pretty_mrn().

name_last

string, Patient's last name, corresponds to Last_Name in RPDR.

name_first

string, Patient's first name, corresponds to First_Name in RPDR.

name_middle

string, Patient's middle name or initial, corresponds to Middle_Name in RPDR.

name_previous

string, Any alternate names on record for this patient, corresponds to Previous_Name in RPDR.

SSN

string, Social Security Number, corresponds to SSN in RPDR.

VIP

character, Special patient statuses as defined by the EMPI group, corresponds to VIP in RPDR.

address1

string, Patient's current address, corresponds to address1 in RPDR.

address2

string, Additional address information, corresponds to address2 in RPDR.

city

string, City of residence, corresponds to City in RPDR.

state

string, State of residence, corresponds to State in RPDR.

country_con

string, Country of residence from con datasource, corresponds to Country in RPDR.

zip_con

numeric, Mailing zip code of primary residence from con datasource, corresponds to Zip in RPDR. Formatted to 5 character zip codes using pretty_numbers().

direct_contact_consent

boolean, Indicates whether the patient has given permission to contact them directly through the RODY program, corresponds to Direct_Contact_Consent in RPDR. Legacy variable.

research_invitations

boolean, Indicates if a patient can be invited to participate in research, corresponds to Research_Invitations in RPDR.

phone_home

number, Patient's home phone number, corresponds to Home_Phone in RPDR. Formatted to 10 digit phone numbers using pretty_numbers().

phone_day

number, Phone number where the patient can be reached during the day, corresponds to Day_Phone in RPDR. Formatted to 10 digit phone numbers using pretty_numbers().

insurance1

string, Patient's primary health insurance carrier and subscriber ID information, corresponds to Insurance_1 in RPDR.

insurance2

string, Patient's secondary health insurance carrier and subscriber ID information, if any, corresponds to Insurance_2 in RPDR.

insurance3

string, Patient's tertiary health insurance carrier and subscriber ID information, if any, corresponds to Insurance_3 in RPDR.

primary_care_physician

string, Comma-delimited list of all primary care providers on record for this patient per institution, along with contact information (if available), corresponds to Primary_Care_Physician in RPDR.

primary_care_physician_resident

string, Comma-delimited list of any Resident primary care providers on record for this patient per institution, along with contact information (if available), corresponds to Resident _Primary_Care_Physician in RPDR.

Examples

## Not run: 
#Using defaults
d_con <- load_con(file = "test_Con.txt")

#Use sequential processing
d_con <- load_con(file = "test_Con.txt", nThread = 1)

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

## End(Not run)