load_enc {parseRPDR}

Loads encounter information into R.

Description

Loads encounter-level detail information into the R environment, both Enc and Exc files.

Usage

load_enc(
  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 Enc.txt or Exc.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 FALSE, as it is not advised to parse these for all data sources as it takes considerable time.

Value

data table, with encounter information.

ID_MERGE

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

ID_enc_EMPI

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

ID_enc_PMRN

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

ID_enc_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().

enc_numb

string, Unique identifier of the record/visit. This values includes the source system, hospital, and a unique identifier within the source system, corresponds to Encounter_number in RPDR.

time_enc_admit

POSIXct, Date when the patient was admitted or entered the facility, corresponds to Admit_Date in RPDR. Converted to POSIXct format.

time_enc_disch

POSIXct, Date when the patient was discharged or left the facility, corresponds to Discharge_Date in RPDR. Converted to POSIXct format.

enc_status

string, Billing account-related notes about the encounter. This will not be populated for all encounters, corresponds to Encounter_Status in RPDR.

enc_hosp

string, Facility where the encounter occurred, corresponds to Hospital in RPDR.

enc_inpatient

string, Classifies the type of encounter as either Inpatient or Outpatient. ED visits are currently classified under the 'Outpatient' label, corresponds to Inpatient_or_Outpatient in RPDR.

enc_service

string, Hospital service line assigned to the encounter, corresponds to Service_Line in RPDR.

enc_attending

string, The attending provider associated with the encounter. For Epic professional billing, this is the billing provider, corresponds to Attending_MD in RPDR.

enc_length

numeric, Length of stay for the encounter, corresponds to LOS_days in RPDR.

enc_clinic

string, Specific department/location where the encounter occured, corresponds to Clinic_Name in RPDR.

enc_admit_src

string, Location where the patient was admitted when entering the hospital/clinic, corresponds to Admit_Source in RPDR.

enc_pat_type

string, Provides information regarding the specific patient classifications and status of the patient visit. This field is only populated for McLean Hospital encounters, corresponds to Patient_Type in RPDR.

enc_ref_disp

string, Location where the patient has been directed for treatment or follow-up by a staff member. This field is only populated for McLean Hospital encounters, corresponds to Referrer_Discipline in RPDR.

enc_disch_disp

string, Patient's anticipated location or status following the encounter, corresponds to Discharge_Disposition in RPDR.

enc_pay

string, Payors responsible for the hospital account. Multiple payors (primary, secondary, etc.) may be listed, corresponds to Payor in RPDR.

enc_diag_admit

string, Initial working diagnosis documented by the admitting or attending physician, corresponds to Admitting_Diagnosis in RPDR.

enc_diag_princ

string, Condition established, after study, to be chiefly responsible for occasioning the admission of the patient to the hospital for care, corresponds to Principle_Diagnosis in RPDR.

enc_diag_1

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_1 in RPDR.

enc_diag_2

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_2 in RPDR.

enc_diag_3

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_3 in RPDR.

enc_diag_4

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_4 in RPDR.

enc_diag_5

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_5 in RPDR.

enc_diag_6

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_6 in RPDR.

enc_diag_7

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_7 in RPDR.

enc_diag_8

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_8 in RPDR.

enc_diag_9

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_9 in RPDR.

enc_diag_10

string, Additional diagnoses associated with this encounter or visit, corresponds to Diagnosis_10 in RPDR.

enc_diag_group

string, Diagnosis-Related Group for the encounter, in the following format: SYSTEM:CODE - Description, corresponds to DRG in RPDR.

Examples

## Not run: 
#Using defaults
d_enc <- load_enc(file = "test_Enc.txt")

#Use sequential processing
d_enc <- load_enc(file = "test_Enc.txt", nThread = 1)

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

## End(Not run)