load_rfv {parseRPDR}

Loads reason for visit data into R.

Description

Loads reason for visit information into the R environment.

Usage

load_rfv(
  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 Rfv.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 reason for visit information.

ID_MERGE

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

ID_rfv_EMPI

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

ID_rfv_PMRN

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

ID_rfv_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().

time_rfv_start

POSIXct, Start date of the encounter, corresponds to Start_Date in RPDR. Converted to POSIXct format.

time_rfv_end

POSIXct, End date of the encounter, corresponds to End_Date in RPDR. Converted to POSIXct format.

rfv_provider

string, Primary provider for the encounter, corresponds to Provider in RPDR.

rfv_hosp

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

rfv_clinic

string, Specific department/location where the patient encounter took place, corresponds to Clinic in RPDR.

rfv_chief_complaint

string, Description of the chief complaint/reason for visit, corresponds to Chief_Complaint in RPDR.

rfv_concept_id

string, Epic identifier for the chief complaint/reason for visit, corresponds to Concept_id in RPDR.

rfv_comment

string, Free-text comments regarding the chief complain/reason for visit, corresponds to Comments in RPDR.

rfv_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.

Examples

## Not run: 
#Using defaults
d_rfv <- load_rfv(file = "test_Rfv.txt")

#Use sequential processing
d_rfv <- load_rfv(file = "test_Rfv.txt", nThread = 1)

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

## End(Not run)