load_med {parseRPDR}

Loads medication order detail into R.

Description

Loads medication order detail information into the R environment, both Med and Mee files.

Usage

load_med(
  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 Med.txt or Mee.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 medication order information.

ID_MERGE

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

ID_med_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_med_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_med_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().

med_enc_numb

string, Unique identifier of the record/visit, displayed in the following format: Source System - Institution Number, corresponds to Encounter_number in RPDR.

time_med

POSIXct, Completion status of the requested test/transfusion. Converted to POSIXct format, corresponds to Medication_Date in RPDR.

time_med_detail

string, To clarify when patients may have stopped taking a medication, this column provides the statuses of 'Listed' or 'Removed'. This is provided on pre-Epic (LMR) medication dates (1997-2017). The 'Listed' value denotes that a medication was on the patient's medication list on the date indicated. The 'Removed' value denotes that a medication was removed from a patient's medication list on the date indicated. Corresponds to Medication_Date_Detail in RPDR.

med

string, Name of the medication. This may be appended with the source system in the case of OnCall and LMR medications, corresponds to Medication in RPDR.

med_code

string, Medication code associated with the "Code_type" value, corresponds to Code in RPDR.

med_code_type

string, Standardized classification system or custom source value used to identify the medication, corresponds to Code_Type in RPDR.

med_quant

string, Number of units of the medication ordered, corresponds to Quantity in RPDR.

med_prov

string, Ordering provider for the medication, corresponds to Provider in RPDR.

med_clinic

string, Specific department/location where the medication was ordered or administered, corresponds to Clinic in RPDR.

med_hosp

string, Facility where the medication was ordered or administered, corresponds to Hospital in RPDR.

med_inpatient

string, Identifies whether the medication was ordered with an Inpatient or Outpatient indication, corresponds to Inpatient_Outpatient in RPDR.

med_add_info

string, Additional administration information about the medication, corresponds to Additional_Info in RPDR.

Examples

## Not run: 
#Using defaults
d_med <- load_med(file = "test_Med.txt")

#Use sequential processing
d_med <- load_med(file = "test_Med.txt", nThread = 1)

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

## End(Not run)