load_phy {parseRPDR}

Loads helath history information into R.

Description

Loads vital signs, social history, immunizations, and various other health history details into the R environment.

Usage

load_phy(
  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 Phy.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 health history information.

ID_MERGE

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

ID_phy_EMPI

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

ID_phy_PMRN

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

ID_phy_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_phy

POSIXct, Date when the diagnosis was noted, corresponds to Date in RPDR. Converted to POSIXct format.

phy_name

string, Type of clinical value/observation recorded, corresponds to Concept_Name in RPDR.

phy_code

string, Source-specific identifier for the specific type of clinical observation, corresponds to Code in RPDR.

phy_code_type

string, Source system for the value, corresponds to Code_type in RPDR.

phy_result

string, Value associated with the clinical observation. Note: BMI results are calculated internally in the RPDR, corresponds to Results in RPDR.

phy_unit

string, Units associated with the clinical observation, corresponds to Units in RPDR.

phy_provider

string, Provider of record for the encounter where the observation was recorded, corresponds to Providers in RPDR.

phy_clinic

string, Specific department/location where the patient observation was recorded, corresponds to Clinic in RPDR.

phy_hosp

string, Facility where the observation was recorded, corresponds to Hospital in RPDR.

phy_inpatient

string, Classifies the type of encounter where the observation was entered, corresponds to Inpatient_Outpatient in RPDR.

phy_enc_num

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

Examples

## Not run: 
#Using defaults
d_phy <- load_phy(file = "test_Phy.txt")

#Use sequential processing
d_phy <- load_phy(file = "test_Phy.txt", nThread = 1)

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

## End(Not run)