load_ptd {parseRPDR}

Loads patient data information into R.

Description

Loads patient data information into the R environment.

Usage

load_ptd(
  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 Ptd.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 patient data information information.

ID_MERGE

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

ID_ptd_EMPI

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

ID_ptd_PMRN

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

ID_ptd_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_ptd_start

POSIXct, Date item was initiated in the record, corresponds to Start_Date in RPDR. Converted to POSIXct format.

time_ptd_end

POSIXct, Date item was finalized in the record, corresponds to End_Date in RPDR. Converted to POSIXct format.

ptd_desc

string, Name of the item being reported, corresponds to Description in RPDR.

ptd_result

string, Result of the item being reported, corresponds to Result in RPDR.

ptd_type

string, Describes the type of data being reported, corresponds to Patient_Data_Type in RPDR.

ptd_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_ptd <- load_ptd(file = "test_Phy.txt")

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

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

## End(Not run)