load_trn {parseRPDR}

Loads transfusion results into R.

Description

Loads transfusion results into the R environment.

Usage

load_trn(
  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 Trn.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 transfusion information.

ID_MERGE

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

ID_trn_EMPI

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

ID_trn_PMRN

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

ID_trn_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_trn

POSIXct, Date when the transfusion was administered or test was performed, corresponds to Transaction_Date_Time in RPDR. Converted to POSIXct format.

trn_descript

string, The type of procedure or product administered, corresponds to Test_Description in RPDR.

trn_result

string, Results of the test or transaction/lot number of transfusion, corresponds to Results in RPDR.

trn_result_abn

string, Denotes an abnormal finding or value, corresponds to Abnormal_Flag in RPDR.

trn_comment

string, Free-text comments about the status of the test/transfusion, corresponds to Comments in RPDR.

trn_status

string, Completion status of the requested test/transfusion, corresponds to Status_Flag in RPDR.

trn_accession

string, Identifier assigned to the test/transfusion for tracking purposes by the blood bank, corresponds to Accession in RPDR.

Examples

## Not run: 
#Using defaults
d_trn <- load_trn(file = "test_Trn.txt")

#Use sequential processing
d_trn <- load_trn(file = "test_Trn.txt", nThread = 1)

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

## End(Not run)