load_lab {parseRPDR}

Loads laboratory results into R.

Description

Loads laboratory results into the R environment, both Lab and Clb files.

Usage

load_lab(
  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 Lab.txt or Clb.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 laboratory exam information.

ID_MERGE

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

ID_lab_EMPI

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

ID_lab_PMRN

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

ID_lab_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_lab_result

POSIXct, Date when the specimen was collected, corresponds to Seq_Date_Time in RPDR. Converted to POSIXct format.

lab_group

string, Higher-level grouping concept used to consolidate similar tests across hospitals, corresponds to Group_ID in RPDR.

lab_loinc

string, Standardized LOINC code for the laboratory test, corresponds to Loinc_Code in RPDR.

lab_testID

string, Internal identifier for the test used by the source system, corresponds to Test_ID in RPDR.

lab_descript

string, Name of the lab test, corresponds to Test_Description in RPDR.

lab_result

string, Result value for the test, corresponds to Result in RPDR.

lab_result_txt

string, Additional information included with the result. This can include instructions for interpretation or comments from the laboratory, corresponds to Result_Text in RPDR.

lab_result_abn

string, Flag for identifying if values are outside of normal ranges or represent a significant deviation from previous values, corresponds to Abnormal_Flag in RPDR.

lab_result_unit

string, Units associated with the result value, corresponds to Reference_Unit in RPDR.

lab_result_range

string, Normal or therapeutic range for this value, corresponds to Reference_Range in RPDR.

lab_result_toxic

string, Reference range of values defined as being toxic to the patient, corresponds to Toxic_Range in RPDR.

lab_spec

string, Type of specimen collected to perform the test, corresponds to Specimen_Type in RPDR.

lab_spec_txt

string, Free-text information about the specimen, its collection or its integrity, corresponds to Specimen_Text in RPDR.

lab_correction

string, Free-text information about any changes made to the results, corresponds to Correction_Flag in RPDR.

lab_status

string, Flag which indicates whether the procedure is pending or complete, corresponds to Test_Status in RPDR.

lab_ord_pys

string, Name of the ordering physician, corresponds to Ordering_Doc in RPDR.

lab_accession

string, Internal tracking number assigned to the specimen for identification in the lab, corresponds to Accession in RPDR.

lab_source

string, Database source, either CDR (Clinical Data Repository) or RPDR (internal RPDR database), corresponds to Source in RPDR.

Examples

## Not run: 
#Using defaults
d_lab <- load_lab(file = "test_Lab.txt")

#Use sequential processing
d_lab <- load_lab(file = "test_Lab.txt", nThread = 1)

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

## End(Not run)