data_lab: Example of processed lab.txt output from RPDR using the load_lab() function.

Description

Result of a lab.txt output from RPDR loaded into a data table in R using load_lab().

**NOTE**: Due to potential issues with PHI and PPI, the example datasets can be downloaded from the Partners Gitlab repository under *parserpdr-sample-data*.

Usage

data_lab

Arguments

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. 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. Punctuation marks and white spaces are removed.
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. Punctuation marks and white spaces are removed.
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. Punctuation marks and white spaces are removed.
lab_result_unit: string, Units associated with the result value, corresponds to Reference_Unit in RPDR. Punctuation marks and white spaces are removed.
lab_result_range: string, Normal or therapeutic range for this value, corresponds to Reference_Range in RPDR. Punctuation marks and white spaces are removed.
lab_result_toxic: string, Reference range of values defined as being toxic to the patient, corresponds to Toxic_Range in RPDR. Punctuation marks and white spaces are removed.
lab_spec: string, Type of specimen collected to perform the test, corresponds to Specimen_Type in RPDR. Punctuation marks and white spaces are removed.
lab_spec_txt: string, Free-text information about the specimen, its collection or its integrity, corresponds to Specimen_Text in RPDR. Punctuation marks and white spaces are removed.
lab_correction: string, Free-text information about any changes made to the results, corresponds to Correction_Flag in RPDR. Punctuation marks and white spaces are removed.
lab_status: string, Flag which indicates whether the procedure is pending or complete, corresponds to Test_Status in RPDR. Punctuation marks and white spaces are removed.
lab_ord_pys: string, Name of the ordering physician, corresponds to Ordering_Doc in RPDR. Punctuation marks are removed.
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. Punctuation marks and white spaces are removed.

Format

data.table