Skip to contents

SEM Laboratory Test Results Dataset (Within 24 Hours of Arrival)

melior_sem_lab_tests_24h.Rd

This dataset contains information about laboratory test results obtained within 24 hours of patient arrival for patients in the SEM cohort from the Melior journal system.

Usage

melior_sem_lab_tests_24h()

Format

A data frame with 10,961,795 observations and 12 variables:

contact_id

Character. Unique identifier for each healthcare contact/encounter, serves as a foreign key to link with other datasets. Original field name: KontaktId

patient_id

Integer. Patient pseudonym identifier, serves as a foreign key to link with other patient-level data. Original field name: Alias

term_name

Character. Term name for the type of laboratory analysis. Contains a single value: "Kemlab analys" for 100% of records. Original field name: Term_Namn

lab_test_name

Character. Abbreviated name of the laboratory test. 732 unique values across the dataset. Most common tests: P-Kalium (5.2%), P-Kreatini (4.8%), B-Hemoglob (4.8%), P-Natrium (4.8%), P-Glukos (4.2%). Original field name: Labanalys_Namn

lab_test_description

Character. Full description of the laboratory test. 822 unique values across the dataset. Most common descriptions: P-Kalium (5.2%), P-Kreatinin (enz) (4.8%), B-Hemoglobin (Hb) (4.8%), P-Natrium (4.8%), P-Glukos (4.2%). Original field name: Labanalys_Beskrivning

test_result_value

Character. Value of the laboratory test result. 14,022 unique values across the dataset. Stored as character since it may contain non-numeric values such as "positive" or "<3". Original field name: Analyssvar_Varde

test_result_unit

Character. Unit of measurement for the test result. 80 unique values across the dataset. 1,189,333 NA values (10.8% of records), primarily for qualitative tests. Most common units: mmol/L (38.7%), % (8.8%), kPa (7.8%), µmol/L (6.3%), µkat/L (5.5%). Original field name: Analyssvar_Enhet

test_result_reference_min

Numeric. Minimum normal reference value for the test. 3,451,693 NA values (31.5% of records). Range: -3 to 1000, with median of 4. Original field name: Analyssvar_ReferensvardeMin

test_result_reference_max

Numeric. Maximum normal reference value for the test. 2,172,705 NA values (19.8% of records). Range: 0 to 3000, with median of 6.3. Original field name: Analyssvar_ReferensvardeMax

test_sampling_date

POSIXct. Date and time when the sample was taken. Date range: 2017-01-01 00:20:00 to 2018-12-31 22:10:00. Distribution by year: 2017 (50.2%), 2018 (49.8%). Original field name: Analyssvar_ProvtagningDatum

sample_type

Character. Type of sample used for the test (e.g., "Blood", "Urine", "Plasma"). Derived from lab_test_name, including handling of "Avd" prefix cases.

pna_test

Logical. Indicates whether the test was performed at point-of-care (PNA) rather than at the central lab. Identified by "Avd" prefix in lab_test_name.

Source

Melior

Details

This file was extracted from the Melior electronic health record system. The original filename indicates it contains information about laboratory analyses (Labanalyser) performed within 24 hours from patient arrival (Inom24TimmarFrånAnkomst). The dataset provides comprehensive laboratory test results for the SEM cohort patients, with nearly 11 million observations covering a wide range of clinical laboratory tests.

The data spans exactly two years (2017-01-01 to 2018-12-31) with an almost equal distribution between both years. This suggests comprehensive and consistent data collection throughout the study period.

Note

  • The test_result_value is stored as character since it may contain non-numeric values such as "positive" or "<3"

  • test_result_unit may contain NA values for qualitative tests that don't have units (10.8% of records)

  • test_result_reference_min and test_result_reference_max may contain NA values when reference ranges are not applicable or not established (31.5% and 19.8% of records, respectively)

  • Several original columns have been removed due to unclear meaning or constant values:

    • lab_test_type (Labanalys_AnalysTyp): Almost entirely "A" with only 3 "B" values for test "CYLHYAL"

    • lab_test_order_type (Labanalys_BestallningTyp): Constant value of 7 for all records

    • test_result_attribute (Analyssvar_Attribut): Values 0 (73.1%), 3 (26.9%), with trace amounts of 1 and 2

    • test_result_reference_type (Analyssvar_Referensvarde): Values 3 (92.1%), 0 (7.9%), with trace amounts of 1 and 2

  • Two derived columns have been added to facilitate analysis:

    • sample_type: Identifies the biological sample type or test category based on the lab_test_name patterns

    • pna_test: Flags whether the test was performed at point-of-care (identified by "Avd" prefix)

  • lab_test_description provides a more complete version of lab_test_name, often with the full name of the test rather than the abbreviated form

  • Common sample type prefixes include:

    • P- (Plasma), B- (Blood), S- (Serum), U- (Urine), Csv- (Cerebrospinal fluid)

    • aB- (Arterial blood), vB- (Venous blood), kB- (Capillary blood)

    • Ledv- (Joint fluid), F- (Feces), tU- (Timed urine collection)

    • These can also appear with an "Avd" prefix for point-of-care tests

  • The most common laboratory tests reflect typical practice in acute care settings: electrolytes (Potassium, Sodium), renal function (Creatinine), blood counts (Hemoglobin), and metabolic parameters (Glucose)

  • For proper analysis, test_result_value should be processed according to its specific test type and converted to numeric values when applicable

Examples