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Generate simulated lab data

dummy_lab_cbc_electrolyte.Rd

This function creates a synthetic dataset with a subset of lab tests that are contained in the GEMINI "lab" table, as seen in GEMINI Data Repository Dictionary. The function currently focuses on simulating two lab tests: hemoglobin and sodium, as they are often used to identify routine blood work tests of complete blood count and electrolytes. This function will return: collection date time, information about the test type, test code, and test result value. It is a long format data table.

Usage

dummy_lab_cbc_electrolyte(
  nid = 1000,
  n_hospitals = 10,
  time_period = c(2015, 2023),
  cohort = NULL,
  seed = NULL
)

Arguments

nid

(integer) Number of unique encounter IDs to simulate. In this data table, each ID occurs once. It is ignored if cohort is provided.

n_hospitals

(integer) Number of hospitals in simulated dataset. It is ignored if cohort is provided

time_period

(numeric): Date range of data, by years or specific dates in either format: ("yyyy-mm-dd", "yyyy-mm-dd") or (yyyy, yyyy). It is ignored if cohort is provided.

cohort

(data.frame or data.table)
Optional, a data frame or data table with columns:

  • genc_id (integer): Mock encounter ID numbers

  • hospital_num (integer): Mock hospital ID numbers

  • admission_date_time (character): Date and time of IP admission in YYYY-MM-DD HH:MM format

  • discharge_date_time (character): Date and time of IP discharge in YYYY-MM-DD HH:MM format. When cohort is not NULL, nid, n_hospitals, and time_period are ignored.

seed

(integer) Optional, a number for setting the seed to get reproducible results.

Value

(data.table)
A data.table object similar to the "lab" table that contains the following fields:

  • genc_id (integer): Mock encounter ID; integers starting from 1 or as seen in cohort

  • hospital_num (integer): Mock hospital ID; integers starting from 1 or as seen in cohort

  • test_type_mapped_omop (character): Test name and code mapped by GEMINI; currently two tests are available: 3000963 (hemoglobin) and 3019550 (sodium)

  • test_name_raw (character): Test name as reported by hospital

  • test_code_raw (character): Test code as reported by hospital

  • result_value (character): Test results

  • collection_date_time (character): Date and time when the sample was collected

Examples

dummy_lab_cbc_electrolyte(nid = 10, n_hospitals = 1, seed = 1)
#>      genc_id hospital_num collection_date_time test_type_mapped_omop
#>        <int>        <int>               <char>                 <num>
#>   1:       1            1     2016-11-06 09:22               3000963
#>   2:       1            1     2016-11-08 08:07               3019550
#>   3:       1            1     2016-11-08 10:25               3000963
#>   4:       1            1     2016-11-06 06:28               3019550
#>   5:       1            1     2016-11-07 09:05               3019550
#>  ---                                                                
#> 149:      10            1     2021-12-29 05:36               3000963
#> 150:      10            1     2021-12-29 11:06               3019550
#> 151:      10            1     2021-12-29 09:58               3000963
#> 152:      10            1     2021-12-29 03:43               3019550
#> 153:      10            1     2021-12-28 08:33               3000963
#>      test_name_raw test_code_raw result_value
#>             <char>        <char>       <char>
#>   1:           CBC          <NA>           84
#>   2:        SODIUM          <NA>          139
#>   3:    HEMOGLOBIN          <NA>           81
#>   4:        SODIUM          <NA>          135
#>   5:        SODIUM          <NA>          138
#>  ---                                         
#> 149:    HEMOGLOBIN           HGB          109
#> 150:        SODIUM          <NA>          135
#> 151:    HEMOGLOBIN    Hemoglobin          139
#> 152:        SODIUM                        140
#> 153:    Hemoglobin          <NA>           89
dummy_lab_cbc_electrolyte(cohort = dummy_admdad())
#>        genc_id hospital_num collection_date_time test_type_mapped_omop
#>          <int>        <int>               <char>                 <num>
#>     1:       1            9     2018-10-13 18:33               3019550
#>     2:       1            9     2018-10-07 10:14               3019550
#>     3:       1            9     2018-10-10 07:24               3000963
#>     4:       1            9     2018-10-31 19:18               3019550
#>     5:       1            9     2018-10-21 05:35               3000963
#>    ---                                                                
#> 15896:    1000            1     2020-04-27 07:40               3000963
#> 15897:    1000            1     2020-04-27 06:27               3000963
#> 15898:    1000            1     2020-04-26 11:06               3019550
#> 15899:    1000            1     2020-04-29 03:27               3000963
#> 15900:    1000            1     2020-04-25 11:50               3000963
#>              test_name_raw test_code_raw result_value
#>                     <char>        <char>       <char>
#>     1:              SODIUM                        133
#>     2: Sodium,Serum,Plasma                        131
#>     3:          HEMOGLOBIN           HGB           97
#>     4:              SODIUM                        139
#>     5:          HEMOGLOBIN        100.06          125
#>    ---                                               
#> 15896:          HEMOGLOBIN            Hb           70
#> 15897:          Hemoglobin          <NA>          130
#> 15898:              SODIUM          NAPL          145
#> 15899:          HEMOGLOBIN          <NA>           76
#> 15900:          HEMOGLOBIN           HGB          122