Loop mLAPS

A wrapper around the mlaps() function which breaks down the calculation of mLAPS on a large number of encounters by hospital-year. This avoids memory issues that can be caused by loading large chunks of the lab table.

Usage

loop_mlaps(
  db,
  cohort = NULL,
  hours_after_admission = 0,
  component_wise = FALSE
)

Arguments

db

(DBIConnection)
RPostgres DB connection.

cohort

(data.frame or data.table)
Containing a column of genc_ids to restrict the calculation to.

hours_after_admission

(numeric)
Consider lab tests collected up to hours_after_admission hours after inpatient admission in the calculation. Default hours_after_admission is set to 0, where only lab tests collected at Emergency Department (before inpatient admission) are considered in mLAPS calculation. Since not all encounters are admitted through Emergency Department, depending on research question, it can be relevant to consider lab tests collected in early inpatient admission. Typically, hours_after_admission can be set to 24 to consider any lab tests collected at Emergency Department and 24 hours after inpatient admission.

component_wise

(logical)
Does not aggregate the score and instead outputs for each LAPS component (test) its contribution to the overall score.

Value

(data.frame)
If output_laps_components == TRUE: genc_id (numeric),
test_type_mapped_omop (character),
mlaps (numeric) max score for this test.

If output_laps_components == FALSE: genc_id (numeric),
mlaps (numeric) sum of max scores for each relevant test for this encounter.

References

When the function is used, please cite the following: https://doi.org/10.1097/MLR.0b013e3181589bb6 https://doi.org/10.1007/s11606-023-08245-w https://doi.org/10.1101/2023.01.06.23284273

Examples

if (FALSE) { # \dontrun{
drv <- DBI::dbDriver("PostgreSQL")
db <- DBI::dbConnect(
  drv,
  dbname = "db_name",
  host = "domain_name.ca",
  port = 1234,
  user = getPass::getPass("Enter Username"),
  password = getPass::getPass("Enter Password")
  )

cohort <- DBI::dbGetQuery(db, "SELECT genc_id FROM public.admdad LIMIT 200;")

laps <- loop_laps(db, cohort = cohort)
} # }