Create a study population

createStudyPopulation(
  plpData,
  population = NULL,
  outcomeId,
  binary = T,
  includeAllOutcomes = T,
  firstExposureOnly = FALSE,
  washoutPeriod = 0,
  removeSubjectsWithPriorOutcome = TRUE,
  priorOutcomeLookback = 99999,
  requireTimeAtRisk = F,
  minTimeAtRisk = 365,
  riskWindowStart = 0,
  startAnchor = "cohort start",
  riskWindowEnd = 365,
  endAnchor = "cohort start",
  verbosity = "INFO",
  addExposureDaysToStart,
  addExposureDaysToEnd,
  ...
)

Arguments

plpData

An object of type plpData as generated using getplpData.

population

If specified, this population will be used as the starting point instead of the cohorts in the plpData object.

outcomeId

The ID of the outcome.

binary

Forces the outcomeCount to be 0 or 1 (use for binary prediction problems)

includeAllOutcomes

(binary) indicating whether to include people with outcomes who are not observed for the whole at risk period

firstExposureOnly

Should only the first exposure per subject be included? Note that this is typically done in the createStudyPopulation function,

washoutPeriod

The mininum required continuous observation time prior to index date for a person to be included in the cohort.

removeSubjectsWithPriorOutcome

Remove subjects that have the outcome prior to the risk window start?

priorOutcomeLookback

How many days should we look back when identifying prior outcomes?

requireTimeAtRisk

Should subject without time at risk be removed?

minTimeAtRisk

The minimum number of days at risk required to be included

riskWindowStart

The start of the risk window (in days) relative to the startAnchor.

startAnchor

The anchor point for the start of the risk window. Can be "cohort start" or "cohort end".

riskWindowEnd

The end of the risk window (in days) relative to the endAnchor parameter

endAnchor

The anchor point for the end of the risk window. Can be "cohort start" or "cohort end".

verbosity

Sets the level of the verbosity. If the log level is at or higher in priority than the logger threshold, a message will print. The levels are:

  • DEBUGHighest verbosity showing all debug statements

  • TRACEShowing information about start and end of steps

  • INFOShow informative information (Default)

  • WARNShow warning messages

  • ERRORShow error messages

  • FATALBe silent except for fatal errors

addExposureDaysToStart

DEPRECATED: Add the length of exposure the start of the risk window? Use startAnchor instead.

addExposureDaysToEnd

DEPRECATED: Add the length of exposure the risk window? Use endAnchor instead.

...

Other inputs

Value

A data frame specifying the study population. This data frame will have the following columns:

rowId

A unique identifier for an exposure

subjectId

The person ID of the subject

cohortStartdate

The index date

outcomeCount

The number of outcomes observed during the risk window

timeAtRisk

The number of days in the risk window

survivalTime

The number of days until either the outcome or the end of the risk window

Details

Create a study population by enforcing certain inclusion and exclusion criteria, defining a risk window, and determining which outcomes fall inside the risk window.