createStudyPopulation: Create a study population

In hxia/plp-git-demo: Package for patient level prediction using data in the OMOP Common Data Model

Description

Create a study population

Usage

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 getDbplpData.
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

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.

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

hxia/plp-git-demo documentation built on March 19, 2021, 1:54 a.m.