createStudyPopulationSettings: create the study population settings

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

Description

create the study population settings

Usage

createStudyPopulationSettings(
  binary = T,
  includeAllOutcomes = T,
  firstExposureOnly = FALSE,
  washoutPeriod = 0,
  removeSubjectsWithPriorOutcome = TRUE,
  priorOutcomeLookback = 99999,
  requireTimeAtRisk = T,
  minTimeAtRisk = 364,
  riskWindowStart = 1,
  startAnchor = "cohort start",
  addExposureDaysToStart,
  riskWindowEnd = 365,
  endAnchor = "cohort start",
  addExposureDaysToEnd,
  verbosity = "INFO"
)

Arguments

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 index date (+ days of exposure if the addExposureDaysToStart parameter is specified).
startAnchor	The anchor point for the start of the risk window. Can be "cohort start" or "cohort end".
addExposureDaysToStart	DEPRECATED: Add the length of exposure the start of the risk window? Use startAnchor instead.
riskWindowEnd	The end of the risk window (in days) relative to the index data (+ days of exposure if the addExposureDaysToEnd parameter is specified).
endAnchor	The anchor point for the end of the risk window. Can be "cohort start" or "cohort end".
addExposureDaysToEnd	DEPRECATED: Add the length of exposure the risk window? Use endAnchor instead.
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 #'

Details

Takes as input the inputs to create study population

Value

A list containing all the settings required for creating the study population

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