Prepare Multi-State Data from an OMOP Cohort Table

Usage

prepareMultistateData(
  cohort,
  trans,
  eventDate = "cohort_start_date",
  censorDate = NULL,
  stateHierarchy = character(),
  stateStep = 0.01
)

Arguments

cohort: A cohort_table object containing one cohort for each state in the multi-state model. Cohort names must match the state names in trans.
trans: Transition matrix describing the states and transitions in the multi-state model. If S is the number of states in the multi-state model, trans should be an S x S matrix, with (i,j)-element a positive integer if a transition from i to j is possible in the multi-state model, NA otherwise. In particular, all diagonal elements should be NA. The integers indicating the possible transitions in the multi-state model should be sequentially numbered, 1,...,K, with K the number of transitions.
eventDate: Name of the date column in cohort that identifies when an individual enters a state.
censorDate: Name of the date column in cohort that identifies the end of follow-up, inclusive. If NULL, the end of each individual's observation period is used.
stateHierarchy: Character vector of state names in the order used to resolve states that occur on the same date, with earlier entries occurring first. An empty character vector applies no hierarchy.
stateStep: Numeric increment used to separate states that occur on the same date according to stateHierarchy.

Value

An msdata object to be used by the mstate package.