Set-up cohort data for Sankey creation — setup

Combines censoring and absorbing variables to determine the min of their occurrence and labels for Sankeys. Converts filter variables if they are not factors.

setup_cohort(
  cohort,
  id_var,
  censor_vars,
  absorbing_vars,
  index_var,
  filt_vars,
  final_stage,
  weight
)

Arguments

cohort: Cohort data.
id_var: String. Variable name of the id/grouping variable.
censor_vars: Character vector. Variable names in cohort that indicate censoring date/day. If multiple, sankey_list_maker will use the minimum. If weight = FALSE the Sankey will use the names of the vector to label the states shown. If unnamed will group together under "Censored".
absorbing_vars: Named character vector. Variables in cohort that indicate date/day of states that members cannot transition out of. Names of the vector will be names of the states shown in the Sankey.
index_var: Date. Indicates cohort_file date or day variable name per subject when event ordering should begin.
filt_vars: All variables that are wanted for filtering.
final_stage: Last timepoint for the Sankeys
weight: Logical. Should Sankey transitions be weighted? Default is FALSE.

Value

tibble with information necessary for Sankey setup.