Flexible Multi-State Survival Models — flexmultistate • ClinicoPath

Flexible parametric multi-state survival models for complex disease progression. Models transition hazards using splines and handles competing risks and intermediate states.

Usage

flexmultistate(
  data,
  time,
  status,
  start_state = NULL,
  predictors,
  model_type = "illness_death",
  hazard_distribution = "royston_parmar",
  spline_knots = 3,
  time_scale = "hazard",
  transition_specific = TRUE,
  shared_effects,
  time_varying_effects,
  prediction_times = "12, 24, 36, 60",
  transition_probabilities = TRUE,
  state_probabilities = TRUE,
  expected_sojourn = TRUE,
  plot_hazards = TRUE,
  plot_cumhaz = TRUE,
  plot_survival = TRUE,
  microsimulation = FALSE,
  n_simulation = 10000,
  confidence_intervals = TRUE
)

Arguments

data: The data as a data frame.
time: Time variable for transitions
status: State or transition status variable
start_state: Variable indicating starting state
predictors: Variables to include in transition models
model_type: Multi-state model configuration
hazard_distribution: Hazard function specification
spline_knots: Spline complexity parameter
time_scale: Transformation scale for splines
transition_specific: Fit separate models for each transition type
shared_effects: Predictors with constrained effects
time_varying_effects: Predictors with time-dependent coefficients
prediction_times: Time points for state occupancy predictions
transition_probabilities: Compute state transition probabilities
state_probabilities: Compute state occupancy probabilities
expected_sojourn: Compute expected sojourn times
plot_hazards: Generate hazard function plots
plot_cumhaz: Generate cumulative hazard plots
plot_survival: Generate state probability plots
microsimulation: Use simulation for state predictions
n_simulation: Sample size for microsimulation
confidence_intervals: Compute uncertainty estimates

Value

A results object containing:

`results$todo`					a html
`results$summary`					a html
`results$transitionMatrix`					a table
`results$transitionModels`					a table
`results$modelComparison`					a table
`results$transitionProbTable`					a table
`results$stateProbTable`					a table
`results$sojournTable`					a table
`results$hazardPlot`					an image
`results$cumhazPlot`					an image
`results$survivalPlot`					an image
`results$transitionDiagram`					an image
`results$microsimResults`					a html
`results$goodnessOfFit`					a html
`results$clinicalInterpretation`					a html

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$transitionMatrix$asDF

as.data.frame(results$transitionMatrix)

Examples

# \donttest{
# Example usage
flexmultistate(
    data = disease_data,
    time = transition_time,
    status = state_variable,
    states = c("Healthy", "Disease", "Death"),
    transition_matrix = transition_def
)
# }