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A multistate system with proportional spline hazards

MultistateSystem.Rd

A multistate system with proportional spline hazards

A multistate system with proportional spline hazards

Methods

Public methods

Method new()

Create model

Usage

MultistateSystem$new(transmat)

Arguments

transmat

A TransitionMatrix.

Method num_states()

Get number of states

Usage

MultistateSystem$num_states()

Returns

integer

Method num_trans()

Get number of transitions

Usage

MultistateSystem$num_trans()

Returns

integer

Method num_weights()

Get number of spline weight parameters

Usage

MultistateSystem$num_weights()

Returns

an integer (num_knots - 2) + self$spline_k

Method num_knots()

Get number of spline knots

Usage

MultistateSystem$num_knots()

Returns

integer, zero if knots have not been set

Method tm()

Get transition matrix

Usage

MultistateSystem$tm()

Method knots_not_set()

Have knots not been set yet?

Usage

MultistateSystem$knots_not_set()

Returns

a logical

Method set_knots()

Set spline knot locations

Usage

MultistateSystem$set_knots(locations)

Arguments

locations

A numeric vector

Method get_knots()

Get knot locations

Usage

MultistateSystem$get_knots()

Returns

a numeric vector

Method get_tmax()

Get max time set for the model

Usage

MultistateSystem$get_tmax()

Returns

a number

Method print()

Print the object

Usage

MultistateSystem$print()

Returns

nothing

Method log_baseline_hazard()

Evaluate log baseline hazard

Usage

MultistateSystem$log_baseline_hazard(t, log_w0, w = NULL, SBF = NULL)

Arguments

t

Output time points. Not used if SBF is given.

log_w0

Intercept (log_scale).

w

Spline weights (log scale). If NULL, will be set to a vector of zeros, meaning that the log hazard is constant at log_w0

SBF

Precomputed basisfunction matrix at t.

Returns

a vector with same length as t

Method basisfun_matrix()

Evaluate basis function matrix for baseline hazard

Usage

MultistateSystem$basisfun_matrix(t)

Arguments

t

Evaluation time points.

Returns

Matrix with shape c(N, L+1) where L is number of knots

Method log_inst_hazard()

Evaluate log instant hazard

Usage

MultistateSystem$log_inst_hazard(t, w, log_w0, log_m, SBF = NULL)

Arguments

t

Time point(s). Not used if SBF is given.

w

Spline basis function weights (vector)

log_w0

Intercept (log)

log_m

Hazard multiplier (log)

SBF

Pre-computed basis function matrix at t.

Method intensity_matrix()

Evaluate transition intensity (generator) matrix at time t

Usage

MultistateSystem$intensity_matrix(t, log_w0, w = NULL, log_m = NULL)

Arguments

t

A number (time point)

log_w0

A vector of length n_trans

w

An array of shape n_trans x n_weights

log_m

A vector of length n_trans

Returns

a matrix with shape n_states x n_states

Method has_self_loops()

Does the system have self loops?

Usage

MultistateSystem$has_self_loops()

Returns

Boolean value

Method max_inst_hazard()

Max instant hazard on interval (t1, t2)

Usage

MultistateSystem$max_inst_hazard(t1, t2, w, log_w0, log_m)

Arguments

t1

Start time point

t2

End time point

w

Spline basis function weights (vector)

log_w0

Intercept (log)

log_m

Hazard multiplier (log)

Method simulate()

Generate paths

Usage

MultistateSystem$simulate(
  w,
  log_w0,
  log_m,
  init_state = 1,
  t_start = 0,
  t_max = NULL,
  n_rep = 1,
  min_t_step = 1e-06
)

Arguments

w

An array of shape n_draws x n_trans x n_weights

log_w0

An array of shape n_draws x n_trans

log_m

An array of shape n_draws x n_trans

init_state

Index of starting state. A single value or a vector with length equal to n_draws.

t_start

Start time.

t_max

Max time. If NULL, the max time of the model is used.

n_rep

Number of repetitions to do for each draw.

min_t_step

Minimal time step.

Returns

A data frame with n_draws x n_rep paths.

Method clone()

The objects of this class are cloneable with this method.

Usage

MultistateSystem$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.