Package index • bmstate

All functions

DosingData: Dosing data class (R6 class)
JointData: Joint data class (R6 class)
MultistateModel: Main model class
MultistateModelFit: Minimal fit class
MultistateSystem: A multistate system with proportional spline hazards
PKModel: One-compartment PK Model
PSSDosingData: Partially steady-state dosing data class (R6 class)
PathData: Path data class (R6 class)
TransitionMatrix: Defines states and possible transitions
as_any_event(): PathData to time-to-event data format for any state other than null state
as_single_event(): PathData to time-to-event data format with a single event
as_survival(): PathData to event-free survival format
bmstate-package bmstate: The 'bmstate' package.
c_index(): Compute concordance index
create_msm(): Create a multistate model
create_scoring_df(): Create a data frame to evaluate state visit probability predictions
create_stan_data(): Creating Stan data list
create_stan_model(): Create the main 'Stan' model
default_stan_filepath(): Get path to default Stan file
df_to_pathdata(): Create 'PathData' from a data frame of one observed path per subject
ensure_exposed_stan_functions(): Expose 'Stan' functions if they are not yet exposed
example_sim_setup_illnessdeath(): Example simulation setup
fit_stan(): Fit a model using 'Stan'
generate_paths(): Path generation for 'MultistateModelFit'
msmfit_exposure(): Compute exposure
msmfit_inst_hazard_param_draws(): Extract and reshape draws of instant hazard related parameters
msmfit_log_hazard_multipliers(): Compute log_hazard multipliers
msmfit_pk_params(): Evaluate PK parameters
p_state_occupancy(): Solve state occupancy probabilities for each subject and draw in 'MultistateModelFit'
p_state_visit(): For each non-source state, compute probability of visiting it at least once before given time
p_state_visit_per_subject(): For each subject, compute probability of visiting a given state at least once before given time
pk_2cpt_pss(): Partially steady-state PK model
plot_stan_data_integral(): Visualize numerical integration of hazard
plot_stan_data_matrix(): Visualize parts of the 'Stan' data
plot_state_occupancy(): Plot mean state occupancy probabilities over time for each subject
potential_covariates(): Look for potential covariates that affect transitions
simulate_dosing(): Simulate dosing data
simulate_example_data(): Simulate example data
solve_time_evolution(): Solve the Kolmogorov forward equation of a Markovian multistate system
solve_trans_prob_matrix(): Solve the transition probability matrix for each given output time
split_data(): Train-test split
transmat_full() transmat_comprisk() transmat_survival() transmat_illnessdeath() transmat_progression() transmat_diamond(): Create a common transition matrix