Simulate a reduced manuscript-style MBMM dataset — mbmm_simulate_manuscript

This public simulation preserves the main manuscript structure while replacing private empirical biomarker and visit-pattern inputs with fully synthetic analogues.

Usage

mbmm_simulate_manuscript_demo(
  n_subjects = 50,
  prevalence = 0.3,
  beta_true = -1.5,
  p_abortive = 0.4,
  n_bank_donors = 8L,
  productive_parameter_bank = NULL,
  visit_schedules = mbmm_demo_visit_schedules(),
  sigma_obs = 0.5,
  lod = 100,
  productive_min_detect = 1L,
  productive_max_tries = 50L,
  seed = NULL
)

Arguments

n_subjects: Number of subjects.
prevalence: Target marginal productive-infection prevalence for the realized synthetic biomarker distribution.
beta_true: True standardized biomarker effect in the logistic gate. Negative values represent protection.
p_abortive: Probability that a nonproductive subject receives an abortive/transient pattern rather than a purely near-background trajectory.
n_bank_donors: Number of productive subjects assigned the complete visit schedule and flagged as bank eligible.
productive_parameter_bank: Optional data frame of productive ODE parameters. When omitted, a synthetic public bank is generated from mbmm_example_eclipse_prior.
visit_schedules: Named list of public visit schedules.
sigma_obs: Observation-noise SD on the log10 scale.
lod: Natural-scale assay limit of detection.
productive_min_detect: Minimum number of detections requested for a productive trajectory.
productive_max_tries: Maximum attempts used to obtain that minimum.
seed: Optional random seed.

Value

A list with:

subject_data: Subject-level covariates and truth.
truth: Alias of subject_data.
observations: Long-format observations.
obs_list: Named per-subject observation data frames.
covariates: Data frame containing id and baseline_antibody.
productive_parameter_bank: Parameter bank used for productive trajectory generation.
settings: Generating settings.

Details

Productive subjects are generated from mbmm_example_eclipse_simulate using parameter draws from mbmm_example_eclipse_prior unless a custom productive parameter bank is supplied.