Define simulation configuration — define_sim

Defines the patterns for various parameters in the epidemic simulation. The number of latent and diagnosis states will be inferred from the simulation specification.

Usage

define_sim_config(
  h_pattern = "constant",
  o_pattern = "constant",
  d_pattern = "constant",
  p_pattern = "constant",
  m_pattern = "constant",
  r_pattern = "constant",
  a_pattern = "constant",
  sim_type = NULL,
  sim_seed = NULL,
  dist = TRUE,
  migration = FALSE,
  rita = FALSE,
  age = FALSE,
  nquar = 40,
  nage = 52,
  q = c(0.0976, 0.115, 0.116, 0.148),
  target_inf = 30000,
  target_mig = 6000,
  abroad_prop = 0.2,
  cd4_completeness = 1,
  rita_completeness = 1,
  rita_completeness_by_state = NULL,
  age_diag_effect = 0,
  mig_diag_offset = NULL,
  frr = 0.019,
  detect_obs_times = NULL,
  gamma_obs_grouped = FALSE,
  gamma_obs_sd = 0,
  gamma_obs_scale = 500,
  abroad_age_trend = 0,
  detect_step_quarter = NULL,
  detect_step_size = 0,
  gamma_obs_scale_trend = 0
)

Arguments

h_pattern: Pattern type for infections ("constant", "increasing", "varying", "varying_2").
o_pattern: Pattern type for omega ("constant", "increasing", "step_change_1", "step_change_2", "none").
d_pattern: Pattern type for diagnosis probabilities ("constant", "varying").
p_pattern: Pattern for the born-abroad:UK-born ratio of UK-acquired incidence ("constant", "increasing").
m_pattern: Pattern type for mu ("constant", "differing", "varying").
r_pattern: Pattern type for RITA data ("constant", "increasing", "none").
a_pattern: Pattern type for age-based data ("constant", "wedge", "varying_wedge").
sim_type: If provided, a preset type of simulation to define patterns for.
sim_seed: Random seed for simulation. If NULL, a random seed is generated.
dist: Logical indicating whether to add stochastic variation.
migration: Logical indicating whether to include migration effects.
rita: Logical indicating whether to simulate RITA (Recent Infection Testing Algorithm) data.
age: Logical indicating whether to simulate age-stratified data.
nquar: Number of time quarters.
nage: Number of age groups.
q: Vector of progression probabilities.
target_inf: Target total number of HIV acquisitions.
target_mig: Target total number of migrations.
abroad_prop: Proportion of infections acquired abroad at the outset.
cd4_completeness: CD4 completeness.
rita_completeness: RITA completeness.
rita_completeness_by_state: Optional numeric vector of length 5 giving state-specific completeness for RITA simulations. Elements correspond to RITA positive, CD4 500 or above, CD4 350–499, CD4 200–349, and CD4 below 200. Use lower values in lower CD4 states to simulate informative missingness.
age_diag_effect: Numeric scalar controlling the strength of age variation in diagnosis probabilities. Applied as a logit-additive offset scaled linearly across ages.
mig_diag_offset: Numeric vector of per-state logit-scale offsets applied to diagnosis probabilities for people born abroad (y = 2). Length must equal the number of diagnosis states (4 for non-RITA, 5 for RITA). NULL (default) applies no offset.
frr: False recency rate for RITA misclassification.
detect_obs_times: Integer vector of quarter indices (1-based) at which external detection-probability observations are generated.
gamma_obs_grouped: Logical scalar or logical vector of length nquar controlling which quarters receive age-stratified external migration observations on the same 4 age groups as ABROAD_group. The scalar gamma_obs series is always simulated; quarters where gamma_obs_grouped is FALSE have -1 rows in gamma_obs_group.
abroad_age_trend: Total logit-scale change (start to end) in the 15-24/25-34 age-group shares of born-abroad arrivals relative to the 45+ reference group; 0 = time-constant age composition.
detect_step_quarter: Quarter index (1-based) of an ascertainment step in detect_prob (e.g. a surveillance reporting change). NULL (default) means no step.
detect_step_size: Logit-scale jump in detect_prob applied from detect_step_quarter onward.
gamma_obs_scale_trend: Total log-scale change (start to end) in the HIV-positive share of the external migration index (gamma_obs_scale); 0 = constant share.

Value

Configuration list.