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Run null mediation simulations to estimate Type I error rates

Source: R/mediation_simulation.R
run_null_mediation_sim.Rd

Sets alpha_M = 0 and beta_M = 0 (no true NIE) while keeping beta_X active (NDE still present). Reports Type I error for both NIE (should be 0 under the null) and NDE (should reflect power for the direct effect).

Usage

run_null_mediation_sim(
  n_iter = 200,
  n_samples = 500,
  n_features = 20,
  beta_X = 0.1,
  conf_str = 0.8,
  w_signal = 0.7,
  mo_confounding = 0.8,
  phi = 0,
  rho_G1 = 0,
  rho_G2 = 0,
  rho_pop = 0,
  lambda_XM = NULL,
  lambda_MY = NULL,
  omega_1 = NULL,
  omega_2 = NULL,
  feat_cor = 0,
  base_seed = 300,
  n_cores = 1,
  alpha = 0.05
)

Arguments

n_iter

Number of replicates. Default 200.

n_samples

Observations per replicate. Default 500.

n_features

Features per replicate. Default 20.

beta_X

Direct effect (NDE, still active under null NIE). Default 0.10.

conf_str

Confounding strength delta. Default 0.80.

w_signal

Proxy quality omega. Default 0.70.

mo_confounding

Strength of U1 -> M. Default 0.80.

phi

Strength of the mediator instrument Gm -> M. 0 = no mediator instrument. Default 0.

rho_G1

Correlation of G1 with conf_XM. Default 0.

rho_G2

Correlation of G2 with conf_MY. Default 0.

rho_pop

Shared population structure. Default 0.

lambda_XM

Optional per-path confounder loading vector (X->M path).

lambda_MY

Optional per-path confounder loading vector (M->Y path).

omega_1

Coverage of conf_XM by W1. NULL = use w_signal.

omega_2

Coverage of conf_MY by W2. NULL = use w_signal.

feat_cor

Within-module correlation for block-diagonal co-expression modules in Y and W. 0 = independent features. Default 0.

base_seed

Seed offset. Default 300.

n_cores

Parallel workers. Default 1.

alpha

Significance threshold. Default 0.05.

Value

A list with rates (data frame: method, NIE_type1, NDE_type1) and raw (full results).

Examples

null <- run_null_mediation_sim(n_iter = 2, n_samples = 100,
  n_features = 5, mo_confounding = 0.8, phi = 0.8)
null$rates
#>    method NIE_type1 NDE_type1
#> 1   UNADJ       0.1       1.0
#> 2  DIRECT       0.0       1.0
#> 3    COCA       0.0       0.0
#> 4  IV2SLS       0.0       0.5
#> 5     PGC       0.0       1.0
#> 6 IV2SLS2       0.0       0.5