Runs simulation sweeps for the empirical NC validity diagnostics
and returns data frames ready for plotting with
plot_nc_validity_diagnostics(). Panels: (A) A1 W perp X | C,
(B) A2 W perp G | C, (C) A2' W perp Gm | C, (D) A3
covariance-capture versus true coverage omega, (E) A3 support
R2(Utilde | W) versus omega.
Usage
sweep_nc_validity(
n_samples = 500,
n_iter = 50,
phi_val = 0.8,
contam_grid = c(0, 0.05, 0.1, 0.15, 0.2, 0.3, 0.5),
meqtl_grid = c(0, 0.05, 0.1, 0.15, 0.2, 0.3, 0.5),
eqtl_grid = c(0, 0.05, 0.1, 0.15, 0.2, 0.3, 0.5),
omega_grid = c(0, 0.1, 0.2, 0.3, 0.5, 0.7, 0.9, 1),
n_perm = 200,
cs_confounders = 2,
include_a3_grid = FALSE,
k_grid = c(1, 2, 3),
n_valid_grid = c(1, 2, 3),
n_cores = 1
)Arguments
- n_samples
Number of synthetic samples per iteration.
- n_iter
Number of replications per sweep point.
- phi_val
Mediator-instrument strength (for the A2' panel and the capture/support sweeps).
- contam_grid
X->W contamination strength grid (A1).
- meqtl_grid
G->W (meQTL) strength grid (A2).
- eqtl_grid
Gm->W (eQTL) strength grid (A2').
- omega_grid
True negative-control coverage grid for the capture (D) and support (E) sweeps. Includes 0 by default so the permutation-null calibration is visible.
- n_perm
Permutations per replicate for the capture test. Default 200, matching
iconic_diagnose().- cs_confounders
Number of latent confounders for the capture/support sweeps (distinct loadings). Default 2.
- include_a3_grid
Logical; also run the legacy A3 dimensional grid (PGC bias over n_valid x k). Default FALSE (no longer plotted).
- k_grid, n_valid_grid
Grids for the legacy A3 dimensional sweep.
- n_cores
Number of parallel workers for the replicate loops. Default 1 (sequential). Uses
parallel::mclapplyon Unix and a PSOCK cluster on Windows.
Value
A list with elements panel_a, panel_b,
panel_d, panel_capture_support (per-replicate raw),
and optionally panel_c when include_a3_grid = TRUE.
Examples
# \donttest{
panels <- sweep_nc_validity(n_samples = 100, n_iter = 2,
contam_grid = c(0, 0.1), meqtl_grid = c(0, 0.1),
eqtl_grid = c(0, 0.1), omega_grid = c(0, 0.5), n_perm = 20)
#> Running NC validity sweeps (n_iter = 2, n = 100) ...
#> Panel A: nc_validity_screen (A1)
#> Panel A replicates: 2 tasks (sequential)
#> NC validity screen: 10 tasks (sequential)
#> NC validity screen: 10% (1/10) [0s]
#> NC validity screen: 20% (2/10) [0s]
#> NC validity screen: 30% (3/10) [0s]
#> NC validity screen: 40% (4/10) [0s]
#> NC validity screen: 50% (5/10) [0s]
#> NC validity screen: 60% (6/10) [0s]
#> NC validity screen: 70% (7/10) [0s]
#> NC validity screen: 80% (8/10) [0s]
#> NC validity screen: 90% (9/10) [0s]
#> NC validity screen: 100% (10/10) [0s]
#> Panel A replicates: 50% (1/2) [0s]
#> NC validity screen: 10 tasks (sequential)
#> NC validity screen: 10% (1/10) [0s]
#> NC validity screen: 20% (2/10) [0s]
#> NC validity screen: 30% (3/10) [0s]
#> NC validity screen: 40% (4/10) [0s]
#> NC validity screen: 50% (5/10) [0s]
#> NC validity screen: 60% (6/10) [0s]
#> NC validity screen: 70% (7/10) [0s]
#> NC validity screen: 80% (8/10) [0s]
#> NC validity screen: 90% (9/10) [0s]
#> NC validity screen: 100% (10/10) [0s]
#> Panel A replicates: 100% (2/2) [0s]
#> Panel A replicates: 2 tasks (sequential)
#> NC validity screen: 10 tasks (sequential)
#> NC validity screen: 10% (1/10) [0s]
#> NC validity screen: 20% (2/10) [0s]
#> NC validity screen: 30% (3/10) [0s]
#> NC validity screen: 40% (4/10) [0s]
#> NC validity screen: 50% (5/10) [0s]
#> NC validity screen: 60% (6/10) [0s]
#> NC validity screen: 70% (7/10) [0s]
#> NC validity screen: 80% (8/10) [0s]
#> NC validity screen: 90% (9/10) [0s]
#> NC validity screen: 100% (10/10) [0s]
#> Panel A replicates: 50% (1/2) [0s]
#> NC validity screen: 10 tasks (sequential)
#> NC validity screen: 10% (1/10) [0s]
#> NC validity screen: 20% (2/10) [0s]
#> NC validity screen: 30% (3/10) [0s]
#> NC validity screen: 40% (4/10) [0s]
#> NC validity screen: 50% (5/10) [0s]
#> NC validity screen: 60% (6/10) [0s]
#> NC validity screen: 70% (7/10) [0s]
#> NC validity screen: 80% (8/10) [0s]
#> NC validity screen: 90% (9/10) [0s]
#> NC validity screen: 100% (10/10) [0s]
#> Panel A replicates: 100% (2/2) [0s]
#> Panel B: nc_independence_check (A2)
#> Panel B replicates: 2 tasks (sequential)
#> NC independence (G): 10 tasks (sequential)
#> NC independence (G): 10% (1/10) [0s]
#> NC independence (G): 20% (2/10) [0s]
#> NC independence (G): 30% (3/10) [0s]
#> NC independence (G): 40% (4/10) [0s]
#> NC independence (G): 50% (5/10) [0s]
#> NC independence (G): 60% (6/10) [0s]
#> NC independence (G): 70% (7/10) [0s]
#> NC independence (G): 80% (8/10) [0s]
#> NC independence (G): 90% (9/10) [0s]
#> NC independence (G): 100% (10/10) [0s]
#> Panel B replicates: 50% (1/2) [0s]
#> NC independence (G): 10 tasks (sequential)
#> NC independence (G): 10% (1/10) [0s]
#> NC independence (G): 20% (2/10) [0s]
#> NC independence (G): 30% (3/10) [0s]
#> NC independence (G): 40% (4/10) [0s]
#> NC independence (G): 50% (5/10) [0s]
#> NC independence (G): 60% (6/10) [0s]
#> NC independence (G): 70% (7/10) [0s]
#> NC independence (G): 80% (8/10) [0s]
#> NC independence (G): 90% (9/10) [0s]
#> NC independence (G): 100% (10/10) [0s]
#> Panel B replicates: 100% (2/2) [0s]
#> Panel B replicates: 2 tasks (sequential)
#> NC independence (G): 10 tasks (sequential)
#> NC independence (G): 10% (1/10) [0s]
#> NC independence (G): 20% (2/10) [0s]
#> NC independence (G): 30% (3/10) [0s]
#> NC independence (G): 40% (4/10) [0s]
#> NC independence (G): 50% (5/10) [0s]
#> NC independence (G): 60% (6/10) [0s]
#> NC independence (G): 70% (7/10) [0s]
#> NC independence (G): 80% (8/10) [0s]
#> NC independence (G): 90% (9/10) [0s]
#> NC independence (G): 100% (10/10) [0s]
#> Panel B replicates: 50% (1/2) [0s]
#> NC independence (G): 10 tasks (sequential)
#> NC independence (G): 10% (1/10) [0s]
#> NC independence (G): 20% (2/10) [0s]
#> NC independence (G): 30% (3/10) [0s]
#> NC independence (G): 40% (4/10) [0s]
#> NC independence (G): 50% (5/10) [0s]
#> NC independence (G): 60% (6/10) [0s]
#> NC independence (G): 70% (7/10) [0s]
#> NC independence (G): 80% (8/10) [0s]
#> NC independence (G): 90% (9/10) [0s]
#> NC independence (G): 100% (10/10) [0s]
#> Panel B replicates: 100% (2/2) [0s]
#> Panel C: nc_independence_check_gm (A2')
#> Panel C replicates: 2 tasks (sequential)
#> NC independence (Gm): 10 tasks (sequential)
#> NC independence (Gm): 10% (1/10) [0s]
#> NC independence (Gm): 20% (2/10) [0s]
#> NC independence (Gm): 30% (3/10) [0s]
#> NC independence (Gm): 40% (4/10) [0s]
#> NC independence (Gm): 50% (5/10) [0s]
#> NC independence (Gm): 60% (6/10) [0s]
#> NC independence (Gm): 70% (7/10) [0s]
#> NC independence (Gm): 80% (8/10) [0s]
#> NC independence (Gm): 90% (9/10) [0s]
#> NC independence (Gm): 100% (10/10) [0s]
#> Panel C replicates: 50% (1/2) [0s]
#> NC independence (Gm): 10 tasks (sequential)
#> NC independence (Gm): 10% (1/10) [0s]
#> NC independence (Gm): 20% (2/10) [0s]
#> NC independence (Gm): 30% (3/10) [0s]
#> NC independence (Gm): 40% (4/10) [0s]
#> NC independence (Gm): 50% (5/10) [0s]
#> NC independence (Gm): 60% (6/10) [0s]
#> NC independence (Gm): 70% (7/10) [0s]
#> NC independence (Gm): 80% (8/10) [0s]
#> NC independence (Gm): 90% (9/10) [0s]
#> NC independence (Gm): 100% (10/10) [0s]
#> Panel C replicates: 100% (2/2) [0s]
#> Panel C replicates: 2 tasks (sequential)
#> NC independence (Gm): 10 tasks (sequential)
#> NC independence (Gm): 10% (1/10) [0s]
#> NC independence (Gm): 20% (2/10) [0s]
#> NC independence (Gm): 30% (3/10) [0s]
#> NC independence (Gm): 40% (4/10) [0s]
#> NC independence (Gm): 50% (5/10) [0s]
#> NC independence (Gm): 60% (6/10) [0s]
#> NC independence (Gm): 70% (7/10) [0s]
#> NC independence (Gm): 80% (8/10) [0s]
#> NC independence (Gm): 90% (9/10) [0s]
#> NC independence (Gm): 100% (10/10) [0s]
#> Panel C replicates: 50% (1/2) [0s]
#> NC independence (Gm): 10 tasks (sequential)
#> NC independence (Gm): 10% (1/10) [0s]
#> NC independence (Gm): 20% (2/10) [0s]
#> NC independence (Gm): 30% (3/10) [0s]
#> NC independence (Gm): 40% (4/10) [0s]
#> NC independence (Gm): 50% (5/10) [0s]
#> NC independence (Gm): 60% (6/10) [0s]
#> NC independence (Gm): 70% (7/10) [0s]
#> NC independence (Gm): 80% (8/10) [0s]
#> NC independence (Gm): 90% (9/10) [0s]
#> NC independence (Gm): 100% (10/10) [0s]
#> Panel C replicates: 100% (2/2) [0s]
#> Panels D-E: nc_completeness_capture + nc_support_check vs omega
#> omega = 0: 2 tasks (sequential)
#> NC capture null: 20 tasks (sequential)
#> NC capture null: 10% (2/20) [0s]
#> NC capture null: 20% (4/20) [0.1s]
#> NC capture null: 30% (6/20) [0.1s]
#> NC capture null: 40% (8/20) [0.2s]
#> NC capture null: 50% (10/20) [0.2s]
#> NC capture null: 60% (12/20) [0.3s]
#> NC capture null: 70% (14/20) [0.3s]
#> NC capture null: 80% (16/20) [0.3s]
#> NC capture null: 90% (18/20) [0.4s]
#> NC capture null: 100% (20/20) [0.4s]
#> omega = 0: 50% (1/2) [0.5s]
#> NC capture null: 20 tasks (sequential)
#> NC capture null: 10% (2/20) [0s]
#> NC capture null: 20% (4/20) [0.1s]
#> NC capture null: 30% (6/20) [0.1s]
#> NC capture null: 40% (8/20) [0.2s]
#> NC capture null: 50% (10/20) [0.2s]
#> NC capture null: 60% (12/20) [0.3s]
#> NC capture null: 70% (14/20) [0.3s]
#> NC capture null: 80% (16/20) [0.4s]
#> NC capture null: 90% (18/20) [0.4s]
#> NC capture null: 100% (20/20) [0.4s]
#> omega = 0: 100% (2/2) [1s]
#> omega = 0.5: 2 tasks (sequential)
#> NC capture null: 20 tasks (sequential)
#> NC capture null: 10% (2/20) [0s]
#> NC capture null: 20% (4/20) [0.1s]
#> NC capture null: 30% (6/20) [0.1s]
#> NC capture null: 40% (8/20) [0.2s]
#> NC capture null: 50% (10/20) [0.2s]
#> NC capture null: 60% (12/20) [0.3s]
#> NC capture null: 70% (14/20) [0.3s]
#> NC capture null: 80% (16/20) [0.4s]
#> NC capture null: 90% (18/20) [0.4s]
#> NC capture null: 100% (20/20) [0.4s]
#> omega = 0.5: 50% (1/2) [0.5s]
#> NC capture null: 20 tasks (sequential)
#> NC capture null: 10% (2/20) [0s]
#> NC capture null: 20% (4/20) [0.1s]
#> NC capture null: 30% (6/20) [0.1s]
#> NC capture null: 40% (8/20) [0.2s]
#> NC capture null: 50% (10/20) [0.2s]
#> NC capture null: 60% (12/20) [0.3s]
#> NC capture null: 70% (14/20) [0.3s]
#> NC capture null: 80% (16/20) [0.4s]
#> NC capture null: 90% (18/20) [0.4s]
#> NC capture null: 100% (20/20) [0.4s]
#> omega = 0.5: 100% (2/2) [1s]
#> Done in 2.2 s
panels$panel_a
#> contamination violated_mean violated_sd confounding_mean confounding_sd
#> 1 0.0 0.0 0.0000000 1 0
#> 2 0.1 0.3 0.1414214 1 0
panels$panel_capture_support
#> omega rep capture_R2 capture_p null_R2 support_R2 frac_adds_coverage
#> 1 0.0 1 0.07755442 0.75 0.10999436 0.11589077 0.0
#> 2 0.0 2 0.04619164 0.90 0.09367601 0.05081462 0.0
#> 3 0.5 1 0.49594649 0.00 0.08636304 0.65417453 0.4
#> 4 0.5 2 0.48886836 0.00 0.10329703 0.63588698 0.2
# }