INFO  [2024-03-07 19:33:39] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-03-07 19:33:39] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-03-07 19:33:39] Will use linear mixed models!
INFO  [2024-03-07 19:33:39] Will use Rfast!
WARN  [2024-03-07 19:33:39] Converting IDs to integer values
WARN  [2024-03-07 19:33:39] The `fold` column is used for stratification
WARN  [2024-03-07 19:33:40] Converting `character` columns to factors
INFO  [2024-03-07 19:33:40] Scaling data with sdall ...
INFO  [2024-03-07 19:33:40] Calculating LMM coefficients
INFO  [2024-03-07 19:33:40] Reducing the number of dimensions with PCA
INFO  [2024-03-07 19:33:41] Keeping 46 components from initial PCA, explaining 95.24 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-03-07 19:33:42] -> Finished the reduction of dimensions!
WARN  [2024-03-07 19:33:42] Keeping 20 of 46 components. Change `max_PC` if necessary.
INFO  [2024-03-07 19:33:42] Starting validation: bootstrap
INFO  [2024-03-07 19:33:43] - Run 1 of 100
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INFO  [2024-03-07 19:41:05] Calculating percentiles for score and loading
INFO  [2024-03-07 19:41:27] ==== ALASCA has finished ====
INFO  [2024-03-07 19:41:27] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
INFO  [2024-03-07 19:41:27] Scree plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1 and 2 and 3 and 4 and 5 and 6 and 7 and 8 and 9 and 10.
INFO  [2024-03-07 19:41:28] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-07 19:41:28] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 19:41:29] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-03-07 19:41:29] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 19:41:30] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-07 19:41:30] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 19:41:31] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-03-07 19:41:31] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 19:41:32] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 19:41:32] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 19:41:33] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 19:41:33] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 19:41:34] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 19:41:34] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-07 19:41:35] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-07 19:41:35] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC2). Use `variable` to specify variables to plot
INFO  [2024-03-07 19:41:37] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-07 19:41:37] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC3). Use `variable` to specify variables to plot
INFO  [2024-03-07 19:41:38] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-07 19:41:38] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC4). Use `variable` to specify variables to plot
INFO  [2024-03-07 19:41:40] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 19:41:40] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC5). Use `variable` to specify variables to plot
INFO  [2024-03-07 19:41:41] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 19:41:41] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC6). Use `variable` to specify variables to plot
INFO  [2024-03-07 19:41:42] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-03-07 19:41:42] Loadings for effect number 1 and principal component(s) 6