INFO  [2024-03-07 18:32:01] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-03-07 18:32:01] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-03-07 18:32:01] Will use linear mixed models!
INFO  [2024-03-07 18:32:01] Will use Rfast!
WARN  [2024-03-07 18:32:01] Converting IDs to integer values
WARN  [2024-03-07 18:32:01] The `fold` column is used for stratification
WARN  [2024-03-07 18:32:01] Converting `character` columns to factors
INFO  [2024-03-07 18:32:01] Scaling data with sdall ...
INFO  [2024-03-07 18:32:02] Calculating LMM coefficients
INFO  [2024-03-07 18:32:02] Reducing the number of dimensions with PCA
INFO  [2024-03-07 18:32:03] Keeping 36 components from initial PCA, explaining 95.31 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-03-07 18:32:03] -> Finished the reduction of dimensions!
WARN  [2024-03-07 18:32:03] Keeping 20 of 36 components. Change `max_PC` if necessary.
INFO  [2024-03-07 18:32:04] Starting validation: bootstrap
INFO  [2024-03-07 18:32:04] - Run 1 of 100
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INFO  [2024-03-07 18:38:51] Calculating percentiles for score and loading
INFO  [2024-03-07 18:39:17] ==== ALASCA has finished ====
INFO  [2024-03-07 18:39:17] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
INFO  [2024-03-07 18:39:25] 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 18:39:30] 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 18:39:44] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-07 18:39:44] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:39:54] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-03-07 18:39:54] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:40:00] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-07 18:40:00] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:40:07] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-03-07 18:40:07] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:40:13] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 18:40:13] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:40:20] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 18:40:20] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:40:32] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-07 18:40:32] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:40:43] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 8.
WARN  [2024-03-07 18:40:43] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:41:07] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 18:41:07] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:41:12] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 8.
WARN  [2024-03-07 18:41:12] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:41:37] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-03-07 18:41:42] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-03-07 18:41:47] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-03-07 18:42:42] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 18:42:42] 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 18:42:46] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-07 18:42:46] 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 18:42:49] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-07 18:42:49] 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 18:42:52] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-07 18:42:52] 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 18:42:55] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 18:42:55] 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 18:42:59] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 18:42:59] 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 18:43:07] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
INFO  [2024-03-07 18:43:07] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC7). Use `variable` to specify variables to plot
INFO  [2024-03-07 18:43:44] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 18:43:44] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 18:43:53] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-03-07 18:43:53] Loadings for effect number 1 and principal component(s) 6