INFO  [2024-07-18 15:09:28] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-07-18 15:09:28] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-07-18 15:09:28] Will use linear mixed models!
INFO  [2024-07-18 15:09:28] Will use Rfast!
WARN  [2024-07-18 15:09:28] Converting IDs to integer values
WARN  [2024-07-18 15:09:28] The `fold` column is used for stratification
WARN  [2024-07-18 15:09:28] Converting `character` columns to factors
INFO  [2024-07-18 15:09:28] Scaling data with sdall ...
INFO  [2024-07-18 15:09:29] Calculating LMM coefficients
INFO  [2024-07-18 15:09:29] Reducing the number of dimensions with PCA
INFO  [2024-07-18 15:09:30] Keeping 46 components from initial PCA, explaining 95.24 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-07-18 15:09:30] -> Finished the reduction of dimensions!
WARN  [2024-07-18 15:09:30] Keeping 20 of 46 components. Change `max_PC` if necessary.
INFO  [2024-07-18 15:09:31] Starting validation: bootstrap
INFO  [2024-07-18 15:09:31] - Run 1 of 100
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INFO  [2024-07-18 15:17:21] Calculating percentiles for score and loading
INFO  [2024-07-18 15:17:45] ==== ALASCA has finished ====
INFO  [2024-07-18 15:17:45] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
INFO  [2024-07-18 15:21:00] 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  [2024-07-18 15:21:02] 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  [2024-07-18 15:21:16] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-07-18 15:21:16] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:21:22] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-07-18 15:21:22] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:21:28] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-07-18 15:21:28] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:21:36] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-07-18 15:21:36] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:21:43] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-07-18 15:21:43] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:21:48] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-07-18 15:21:48] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:21:53] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-07-18 15:21:53] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:21:57] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-07-18 15:21:57] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:22:02] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-07-18 15:22:02] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:22:04] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-07-18 15:22:04] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:22:09] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-07-18 15:22:09] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:22:13] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-07-18 15:22:13] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:22:17] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-07-18 15:22:17] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:22:24] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-07-18 15:22:24] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:22:39] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-07-18 15:22:39] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-07-18 15:22:42] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-07-18 15:22:42] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC2). Use `variable` to specify variables to plot
INFO  [2024-07-18 15:22:46] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-07-18 15:22:46] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC3). Use `variable` to specify variables to plot
INFO  [2024-07-18 15:22:51] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-07-18 15:22:51] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC4). Use `variable` to specify variables to plot
INFO  [2024-07-18 15:22:55] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-07-18 15:22:55] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC5). Use `variable` to specify variables to plot
INFO  [2024-07-18 15:22:59] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-07-18 15:22:59] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC6). Use `variable` to specify variables to plot
INFO  [2024-07-18 15:23:02] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-07-18 15:23:02] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC5). Use `variable` to specify variables to plot
INFO  [2024-07-18 15:23:40] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-07-18 15:23:40] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-07-18 15:23:51] Loadings for effect number 1 and principal component(s) 1
INFO  [2024-07-18 15:23:51] Loadings for effect number 1 and principal component(s) 2
INFO  [2024-07-18 15:23:51] Loadings for effect number 1 and principal component(s) 3
INFO  [2024-07-18 15:23:51] Loadings for effect number 1 and principal component(s) 4
INFO  [2024-07-18 15:49:20] Loadings for effect number 1 and principal component(s) 1
INFO  [2024-07-18 15:49:20] Loadings for effect number 1 and principal component(s) 2
INFO  [2024-07-18 15:49:20] Loadings for effect number 1 and principal component(s) 3
INFO  [2024-07-18 15:49:20] Loadings for effect number 1 and principal component(s) 4