INFO  [2024-07-18 15:39:55] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-07-18 15:39:55] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-07-18 15:39:55] Will use linear mixed models!
INFO  [2024-07-18 15:39:55] Will use Rfast!
WARN  [2024-07-18 15:39:55] Converting IDs to integer values
WARN  [2024-07-18 15:39:55] The `fold` column is used for stratification
WARN  [2024-07-18 15:39:55] Converting `character` columns to factors
INFO  [2024-07-18 15:39:55] Scaling data with sdall ...
INFO  [2024-07-18 15:39:56] Calculating LMM coefficients
INFO  [2024-07-18 15:39:56] Reducing the number of dimensions with PCA
INFO  [2024-07-18 15:39:57] Keeping 36 components from initial PCA, explaining 95.31 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-07-18 15:39:57] -> Finished the reduction of dimensions!
WARN  [2024-07-18 15:39:57] Keeping 20 of 36 components. Change `max_PC` if necessary.
INFO  [2024-07-18 15:39:58] Starting validation: bootstrap
INFO  [2024-07-18 15:39:58] - Run 1 of 100
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INFO  [2024-07-18 15:46:47] Calculating percentiles for score and loading
INFO  [2024-07-18 15:47:13] ==== ALASCA has finished ====
INFO  [2024-07-18 15:47:13] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
INFO  [2024-07-18 15:47:43] 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 15:47:45] 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 15:47:48] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-07-18 15:47:48] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:47:50] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-07-18 15:47:50] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:47:56] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-07-18 15:47:56] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:47:58] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-07-18 15:47:58] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:47:59] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-07-18 15:47:59] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:00] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-07-18 15:48:00] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:01] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-07-18 15:48:01] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:04] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-07-18 15:48:04] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:07] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-07-18 15:48:07] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:16] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-07-18 15:48:16] Showing 10 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:19] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-07-18 15:48:19] Showing 10 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:23] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-07-18 15:48:23] Showing 10 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:27] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-07-18 15:48:27] Showing 10 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:31] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-07-18 15:48:31] Showing 10 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:36] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-07-18 15:48:36] Showing 10 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-07-18 15:48:40] Scores for effect number 1 and principal component(s) 6
INFO  [2024-07-18 15:48:46] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-07-18 15:48:46] 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 15:48:50] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-07-18 15:48:50] 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 15:48:54] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-07-18 15:48:54] 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 15:48:58] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-07-18 15:48:58] 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 15:49:00] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-07-18 15:49:00] 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 15:49:05] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-07-18 15:49:05] 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 15:49:08] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-07-18 15:49:08] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-07-18 15:49:10] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-07-18 15:49:10] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-07-18 15:49:11] Loadings for effect number 1 and principal component(s) 1
INFO  [2024-07-18 15:49:11] Loadings for effect number 1 and principal component(s) 2
INFO  [2024-07-18 15:49:11] Loadings for effect number 1 and principal component(s) 3
INFO  [2024-07-18 15:49:11] Loadings for effect number 1 and principal component(s) 4