INFO  [2024-03-07 20:13:43] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-03-07 20:13:43] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-03-07 20:13:43] Will use linear mixed models!
INFO  [2024-03-07 20:13:43] Will use Rfast!
WARN  [2024-03-07 20:13:43] Converting IDs to integer values
WARN  [2024-03-07 20:13:43] The `fold` column is used for stratification
WARN  [2024-03-07 20:13:43] Converting `character` columns to factors
INFO  [2024-03-07 20:13:43] Scaling data with sdall ...
INFO  [2024-03-07 20:13:44] Calculating LMM coefficients
INFO  [2024-03-07 20:13:44] Reducing the number of dimensions with PCA
INFO  [2024-03-07 20:13:45] Keeping 36 components from initial PCA, explaining 95.31 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-03-07 20:13:45] -> Finished the reduction of dimensions!
WARN  [2024-03-07 20:13:45] Keeping 20 of 36 components. Change `max_PC` if necessary.
INFO  [2024-03-07 20:13:46] Starting validation: bootstrap
INFO  [2024-03-07 20:13:46] - Run 1 of 100
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INFO  [2024-03-07 20:20:07] Calculating percentiles for score and loading
INFO  [2024-03-07 20:20:31] ==== ALASCA has finished ====
INFO  [2024-03-07 20:20:31] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
INFO  [2024-03-07 20:20:31] 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 20:20:31] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-07 20:20:32] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:20:32] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-03-07 20:20:32] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:20:33] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-07 20:20:33] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:20:34] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-03-07 20:20:34] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:20:35] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 20:20:35] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:20:36] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 20:20:36] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:20:37] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 20:20:37] 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 20:20:39] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-07 20:20:39] 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 20:20:40] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-07 20:20:40] 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 20:20:41] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-07 20:20:41] 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 20:20:42] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 20:20:42] 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 20:20:43] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 20:20:43] 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 20:20:45] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-03-07 20:20:45] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-03-08 07:43:29] Scores for effect number 1 and principal component(s) 1
INFO  [2024-03-08 07:45:19] Scores for effect number 1 and principal component(s) 1
INFO  [2024-03-08 07:45:29] Scores for effect number 1 and principal component(s) 6
INFO  [2024-03-08 07:45:43] Scores for effect number 1 and principal component(s) 5
INFO  [2024-03-08 07:45:46] Scores for effect number 1 and principal component(s) 5
INFO  [2024-03-08 07:47:00] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 07:47:00] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:47:37] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-08 07:47:37] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:47:53] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 07:47:53] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:48:01] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-08 07:48:01] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC6). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:56:19] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-08 07:56:19] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:56:37] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-03-08 07:56:37] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:56:55] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-08 07:56:55] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:57:05] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-03-08 07:57:05] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:57:20] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-08 07:57:20] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:57:33] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 07:57:33] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:58:31] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:58:31] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:58:50] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-08 07:58:50] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC2). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:59:04] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-08 07:59:04] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC3). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:59:18] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-08 07:59:18] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC3). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:59:27] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-08 07:59:27] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC4). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:59:47] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-08 07:59:47] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC5). Use `variable` to specify variables to plot
INFO  [2024-03-08 08:00:07] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-08 08:00:07] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC6). Use `variable` to specify variables to plot
INFO  [2024-03-08 08:35:25] Loadings for effect number 1 and principal component(s) 1
INFO  [2024-03-08 08:35:29] Loadings for effect number 1 and principal component(s) 2
INFO  [2024-03-08 08:35:30] Loadings for effect number 1 and principal component(s) 3
INFO  [2024-03-08 08:35:33] Loadings for effect number 1 and principal component(s) 4
INFO  [2024-03-08 08:36:16] Loadings for effect number 1 and principal component(s) 1
INFO  [2024-03-08 08:36:16] Loadings for effect number 1 and principal component(s) 2
INFO  [2024-03-08 08:36:16] Loadings for effect number 1 and principal component(s) 3
INFO  [2024-03-08 08:36:16] Loadings for effect number 1 and principal component(s) 4
INFO  [2024-03-08 09:55:49] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-08 09:55:49] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 13:35:26] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-08 13:35:26] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 13:35:35] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 13:35:35] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 13:35:50] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-08 13:35:50] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 13:35:56] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 13:35:56] Showing 20 of 12641 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 20:47:58] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-08 20:47:58] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC5). Use `variable` to specify variables to plot