INFO  [2024-03-07 20:04:39] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-03-07 20:04:39] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-03-07 20:04:39] Will use linear mixed models!
INFO  [2024-03-07 20:04:39] Will use Rfast!
WARN  [2024-03-07 20:04:39] Converting IDs to integer values
WARN  [2024-03-07 20:04:39] The `fold` column is used for stratification
WARN  [2024-03-07 20:04:39] Converting `character` columns to factors
INFO  [2024-03-07 20:04:40] Scaling data with sdall ...
INFO  [2024-03-07 20:04:40] Calculating LMM coefficients
INFO  [2024-03-07 20:04:40] Reducing the number of dimensions with PCA
INFO  [2024-03-07 20:04:41] Keeping 46 components from initial PCA, explaining 95.24 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-03-07 20:04:41] -> Finished the reduction of dimensions!
WARN  [2024-03-07 20:04:41] Keeping 20 of 46 components. Change `max_PC` if necessary.
INFO  [2024-03-07 20:04:42] Starting validation: bootstrap
INFO  [2024-03-07 20:04:42] - Run 1 of 100
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INFO  [2024-03-07 20:12:00] Calculating percentiles for score and loading
INFO  [2024-03-07 20:12:22] ==== ALASCA has finished ====
INFO  [2024-03-07 20:12:22] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
INFO  [2024-03-07 20:12:22] 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 20:12:23] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-07 20:12:23] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:12:24] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-03-07 20:12:24] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:12:25] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-07 20:12:25] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:12:26] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-03-07 20:12:27] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:12:28] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 20:12:28] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:12:29] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 20:12:29] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 20:12:31] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 20:12:31] 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 20:12:32] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-07 20:12:32] 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 20:12:34] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-07 20:12:34] 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 20:12:35] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-07 20:12:35] 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 20:12:36] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 20:12:36] 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 20:12:37] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 20:12:37] 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 20:12:38] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-03-07 20:12:38] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-03-08 07:49:21] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-08 07:49:21] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:49:32] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-08 07:49:32] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:49:53] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-08 07:49:53] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:50:16] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-03-08 07:50:17] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:50:37] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-08 07:50:37] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:51:00] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-03-08 07:51:00] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:51:19] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-08 07:51:19] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:51:39] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 07:51:39] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 07:52:07] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:52:07] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:52:16] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:52:16] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:52:26] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:52:26] Selecting the 5 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:52:49] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:52:49] Selecting the 6 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-08 07:53:07] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:53:07] 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 07:53:23] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:53:23] 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 07:53:46] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-08 07:53:46] 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 07:53:53] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-08 07:53:53] 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 07:53:57] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-08 07:53:57] 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 07:54:19] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-08 07:54:19] 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 07:54:48] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-08 07:54:48] 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 07:54:50] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-08 07:54:50] 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 07:55:01] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-08 07:55:01] 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 07:55:22] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-08 07:55:22] 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 08:34:18] Loadings for effect number 1 and principal component(s) 1
INFO  [2024-03-08 08:34:21] Loadings for effect number 1 and principal component(s) 2
INFO  [2024-03-08 08:34:24] Loadings for effect number 1 and principal component(s) 3
INFO  [2024-03-08 08:34:25] Loadings for effect number 1 and principal component(s) 4
INFO  [2024-03-08 09:56:14] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-08 09:56:14] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 09:56:23] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 09:56:23] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-08 13:29:57] 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  [2024-03-08 13:30:08] 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  [2024-03-08 13:30:12] 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  [2024-03-08 13:30:39] 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  [2024-03-08 13:35:07] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-08 13:35:07] Showing 20 of 11270 variables. Adjust the number with `n_limit`