INFO  [2024-03-07 16:33:53] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-03-07 16:33:53] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-03-07 16:33:53] Will use linear mixed models!
INFO  [2024-03-07 16:33:53] Will use Rfast!
WARN  [2024-03-07 16:33:53] Converting IDs to integer values
WARN  [2024-03-07 16:33:53] The `fold` column is used for stratification
WARN  [2024-03-07 16:33:54] Converting `character` columns to factors
INFO  [2024-03-07 16:33:54] Scaling data with sdall ...
INFO  [2024-03-07 16:33:55] Calculating LMM coefficients
INFO  [2024-03-07 16:33:55] Reducing the number of dimensions with PCA
INFO  [2024-03-07 16:33:56] Keeping 46 components from initial PCA, explaining 95.24 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-03-07 16:33:56] -> Finished the reduction of dimensions!
WARN  [2024-03-07 16:33:56] Keeping 20 of 46 components. Change `max_PC` if necessary.
INFO  [2024-03-07 16:33:57] Starting validation: bootstrap
INFO  [2024-03-07 16:33:57] - Run 1 of 100
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INFO  [2024-03-07 16:34:56] - Run 14 of 100
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INFO  [2024-03-07 16:35:00] - Run 15 of 100
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INFO  [2024-03-07 16:35:05] - Run 16 of 100
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INFO  [2024-03-07 16:35:22] - Run 20 of 100
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INFO  [2024-03-07 16:41:10] - Run 100 of 100
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INFO  [2024-03-07 16:41:15] Calculating percentiles for score and loading
INFO  [2024-03-07 16:41:38] ==== ALASCA has finished ====
INFO  [2024-03-07 16:41:38] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
INFO  [2024-03-07 16:41:44] 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 16:41:52] 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 16:43:13] Loadings for effect number 1 and principal component(s) 1
INFO  [2024-03-07 16:44:24] 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 16:44:57] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-07 16:44:57] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:45:13] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
WARN  [2024-03-07 16:45:13] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:45:24] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-07 16:45:24] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:45:36] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-07 16:45:36] Showing 200 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:45:40] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
WARN  [2024-03-07 16:45:40] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:45:53] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
WARN  [2024-03-07 16:45:53] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:46:04] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 16:46:04] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:46:16] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 16:46:16] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:46:30] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-07 16:46:30] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:46:37] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 8.
WARN  [2024-03-07 16:46:37] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:46:43] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 9.
WARN  [2024-03-07 16:46:43] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:47:19] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 16:47:19] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:47:37] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 16:47:37] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:47:41] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 16:47:41] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:47:56] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
WARN  [2024-03-07 16:47:56] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:48:02] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 16:48:02] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:48:06] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-07 16:48:06] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:49:51] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 16:49:51] 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 16:50:06] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 16:50:07] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC5). Use `variable` to specify variables to plot
INFO  [2024-03-07 16:50:12] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 16:50:32] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 16:50:36] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 16:50:43] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 16:50:51] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 16:51:32] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 16:51:45] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 16:52:08] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 16:52:08] Selecting the 2 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-07 16:52:14] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 16:52:14] 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 16:52:33] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-07 16:52:33] Showing 10 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:52:42] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
WARN  [2024-03-07 16:52:42] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:52:49] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 16:52:49] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-07 16:52:56] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-07 16:52:56] 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 16:53:17] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 2.
INFO  [2024-03-07 16:53:17] 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 16:53:26] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 3.
INFO  [2024-03-07 16:53:26] 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 16:53:32] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-07 16:53:32] 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 16:53:38] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 16:53:38] 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 16:53:47] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 16:53:47] 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 16:53:53] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
INFO  [2024-03-07 16:53:53] 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 16:54:07] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 7.
INFO  [2024-03-07 16:54:07] 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 16:54:15] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 16:54:15] 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 16:54:31] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 16:54:31] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:55:49] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 16:55:49] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:58:53] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 16:58:53] 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 16:59:03] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 16:59:03] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 16:59:14] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 16:59:14] 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 17:04:38] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-07 17:04:38] 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 17:04:44] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 4.
INFO  [2024-03-07 17:04:44] 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 17:04:47] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
INFO  [2024-03-07 17:04:47] 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 17:05:46] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-03-07 17:05:59] Loadings for effect number 5 and principal component(s) 6
INFO  [2024-03-07 17:06:04] Loadings for effect number 5 and principal component(s) 6
INFO  [2024-03-07 17:06:05] Loadings for effect number 5 and principal component(s) 6
INFO  [2024-03-07 17:06:13] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-03-07 17:06:49] Loadings for effect number 1 and principal component(s) 6
INFO  [2024-03-07 17:06:59] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 6.
WARN  [2024-03-07 17:06:59] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-07 17:07:56] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-03-07 17:08:14] Loadings for effect number 1 and principal component(s) 5
INFO  [2024-03-07 17:08:15] Loadings for effect number 1 and principal component(s) 6