INFO  [2024-03-08 17:15:55] Initializing ALASCA (v1.0.15, 2024-02-07)
WARN  [2024-03-08 17:15:55] Guessing effects: `fold+fold:treatment+treatment`
INFO  [2024-03-08 17:15:55] Will use linear mixed models!
INFO  [2024-03-08 17:15:55] Will use Rfast!
WARN  [2024-03-08 17:15:55] Converting IDs to integer values
WARN  [2024-03-08 17:15:55] The `fold` column is used for stratification
WARN  [2024-03-08 17:15:55] Converting `character` columns to factors
INFO  [2024-03-08 17:15:56] Scaling data with sdall ...
INFO  [2024-03-08 17:15:56] Calculating LMM coefficients
INFO  [2024-03-08 17:15:56] Reducing the number of dimensions with PCA
INFO  [2024-03-08 17:15:57] Keeping 46 components from initial PCA, explaining 95.24 % of variation. The limit can be changed with `reduce_dimensions.limit`
INFO  [2024-03-08 17:15:57] -> Finished the reduction of dimensions!
WARN  [2024-03-08 17:15:57] Keeping 20 of 46 components. Change `max_PC` if necessary.
INFO  [2024-03-08 17:15:58] Starting validation: bootstrap
INFO  [2024-03-08 17:15:59] - Run 1 of 100
INFO  [2024-03-08 17:16:03] --- Used 4.79 seconds. Est. time remaining: 476.65 seconds
INFO  [2024-03-08 17:16:03] - Run 2 of 100
INFO  [2024-03-08 17:16:07] --- Used 4.06 seconds. Est. time remaining: 435.04 seconds
INFO  [2024-03-08 17:16:07] - Run 3 of 100
INFO  [2024-03-08 17:16:11] --- Used 4.09 seconds. Est. time remaining: 419.4 seconds
INFO  [2024-03-08 17:16:11] - Run 4 of 100
INFO  [2024-03-08 17:16:15] --- Used 3.99 seconds. Est. time remaining: 407.13 seconds
INFO  [2024-03-08 17:16:15] - Run 5 of 100
INFO  [2024-03-08 17:16:19] --- Used 3.98 seconds. Est. time remaining: 398.02 seconds
INFO  [2024-03-08 17:16:19] - Run 6 of 100
INFO  [2024-03-08 17:16:23] --- Used 3.95 seconds. Est. time remaining: 390.07 seconds
INFO  [2024-03-08 17:16:23] - Run 7 of 100
INFO  [2024-03-08 17:16:28] --- Used 4.15 seconds. Est. time remaining: 385.98 seconds
INFO  [2024-03-08 17:16:28] - Run 8 of 100
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INFO  [2024-03-08 17:16:32] - Run 9 of 100
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INFO  [2024-03-08 17:16:36] - Run 10 of 100
INFO  [2024-03-08 17:16:40] --- Used 4.05 seconds. Est. time remaining: 371.46 seconds
INFO  [2024-03-08 17:16:40] - Run 11 of 100
INFO  [2024-03-08 17:16:44] --- Used 4.03 seconds. Est. time remaining: 366.57 seconds
INFO  [2024-03-08 17:16:44] - Run 12 of 100
INFO  [2024-03-08 17:16:48] --- Used 4.16 seconds. Est. time remaining: 362.74 seconds
INFO  [2024-03-08 17:16:48] - Run 13 of 100
INFO  [2024-03-08 17:16:52] --- Used 4.09 seconds. Est. time remaining: 358.43 seconds
INFO  [2024-03-08 17:16:52] - Run 14 of 100
INFO  [2024-03-08 17:16:56] --- Used 3.97 seconds. Est. time remaining: 353.38 seconds
INFO  [2024-03-08 17:16:56] - Run 15 of 100
INFO  [2024-03-08 17:17:00] --- Used 4.06 seconds. Est. time remaining: 349.02 seconds
INFO  [2024-03-08 17:17:00] - Run 16 of 100
INFO  [2024-03-08 17:17:04] --- Used 4.08 seconds. Est. time remaining: 344.78 seconds
INFO  [2024-03-08 17:17:04] - Run 17 of 100
INFO  [2024-03-08 17:17:08] --- Used 4.09 seconds. Est. time remaining: 340.58 seconds
INFO  [2024-03-08 17:17:08] - Run 18 of 100
INFO  [2024-03-08 17:17:12] --- Used 4.19 seconds. Est. time remaining: 336.86 seconds
INFO  [2024-03-08 17:17:12] - Run 19 of 100
INFO  [2024-03-08 17:17:17] --- Used 4.21 seconds. Est. time remaining: 333.21 seconds
INFO  [2024-03-08 17:17:17] - Run 20 of 100
INFO  [2024-03-08 17:17:21] --- Used 4.18 seconds. Est. time remaining: 329.36 seconds
INFO  [2024-03-08 17:17:21] - Run 21 of 100
INFO  [2024-03-08 17:17:25] --- Used 4.09 seconds. Est. time remaining: 325.14 seconds
INFO  [2024-03-08 17:17:25] - Run 22 of 100
INFO  [2024-03-08 17:17:29] --- Used 4.17 seconds. Est. time remaining: 321.21 seconds
INFO  [2024-03-08 17:17:29] - Run 23 of 100
INFO  [2024-03-08 17:17:33] --- Used 4.25 seconds. Est. time remaining: 317.53 seconds
INFO  [2024-03-08 17:17:33] - Run 24 of 100
INFO  [2024-03-08 17:17:38] --- Used 4.18 seconds. Est. time remaining: 313.6 seconds
INFO  [2024-03-08 17:17:38] - Run 25 of 100
INFO  [2024-03-08 17:17:42] --- Used 4.21 seconds. Est. time remaining: 309.73 seconds
INFO  [2024-03-08 17:17:42] - Run 26 of 100
INFO  [2024-03-08 17:17:46] --- Used 4.49 seconds. Est. time remaining: 306.63 seconds
INFO  [2024-03-08 17:17:46] - Run 27 of 100
INFO  [2024-03-08 17:17:51] --- Used 4.8 seconds. Est. time remaining: 304.27 seconds
INFO  [2024-03-08 17:17:51] - Run 28 of 100
INFO  [2024-03-08 17:17:55] --- Used 3.97 seconds. Est. time remaining: 299.59 seconds
INFO  [2024-03-08 17:17:55] - Run 29 of 100
INFO  [2024-03-08 17:17:59] --- Used 3.99 seconds. Est. time remaining: 295.01 seconds
INFO  [2024-03-08 17:17:59] - Run 30 of 100
INFO  [2024-03-08 17:18:03] --- Used 3.98 seconds. Est. time remaining: 290.43 seconds
INFO  [2024-03-08 17:18:03] - Run 31 of 100
INFO  [2024-03-08 17:18:07] --- Used 4.07 seconds. Est. time remaining: 286.11 seconds
INFO  [2024-03-08 17:18:07] - Run 32 of 100
INFO  [2024-03-08 17:18:11] --- Used 4.16 seconds. Est. time remaining: 282.01 seconds
INFO  [2024-03-08 17:18:11] - Run 33 of 100
INFO  [2024-03-08 17:18:15] --- Used 4.27 seconds. Est. time remaining: 278.12 seconds
INFO  [2024-03-08 17:18:15] - Run 34 of 100
INFO  [2024-03-08 17:18:20] --- Used 4.25 seconds. Est. time remaining: 274.16 seconds
INFO  [2024-03-08 17:18:20] - Run 35 of 100
INFO  [2024-03-08 17:18:24] --- Used 4.28 seconds. Est. time remaining: 270.25 seconds
INFO  [2024-03-08 17:18:24] - Run 36 of 100
INFO  [2024-03-08 17:18:28] --- Used 4.05 seconds. Est. time remaining: 265.89 seconds
INFO  [2024-03-08 17:18:28] - Run 37 of 100
INFO  [2024-03-08 17:18:32] --- Used 4.03 seconds. Est. time remaining: 261.53 seconds
INFO  [2024-03-08 17:18:32] - Run 38 of 100
INFO  [2024-03-08 17:18:36] --- Used 4.11 seconds. Est. time remaining: 257.31 seconds
INFO  [2024-03-08 17:18:36] - Run 39 of 100
INFO  [2024-03-08 17:18:40] --- Used 4.1 seconds. Est. time remaining: 253.08 seconds
INFO  [2024-03-08 17:18:40] - Run 40 of 100
INFO  [2024-03-08 17:18:45] --- Used 4.79 seconds. Est. time remaining: 249.9 seconds
INFO  [2024-03-08 17:18:45] - Run 41 of 100
INFO  [2024-03-08 17:18:49] --- Used 4.14 seconds. Est. time remaining: 245.7 seconds
INFO  [2024-03-08 17:18:49] - Run 42 of 100
INFO  [2024-03-08 17:18:53] --- Used 4.11 seconds. Est. time remaining: 241.46 seconds
INFO  [2024-03-08 17:18:53] - Run 43 of 100
INFO  [2024-03-08 17:18:58] --- Used 4.26 seconds. Est. time remaining: 237.43 seconds
INFO  [2024-03-08 17:18:58] - Run 44 of 100
INFO  [2024-03-08 17:19:02] --- Used 4.16 seconds. Est. time remaining: 233.25 seconds
INFO  [2024-03-08 17:19:02] - Run 45 of 100
INFO  [2024-03-08 17:19:06] --- Used 4.19 seconds. Est. time remaining: 229.12 seconds
INFO  [2024-03-08 17:19:06] - Run 46 of 100
INFO  [2024-03-08 17:19:10] --- Used 4.07 seconds. Est. time remaining: 224.84 seconds
INFO  [2024-03-08 17:19:10] - Run 47 of 100
INFO  [2024-03-08 17:19:15] --- Used 4.77 seconds. Est. time remaining: 221.36 seconds
INFO  [2024-03-08 17:19:15] - Run 48 of 100
INFO  [2024-03-08 17:19:19] --- Used 4.07 seconds. Est. time remaining: 217.08 seconds
INFO  [2024-03-08 17:19:19] - Run 49 of 100
INFO  [2024-03-08 17:19:24] --- Used 4.72 seconds. Est. time remaining: 213.47 seconds
INFO  [2024-03-08 17:19:24] - Run 50 of 100
INFO  [2024-03-08 17:19:28] --- Used 4.04 seconds. Est. time remaining: 209.14 seconds
INFO  [2024-03-08 17:19:28] - Run 51 of 100
INFO  [2024-03-08 17:19:32] --- Used 4.13 seconds. Est. time remaining: 204.9 seconds
INFO  [2024-03-08 17:19:32] - Run 52 of 100
INFO  [2024-03-08 17:19:37] --- Used 4.78 seconds. Est. time remaining: 201.28 seconds
INFO  [2024-03-08 17:19:37] - Run 53 of 100
INFO  [2024-03-08 17:19:41] --- Used 4.01 seconds. Est. time remaining: 196.93 seconds
INFO  [2024-03-08 17:19:41] - Run 54 of 100
INFO  [2024-03-08 17:19:45] --- Used 4.68 seconds. Est. time remaining: 193.15 seconds
INFO  [2024-03-08 17:19:45] - Run 55 of 100
INFO  [2024-03-08 17:19:50] --- Used 4.74 seconds. Est. time remaining: 189.39 seconds
INFO  [2024-03-08 17:19:50] - Run 56 of 100
INFO  [2024-03-08 17:19:54] --- Used 4.21 seconds. Est. time remaining: 185.19 seconds
INFO  [2024-03-08 17:19:54] - Run 57 of 100
INFO  [2024-03-08 17:19:58] --- Used 4.14 seconds. Est. time remaining: 180.93 seconds
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INFO  [2024-03-08 17:20:07] - Run 60 of 100
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INFO  [2024-03-08 17:20:36] --- Used 4.09 seconds. Est. time remaining: 142.93 seconds
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INFO  [2024-03-08 17:20:49] --- Used 4.18 seconds. Est. time remaining: 130.49 seconds
INFO  [2024-03-08 17:20:49] - Run 70 of 100
INFO  [2024-03-08 17:20:53] --- Used 4.24 seconds. Est. time remaining: 126.29 seconds
INFO  [2024-03-08 17:20:53] - Run 71 of 100
INFO  [2024-03-08 17:20:57] --- Used 4.22 seconds. Est. time remaining: 122.09 seconds
INFO  [2024-03-08 17:20:57] - Run 72 of 100
INFO  [2024-03-08 17:21:02] --- Used 4.79 seconds. Est. time remaining: 118.1 seconds
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INFO  [2024-03-08 17:21:06] --- Used 4.21 seconds. Est. time remaining: 113.88 seconds
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INFO  [2024-03-08 17:21:11] --- Used 4.27 seconds. Est. time remaining: 109.68 seconds
INFO  [2024-03-08 17:21:11] - Run 75 of 100
INFO  [2024-03-08 17:21:15] --- Used 4.15 seconds. Est. time remaining: 105.44 seconds
INFO  [2024-03-08 17:21:15] - Run 76 of 100
INFO  [2024-03-08 17:21:20] --- Used 4.76 seconds. Est. time remaining: 101.4 seconds
INFO  [2024-03-08 17:21:20] - Run 77 of 100
INFO  [2024-03-08 17:21:24] --- Used 4.11 seconds. Est. time remaining: 97.14 seconds
INFO  [2024-03-08 17:21:24] - Run 78 of 100
INFO  [2024-03-08 17:21:28] --- Used 4.02 seconds. Est. time remaining: 92.85 seconds
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INFO  [2024-03-08 17:21:32] --- Used 4.23 seconds. Est. time remaining: 88.64 seconds
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INFO  [2024-03-08 17:21:36] --- Used 4.13 seconds. Est. time remaining: 84.39 seconds
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INFO  [2024-03-08 17:21:49] --- Used 4.87 seconds. Est. time remaining: 71.87 seconds
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INFO  [2024-03-08 17:21:58] - Run 86 of 100
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INFO  [2024-03-08 17:22:36] - Run 95 of 100
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INFO  [2024-03-08 17:22:41] - Run 96 of 100
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INFO  [2024-03-08 17:22:45] - Run 97 of 100
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INFO  [2024-03-08 17:22:49] - Run 98 of 100
INFO  [2024-03-08 17:22:54] --- Used 4.91 seconds. Est. time remaining: 8.48 seconds
INFO  [2024-03-08 17:22:54] - Run 99 of 100
INFO  [2024-03-08 17:22:58] --- Used 4.2 seconds. Est. time remaining: 4.24 seconds
INFO  [2024-03-08 17:22:58] - Run 100 of 100
INFO  [2024-03-08 17:23:02] --- Used 4.25 seconds. Est. time remaining: 0 seconds
INFO  [2024-03-08 17:23:03] Calculating percentiles for score and loading
INFO  [2024-03-08 17:23:25] ==== ALASCA has finished ====
INFO  [2024-03-08 17:23:25] To visualize the model, try `plot(<object>, effect = 1, component = 1, type = 'effect')`
ERROR [2024-03-08 20:16:47] The effect you wanted to plot does not exist!
INFO  [2024-03-08 20:16:51] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-08 20:16:51] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-09 21:37:50] Effect plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
WARN  [2024-03-09 21:37:50] Showing 20 of 11270 variables. Adjust the number with `n_limit`
INFO  [2024-03-09 21:38:48] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 1.
INFO  [2024-03-09 21:38:48] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC1). Use `variable` to specify variables to plot
INFO  [2024-03-09 21:39:05] Prediction plot. Selected effect (nr 1): `fold+fold:treatment+treatment`. Component: 5.
INFO  [2024-03-09 21:39:05] Selecting the 10 variables with highest/lowest loading on `fold+fold:treatment+treatment` (PC5). Use `variable` to specify variables to plot