Access method for bru_log objects.
Note: Up to version 2.8.0, bru_log() was a deprecated alias for
bru_log_message(). When running on 2.8.0 or earlier, use bru_log_get()
to access the global log, and cat(fit$bru_iinla$log, sep = "\n") to print a
stored estimation object log.
After version 2.8.0, use bru_log() to access the global log, and
bru_log(fit) to access a stored estimation log.
Usage
bru_log(x = NULL, verbosity = NULL)
# S3 method for class 'character'
bru_log(x, verbosity = NULL)
# S3 method for class 'bru_log'
bru_log(x, verbosity = NULL)
# S3 method for class 'iinla'
bru_log(x, verbosity = NULL)
# S3 method for class 'bru'
bru_log(x, verbosity = NULL)
# S3 method for class 'bru_log'
format(x, ..., timestamp = TRUE, verbosity = FALSE)
# S3 method for class 'bru_log'
print(x, ..., timestamp = TRUE, verbosity = FALSE)
# S3 method for class 'bru_log'
as.character(x, ...)
# S3 method for class 'bru_log'
x[i]
# S3 method for class 'bru_log'
c(...)
# S3 method for class 'bru_log'
length(x)Arguments
- x
An object that is, contains, or can be converted to, a
bru_logobject. IfNULL, refers to the globalinlabrulog.- verbosity
integer value for limiting the highest verbosity level being returned.
- ...
further arguments passed to or from other methods.
- timestamp
If
TRUE, include the timestamp of each message. DefaultTRUE.- i
indices specifying elements to extract. If
character, denotes the sequence between bookmarkiand the next bookmark (or the end of the log ifiis the last bookmark)
Value
bru_log A bru_log object, containing a
character vector of log messages, and potentially a vector of bookmarks.
Methods (by generic)
format(bru_log): Format abru_logobject for printing. IfverbosityisTRUE, include the verbosity level of each message.print(bru_log): Print abru_logobject withcat(x, sep = "\n"). IfverbosityisTRUE, include the verbosity level of each message.as.character(bru_log): Convertbru_logobject to a plaincharactervector[: Extract a subset of abru_logobjectc(bru_log): Concatenate severalbru_logorcharacterobjects into abru_logobject.length(bru_log): Obtain the number of log entries into abru_logobject.
Functions
bru_log(): Extract stored log messages. If non-NULL, theverbosityargument determines the maximum verbosity level of the messages to extract.
See also
Other inlabru log methods:
bru_log_bookmark(),
bru_log_message(),
bru_log_new(),
bru_log_offset(),
bru_log_reset()
Examples
bru_log(verbosity = 2L)
#> 2025-05-20 17:02:19.293311: inlabru loaded
#> 2025-05-20 17:02:19.293854: Clear override options
#> 2025-05-20 17:02:24.325026: bru: Preprocessing
#> 2025-05-20 17:02:24.586822: iinla: Iteration 1 [max:1]
#> 2025-05-20 17:02:25.316015: bru: Preprocessing
#> 2025-05-20 17:02:25.470821: iinla: Iteration 1 [max:1]
#> 2025-05-20 17:02:26.092287: bru: Preprocessing
#> 2025-05-20 17:02:26.249773: iinla: Iteration 1 [max:10]
#> 2025-05-20 17:02:26.807577: iinla: Step rescaling: 27.1% (norm0 = 184.8, norm1 = 228.4, norm01 = 351.8)
#> 2025-05-20 17:02:26.856121: iinla: Iteration 2 [max:10]
#> 2025-05-20 17:02:27.668572: iinla: Step rescaling: 99.5% (norm0 = 227.7, norm1 = 11.96, norm01 = 228.6)
#> 2025-05-20 17:02:27.709174: iinla: Max deviation from previous: 47200% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-05-20 17:02:27.710964: iinla: Iteration 3 [max:10]
#> 2025-05-20 17:02:28.267547: iinla: Step rescaling: 102% (norm0 = 11.95, norm1 = 0.01917, norm01 = 11.95)
#> 2025-05-20 17:02:28.308321: iinla: Max deviation from previous: 555% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-05-20 17:02:28.310061: iinla: Iteration 4 [max:10]
#> 2025-05-20 17:02:28.917312: iinla: Max deviation from previous: 9.69% of SD, and line search is inactive
#> [stop if: <10% and line search inactive]
#> 2025-05-20 17:02:28.918522: iinla: Convergence criterion met.
#> Running final INLA integration step with known theta mode.
#> 2025-05-20 17:02:28.920253: iinla: Iteration 5 [max:10]
#> 2025-05-20 17:02:30.398266: bru: Preprocessing
#> 2025-05-20 17:02:30.507348: iinla: Iteration 1 [max:1]
#> 2025-05-20 17:02:36.85247: bru: Preprocessing
#> 2025-05-20 17:02:37.00406: iinla: Iteration 1 [max:1]
format(bru_log())
#> [1] "2025-05-20 17:02:19.293311: inlabru loaded"
#> [2] "2025-05-20 17:02:19.293854: Clear override options"
#> [3] "2025-05-20 17:02:24.325026: bru: Preprocessing"
#> [4] "2025-05-20 17:02:24.333313: Evaluate component inputs for each observation model"
#> [5] "2025-05-20 17:02:24.334675: input_eval.component_list"
#> [6] "2025-05-20 17:02:24.335974: input_eval.component(x)"
#> [7] "2025-05-20 17:02:24.337468: input_eval.bru_input(x)"
#> [8] "2025-05-20 17:02:24.344736: input_eval.bru_input(x.group)"
#> [9] "2025-05-20 17:02:24.3499: input_eval.bru_input(x.repl)"
#> [10] "2025-05-20 17:02:24.354942: input_eval.component(Intercept)"
#> [11] "2025-05-20 17:02:24.35616: input_eval.bru_input(Intercept)"
#> [12] "2025-05-20 17:02:24.361265: input_eval.bru_input(Intercept.group)"
#> [13] "2025-05-20 17:02:24.367024: input_eval.bru_input(Intercept.repl)"
#> [14] "2025-05-20 17:02:24.484476: iinla: Start"
#> [15] "2025-05-20 17:02:24.485712: iinla: Evaluate component linearisations"
#> [16] "2025-05-20 17:02:24.486982: Linearise components for each observation model"
#> [17] "2025-05-20 17:02:24.488285: Linearise components"
#> [18] "2025-05-20 17:02:24.48949: Linearise component 'x'"
#> [19] "2025-05-20 17:02:24.518736: Linearise component 'Intercept'"
#> [20] "2025-05-20 17:02:24.527955: iinla: Evaluate component simplifications"
#> [21] "2025-05-20 17:02:24.529266: Simplify model components"
#> [22] "2025-05-20 17:02:24.530602: Simplify component 'x'"
#> [23] "2025-05-20 17:02:24.540252: Simplify component 'Intercept'"
#> [24] "2025-05-20 17:02:24.549324: iinla: Evaluate predictor linearisation"
#> [25] "2025-05-20 17:02:24.562361: iinla: Construct inla stack"
#> [26] "2025-05-20 17:02:24.585541: iinla: Model initialisation completed"
#> [27] "2025-05-20 17:02:24.586822: iinla: Iteration 1 [max:1]"
#> [28] "2025-05-20 17:02:25.316015: bru: Preprocessing"
#> [29] "2025-05-20 17:02:25.318591: Evaluate component inputs for each observation model"
#> [30] "2025-05-20 17:02:25.319918: input_eval.component_list"
#> [31] "2025-05-20 17:02:25.321165: input_eval.component(x)"
#> [32] "2025-05-20 17:02:25.322374: input_eval.bru_input(x)"
#> [33] "2025-05-20 17:02:25.330273: input_eval.bru_input(x.group)"
#> [34] "2025-05-20 17:02:25.336064: input_eval.bru_input(x.repl)"
#> [35] "2025-05-20 17:02:25.341216: input_eval.component(Intercept)"
#> [36] "2025-05-20 17:02:25.342437: input_eval.bru_input(Intercept)"
#> [37] "2025-05-20 17:02:25.347337: input_eval.bru_input(Intercept.group)"
#> [38] "2025-05-20 17:02:25.352231: input_eval.bru_input(Intercept.repl)"
#> [39] "2025-05-20 17:02:25.397276: iinla: Start"
#> [40] "2025-05-20 17:02:25.39849: iinla: Evaluate component linearisations"
#> [41] "2025-05-20 17:02:25.399681: Linearise components for each observation model"
#> [42] "2025-05-20 17:02:25.400933: Linearise components"
#> [43] "2025-05-20 17:02:25.402112: Linearise component 'x'"
#> [44] "2025-05-20 17:02:25.420434: Linearise component 'Intercept'"
#> [45] "2025-05-20 17:02:25.429284: iinla: Evaluate component simplifications"
#> [46] "2025-05-20 17:02:25.43051: Simplify model components"
#> [47] "2025-05-20 17:02:25.4318: Simplify component 'x'"
#> [48] "2025-05-20 17:02:25.441248: Simplify component 'Intercept'"
#> [49] "2025-05-20 17:02:25.450445: iinla: Evaluate predictor linearisation"
#> [50] "2025-05-20 17:02:25.456513: iinla: Construct inla stack"
#> [51] "2025-05-20 17:02:25.469536: iinla: Model initialisation completed"
#> [52] "2025-05-20 17:02:25.470821: iinla: Iteration 1 [max:1]"
#> [53] "2025-05-20 17:02:26.092287: bru: Preprocessing"
#> [54] "2025-05-20 17:02:26.094878: Evaluate component inputs for each observation model"
#> [55] "2025-05-20 17:02:26.096175: input_eval.component_list"
#> [56] "2025-05-20 17:02:26.097448: input_eval.component(z)"
#> [57] "2025-05-20 17:02:26.098718: input_eval.bru_input(z)"
#> [58] "2025-05-20 17:02:26.106634: input_eval.bru_input(z.group)"
#> [59] "2025-05-20 17:02:26.1123: input_eval.bru_input(z.repl)"
#> [60] "2025-05-20 17:02:26.117485: input_eval.component(Intercept)"
#> [61] "2025-05-20 17:02:26.118751: input_eval.bru_input(Intercept)"
#> [62] "2025-05-20 17:02:26.123806: input_eval.bru_input(Intercept.group)"
#> [63] "2025-05-20 17:02:26.128738: input_eval.bru_input(Intercept.repl)"
#> [64] "2025-05-20 17:02:26.175679: iinla: Start"
#> [65] "2025-05-20 17:02:26.176922: iinla: Evaluate component linearisations"
#> [66] "2025-05-20 17:02:26.178146: Linearise components for each observation model"
#> [67] "2025-05-20 17:02:26.179438: Linearise components"
#> [68] "2025-05-20 17:02:26.180661: Linearise component 'z'"
#> [69] "2025-05-20 17:02:26.190317: Linearise component 'Intercept'"
#> [70] "2025-05-20 17:02:26.199591: iinla: Evaluate component simplifications"
#> [71] "2025-05-20 17:02:26.200885: Simplify model components"
#> [72] "2025-05-20 17:02:26.202173: Simplify component 'z'"
#> [73] "2025-05-20 17:02:26.211407: Simplify component 'Intercept'"
#> [74] "2025-05-20 17:02:26.225837: iinla: Evaluate predictor linearisation"
#> [75] "2025-05-20 17:02:26.22836: Linearise with respect to component 'z'"
#> [76] "2025-05-20 17:02:26.232791: Linearise with respect to component 'Intercept'"
#> [77] "2025-05-20 17:02:26.23595: iinla: Construct inla stack"
#> [78] "2025-05-20 17:02:26.248505: iinla: Model initialisation completed"
#> [79] "2025-05-20 17:02:26.249773: iinla: Iteration 1 [max:10]"
#> [80] "2025-05-20 17:02:26.800024: iinla: Step rescaling: 61.8%, Contract (norm0 = 2076, norm1 = 1910, norm01 = 351.8)"
#> [81] "2025-05-20 17:02:26.802144: iinla: Step rescaling: 38.2%, Contract (norm0 = 413.9, norm1 = 304.9, norm01 = 351.8)"
#> [82] "2025-05-20 17:02:26.805067: iinla: Step rescaling: 27.06%, Approx Optimisation (norm0 = 184.8, norm1 = 228.4, norm01 = 351.8)"
#> [83] "2025-05-20 17:02:26.806365: iinla: |lin1-lin0| = 351.8\n <eta-lin1,delta>/|delta| = -201.5\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 107.4"
#> [84] "2025-05-20 17:02:26.807577: iinla: Step rescaling: 27.1% (norm0 = 184.8, norm1 = 228.4, norm01 = 351.8)"
#> [85] "2025-05-20 17:02:26.809282: iinla: Evaluate component linearisations"
#> [86] "2025-05-20 17:02:26.810467: Linearise components for each observation model"
#> [87] "2025-05-20 17:02:26.811822: Linearise components"
#> [88] "2025-05-20 17:02:26.813039: Linearise component 'z'"
#> [89] "2025-05-20 17:02:26.82843: Linearise component 'Intercept'"
#> [90] "2025-05-20 17:02:26.837419: iinla: Evaluate predictor linearisation"
#> [91] "2025-05-20 17:02:26.839484: Linearise with respect to component 'z'"
#> [92] "2025-05-20 17:02:26.842864: Linearise with respect to component 'Intercept'"
#> [93] "2025-05-20 17:02:26.856121: iinla: Iteration 2 [max:10]"
#> [94] "2025-05-20 17:02:27.666028: iinla: Step rescaling: 99.54%, Approx Optimisation (norm0 = 227.7, norm1 = 11.96, norm01 = 228.6)"
#> [95] "2025-05-20 17:02:27.667361: iinla: |lin1-lin0| = 228.6\n <eta-lin1,delta>/|delta| = -1.246\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 11.89"
#> [96] "2025-05-20 17:02:27.668572: iinla: Step rescaling: 99.5% (norm0 = 227.7, norm1 = 11.96, norm01 = 228.6)"
#> [97] "2025-05-20 17:02:27.67027: iinla: Evaluate component linearisations"
#> [98] "2025-05-20 17:02:27.671407: Linearise components for each observation model"
#> [99] "2025-05-20 17:02:27.672591: Linearise components"
#> [100] "2025-05-20 17:02:27.673749: Linearise component 'z'"
#> [101] "2025-05-20 17:02:27.682701: Linearise component 'Intercept'"
#> [102] "2025-05-20 17:02:27.691376: iinla: Evaluate predictor linearisation"
#> [103] "2025-05-20 17:02:27.693311: Linearise with respect to component 'z'"
#> [104] "2025-05-20 17:02:27.696679: Linearise with respect to component 'Intercept'"
#> [105] "2025-05-20 17:02:27.709174: iinla: Max deviation from previous: 47200% of SD, and line search is active\n [stop if: <10% and line search inactive]"
#> [106] "2025-05-20 17:02:27.710964: iinla: Iteration 3 [max:10]"
#> [107] "2025-05-20 17:02:28.25452: iinla: Step rescaling: 162%, Expand (norm0 = 18.8, norm1 = 6.846, norm01 = 11.95)"
#> [108] "2025-05-20 17:02:28.262503: iinla: Step rescaling: 100%, Overstep (norm0 = 11.74, norm1 = 0.2094, norm01 = 11.95)"
#> [109] "2025-05-20 17:02:28.265148: iinla: Step rescaling: 101.8%, Approx Optimisation (norm0 = 11.95, norm1 = 0.01917, norm01 = 11.95)"
#> [110] "2025-05-20 17:02:28.266382: iinla: |lin1-lin0| = 11.95\n <eta-lin1,delta>/|delta| = -4e-05\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 0.01917"
#> [111] "2025-05-20 17:02:28.267547: iinla: Step rescaling: 102% (norm0 = 11.95, norm1 = 0.01917, norm01 = 11.95)"
#> [112] "2025-05-20 17:02:28.269199: iinla: Evaluate component linearisations"
#> [113] "2025-05-20 17:02:28.270332: Linearise components for each observation model"
#> [114] "2025-05-20 17:02:28.271527: Linearise components"
#> [115] "2025-05-20 17:02:28.272676: Linearise component 'z'"
#> [116] "2025-05-20 17:02:28.281698: Linearise component 'Intercept'"
#> [117] "2025-05-20 17:02:28.290421: iinla: Evaluate predictor linearisation"
#> [118] "2025-05-20 17:02:28.292449: Linearise with respect to component 'z'"
#> [119] "2025-05-20 17:02:28.295805: Linearise with respect to component 'Intercept'"
#> [120] "2025-05-20 17:02:28.308321: iinla: Max deviation from previous: 555% of SD, and line search is active\n [stop if: <10% and line search inactive]"
#> [121] "2025-05-20 17:02:28.310061: iinla: Iteration 4 [max:10]"
#> [122] "2025-05-20 17:02:28.86514: iinla: Step rescaling: 162%, Expand (norm0 = 0.03103, norm1 = 0.01185, norm01 = 0.01917)"
#> [123] "2025-05-20 17:02:28.867123: iinla: Step rescaling: 100%, Overstep (norm0 = 0.01917, norm1 = 1.444e-07, norm01 = 0.01917)"
#> [124] "2025-05-20 17:02:28.86982: iinla: Step rescaling: 100%, Approx Optimisation (norm0 = 0.01917, norm1 = 1.438e-07, norm01 = 0.01917)"
#> [125] "2025-05-20 17:02:28.87102: iinla: |lin1-lin0| = 0.01917\n <eta-lin1,delta>/|delta| = 2.759e-10\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 1.438e-07"
#> [126] "2025-05-20 17:02:28.872694: iinla: Evaluate component linearisations"
#> [127] "2025-05-20 17:02:28.87383: Linearise components for each observation model"
#> [128] "2025-05-20 17:02:28.875011: Linearise components"
#> [129] "2025-05-20 17:02:28.876128: Linearise component 'z'"
#> [130] "2025-05-20 17:02:28.885798: Linearise component 'Intercept'"
#> [131] "2025-05-20 17:02:28.899522: iinla: Evaluate predictor linearisation"
#> [132] "2025-05-20 17:02:28.901507: Linearise with respect to component 'z'"
#> [133] "2025-05-20 17:02:28.904892: Linearise with respect to component 'Intercept'"
#> [134] "2025-05-20 17:02:28.917312: iinla: Max deviation from previous: 9.69% of SD, and line search is inactive\n [stop if: <10% and line search inactive]"
#> [135] "2025-05-20 17:02:28.918522: iinla: Convergence criterion met.\n Running final INLA integration step with known theta mode."
#> [136] "2025-05-20 17:02:28.920253: iinla: Iteration 5 [max:10]"
#> [137] "2025-05-20 17:02:30.398266: bru: Preprocessing"
#> [138] "2025-05-20 17:02:30.403213: Evaluate component inputs for each observation model"
#> [139] "2025-05-20 17:02:30.404474: input_eval.component_list"
#> [140] "2025-05-20 17:02:30.405703: input_eval.component(field)"
#> [141] "2025-05-20 17:02:30.406892: input_eval.bru_input(field)"
#> [142] "2025-05-20 17:02:30.415253: input_eval.bru_input(field.group)"
#> [143] "2025-05-20 17:02:30.422039: input_eval.bru_input(field.repl)"
#> [144] "2025-05-20 17:02:30.450392: iinla: Start"
#> [145] "2025-05-20 17:02:30.451613: iinla: Evaluate component linearisations"
#> [146] "2025-05-20 17:02:30.452853: Linearise components for each observation model"
#> [147] "2025-05-20 17:02:30.454098: Linearise components"
#> [148] "2025-05-20 17:02:30.455299: Linearise component 'field'"
#> [149] "2025-05-20 17:02:30.479026: iinla: Evaluate component simplifications"
#> [150] "2025-05-20 17:02:30.480313: Simplify model components"
#> [151] "2025-05-20 17:02:30.481566: Simplify component 'field'"
#> [152] "2025-05-20 17:02:30.492422: iinla: Evaluate predictor linearisation"
#> [153] "2025-05-20 17:02:30.495399: iinla: Construct inla stack"
#> [154] "2025-05-20 17:02:30.506115: iinla: Model initialisation completed"
#> [155] "2025-05-20 17:02:30.507348: iinla: Iteration 1 [max:1]"
#> [156] "2025-05-20 17:02:33.184556: input_eval.component_list"
#> [157] "2025-05-20 17:02:36.85247: bru: Preprocessing"
#> [158] "2025-05-20 17:02:36.865775: Evaluate component inputs for each observation model"
#> [159] "2025-05-20 17:02:36.867008: input_eval.component_list"
#> [160] "2025-05-20 17:02:36.868182: input_eval.component(x)"
#> [161] "2025-05-20 17:02:36.869362: input_eval.bru_input(x)"
#> [162] "2025-05-20 17:02:36.875779: input_eval.bru_input(x.group)"
#> [163] "2025-05-20 17:02:36.880942: input_eval.bru_input(x.repl)"
#> [164] "2025-05-20 17:02:36.886088: input_eval.component_list"
#> [165] "2025-05-20 17:02:36.887257: input_eval.component(x)"
#> [166] "2025-05-20 17:02:36.888412: input_eval.bru_input(x)"
#> [167] "2025-05-20 17:02:36.893656: input_eval.bru_input(x.group)"
#> [168] "2025-05-20 17:02:36.898849: input_eval.bru_input(x.repl)"
#> [169] "2025-05-20 17:02:36.925966: iinla: Start"
#> [170] "2025-05-20 17:02:36.927164: iinla: Evaluate component linearisations"
#> [171] "2025-05-20 17:02:36.92834: Linearise components for each observation model"
#> [172] "2025-05-20 17:02:36.929574: Linearise components"
#> [173] "2025-05-20 17:02:36.930785: Linearise component 'x'"
#> [174] "2025-05-20 17:02:36.942208: Linearise components"
#> [175] "2025-05-20 17:02:36.943432: Linearise component 'x'"
#> [176] "2025-05-20 17:02:36.952892: iinla: Evaluate component simplifications"
#> [177] "2025-05-20 17:02:36.954095: Simplify model components"
#> [178] "2025-05-20 17:02:36.955339: Simplify component 'x'"
#> [179] "2025-05-20 17:02:36.964736: Simplify component 'x'"
#> [180] "2025-05-20 17:02:36.974164: iinla: Evaluate predictor linearisation"
#> [181] "2025-05-20 17:02:36.981042: iinla: Construct inla stack"
#> [182] "2025-05-20 17:02:37.002827: iinla: Model initialisation completed"
#> [183] "2025-05-20 17:02:37.00406: iinla: Iteration 1 [max:1]"
bru_log(verbosity = 2L)
#> 2025-05-20 17:02:19.293311: inlabru loaded
#> 2025-05-20 17:02:19.293854: Clear override options
#> 2025-05-20 17:02:24.325026: bru: Preprocessing
#> 2025-05-20 17:02:24.586822: iinla: Iteration 1 [max:1]
#> 2025-05-20 17:02:25.316015: bru: Preprocessing
#> 2025-05-20 17:02:25.470821: iinla: Iteration 1 [max:1]
#> 2025-05-20 17:02:26.092287: bru: Preprocessing
#> 2025-05-20 17:02:26.249773: iinla: Iteration 1 [max:10]
#> 2025-05-20 17:02:26.807577: iinla: Step rescaling: 27.1% (norm0 = 184.8, norm1 = 228.4, norm01 = 351.8)
#> 2025-05-20 17:02:26.856121: iinla: Iteration 2 [max:10]
#> 2025-05-20 17:02:27.668572: iinla: Step rescaling: 99.5% (norm0 = 227.7, norm1 = 11.96, norm01 = 228.6)
#> 2025-05-20 17:02:27.709174: iinla: Max deviation from previous: 47200% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-05-20 17:02:27.710964: iinla: Iteration 3 [max:10]
#> 2025-05-20 17:02:28.267547: iinla: Step rescaling: 102% (norm0 = 11.95, norm1 = 0.01917, norm01 = 11.95)
#> 2025-05-20 17:02:28.308321: iinla: Max deviation from previous: 555% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-05-20 17:02:28.310061: iinla: Iteration 4 [max:10]
#> 2025-05-20 17:02:28.917312: iinla: Max deviation from previous: 9.69% of SD, and line search is inactive
#> [stop if: <10% and line search inactive]
#> 2025-05-20 17:02:28.918522: iinla: Convergence criterion met.
#> Running final INLA integration step with known theta mode.
#> 2025-05-20 17:02:28.920253: iinla: Iteration 5 [max:10]
#> 2025-05-20 17:02:30.398266: bru: Preprocessing
#> 2025-05-20 17:02:30.507348: iinla: Iteration 1 [max:1]
#> 2025-05-20 17:02:36.85247: bru: Preprocessing
#> 2025-05-20 17:02:37.00406: iinla: Iteration 1 [max:1]
print(bru_log(), timestamp = TRUE, verbosity = TRUE)
#> 2025-05-20 17:02:19.293311: inlabru loaded (level 1)
#> 2025-05-20 17:02:19.293854: Clear override options (level 1)
#> 2025-05-20 17:02:24.325026: bru: Preprocessing (level 1)
#> 2025-05-20 17:02:24.333313: Evaluate component inputs for each observation model (level 3)
#> 2025-05-20 17:02:24.334675: input_eval.component_list (level 4)
#> 2025-05-20 17:02:24.335974: input_eval.component(x) (level 4)
#> 2025-05-20 17:02:24.337468: input_eval.bru_input(x) (level 5)
#> 2025-05-20 17:02:24.344736: input_eval.bru_input(x.group) (level 5)
#> 2025-05-20 17:02:24.3499: input_eval.bru_input(x.repl) (level 5)
#> 2025-05-20 17:02:24.354942: input_eval.component(Intercept) (level 4)
#> 2025-05-20 17:02:24.35616: input_eval.bru_input(Intercept) (level 5)
#> 2025-05-20 17:02:24.361265: input_eval.bru_input(Intercept.group) (level 5)
#> 2025-05-20 17:02:24.367024: input_eval.bru_input(Intercept.repl) (level 5)
#> 2025-05-20 17:02:24.484476: iinla: Start (level 3)
#> 2025-05-20 17:02:24.485712: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:24.486982: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:24.488285: Linearise components (level 5)
#> 2025-05-20 17:02:24.48949: Linearise component 'x' (level 5)
#> 2025-05-20 17:02:24.518736: Linearise component 'Intercept' (level 5)
#> 2025-05-20 17:02:24.527955: iinla: Evaluate component simplifications (level 3)
#> 2025-05-20 17:02:24.529266: Simplify model components (level 3)
#> 2025-05-20 17:02:24.530602: Simplify component 'x' (level 4)
#> 2025-05-20 17:02:24.540252: Simplify component 'Intercept' (level 4)
#> 2025-05-20 17:02:24.549324: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:24.562361: iinla: Construct inla stack (level 3)
#> 2025-05-20 17:02:24.585541: iinla: Model initialisation completed (level 3)
#> 2025-05-20 17:02:24.586822: iinla: Iteration 1 [max:1] (level 1)
#> 2025-05-20 17:02:25.316015: bru: Preprocessing (level 1)
#> 2025-05-20 17:02:25.318591: Evaluate component inputs for each observation model (level 3)
#> 2025-05-20 17:02:25.319918: input_eval.component_list (level 4)
#> 2025-05-20 17:02:25.321165: input_eval.component(x) (level 4)
#> 2025-05-20 17:02:25.322374: input_eval.bru_input(x) (level 5)
#> 2025-05-20 17:02:25.330273: input_eval.bru_input(x.group) (level 5)
#> 2025-05-20 17:02:25.336064: input_eval.bru_input(x.repl) (level 5)
#> 2025-05-20 17:02:25.341216: input_eval.component(Intercept) (level 4)
#> 2025-05-20 17:02:25.342437: input_eval.bru_input(Intercept) (level 5)
#> 2025-05-20 17:02:25.347337: input_eval.bru_input(Intercept.group) (level 5)
#> 2025-05-20 17:02:25.352231: input_eval.bru_input(Intercept.repl) (level 5)
#> 2025-05-20 17:02:25.397276: iinla: Start (level 3)
#> 2025-05-20 17:02:25.39849: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:25.399681: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:25.400933: Linearise components (level 5)
#> 2025-05-20 17:02:25.402112: Linearise component 'x' (level 5)
#> 2025-05-20 17:02:25.420434: Linearise component 'Intercept' (level 5)
#> 2025-05-20 17:02:25.429284: iinla: Evaluate component simplifications (level 3)
#> 2025-05-20 17:02:25.43051: Simplify model components (level 3)
#> 2025-05-20 17:02:25.4318: Simplify component 'x' (level 4)
#> 2025-05-20 17:02:25.441248: Simplify component 'Intercept' (level 4)
#> 2025-05-20 17:02:25.450445: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:25.456513: iinla: Construct inla stack (level 3)
#> 2025-05-20 17:02:25.469536: iinla: Model initialisation completed (level 3)
#> 2025-05-20 17:02:25.470821: iinla: Iteration 1 [max:1] (level 1)
#> 2025-05-20 17:02:26.092287: bru: Preprocessing (level 1)
#> 2025-05-20 17:02:26.094878: Evaluate component inputs for each observation model (level 3)
#> 2025-05-20 17:02:26.096175: input_eval.component_list (level 4)
#> 2025-05-20 17:02:26.097448: input_eval.component(z) (level 4)
#> 2025-05-20 17:02:26.098718: input_eval.bru_input(z) (level 5)
#> 2025-05-20 17:02:26.106634: input_eval.bru_input(z.group) (level 5)
#> 2025-05-20 17:02:26.1123: input_eval.bru_input(z.repl) (level 5)
#> 2025-05-20 17:02:26.117485: input_eval.component(Intercept) (level 4)
#> 2025-05-20 17:02:26.118751: input_eval.bru_input(Intercept) (level 5)
#> 2025-05-20 17:02:26.123806: input_eval.bru_input(Intercept.group) (level 5)
#> 2025-05-20 17:02:26.128738: input_eval.bru_input(Intercept.repl) (level 5)
#> 2025-05-20 17:02:26.175679: iinla: Start (level 3)
#> 2025-05-20 17:02:26.176922: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:26.178146: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:26.179438: Linearise components (level 5)
#> 2025-05-20 17:02:26.180661: Linearise component 'z' (level 5)
#> 2025-05-20 17:02:26.190317: Linearise component 'Intercept' (level 5)
#> 2025-05-20 17:02:26.199591: iinla: Evaluate component simplifications (level 3)
#> 2025-05-20 17:02:26.200885: Simplify model components (level 3)
#> 2025-05-20 17:02:26.202173: Simplify component 'z' (level 4)
#> 2025-05-20 17:02:26.211407: Simplify component 'Intercept' (level 4)
#> 2025-05-20 17:02:26.225837: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:26.22836: Linearise with respect to component 'z' (level 5)
#> 2025-05-20 17:02:26.232791: Linearise with respect to component 'Intercept' (level 5)
#> 2025-05-20 17:02:26.23595: iinla: Construct inla stack (level 3)
#> 2025-05-20 17:02:26.248505: iinla: Model initialisation completed (level 3)
#> 2025-05-20 17:02:26.249773: iinla: Iteration 1 [max:10] (level 1)
#> 2025-05-20 17:02:26.800024: iinla: Step rescaling: 61.8%, Contract (norm0 = 2076, norm1 = 1910, norm01 = 351.8) (level 3)
#> 2025-05-20 17:02:26.802144: iinla: Step rescaling: 38.2%, Contract (norm0 = 413.9, norm1 = 304.9, norm01 = 351.8) (level 3)
#> 2025-05-20 17:02:26.805067: iinla: Step rescaling: 27.06%, Approx Optimisation (norm0 = 184.8, norm1 = 228.4, norm01 = 351.8) (level 3)
#> 2025-05-20 17:02:26.806365: iinla: |lin1-lin0| = 351.8
#> <eta-lin1,delta>/|delta| = -201.5
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 107.4 (level 4)
#> 2025-05-20 17:02:26.807577: iinla: Step rescaling: 27.1% (norm0 = 184.8, norm1 = 228.4, norm01 = 351.8) (level 2)
#> 2025-05-20 17:02:26.809282: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:26.810467: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:26.811822: Linearise components (level 5)
#> 2025-05-20 17:02:26.813039: Linearise component 'z' (level 5)
#> 2025-05-20 17:02:26.82843: Linearise component 'Intercept' (level 5)
#> 2025-05-20 17:02:26.837419: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:26.839484: Linearise with respect to component 'z' (level 5)
#> 2025-05-20 17:02:26.842864: Linearise with respect to component 'Intercept' (level 5)
#> 2025-05-20 17:02:26.856121: iinla: Iteration 2 [max:10] (level 1)
#> 2025-05-20 17:02:27.666028: iinla: Step rescaling: 99.54%, Approx Optimisation (norm0 = 227.7, norm1 = 11.96, norm01 = 228.6) (level 3)
#> 2025-05-20 17:02:27.667361: iinla: |lin1-lin0| = 228.6
#> <eta-lin1,delta>/|delta| = -1.246
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 11.89 (level 4)
#> 2025-05-20 17:02:27.668572: iinla: Step rescaling: 99.5% (norm0 = 227.7, norm1 = 11.96, norm01 = 228.6) (level 2)
#> 2025-05-20 17:02:27.67027: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:27.671407: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:27.672591: Linearise components (level 5)
#> 2025-05-20 17:02:27.673749: Linearise component 'z' (level 5)
#> 2025-05-20 17:02:27.682701: Linearise component 'Intercept' (level 5)
#> 2025-05-20 17:02:27.691376: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:27.693311: Linearise with respect to component 'z' (level 5)
#> 2025-05-20 17:02:27.696679: Linearise with respect to component 'Intercept' (level 5)
#> 2025-05-20 17:02:27.709174: iinla: Max deviation from previous: 47200% of SD, and line search is active
#> [stop if: <10% and line search inactive] (level 1)
#> 2025-05-20 17:02:27.710964: iinla: Iteration 3 [max:10] (level 1)
#> 2025-05-20 17:02:28.25452: iinla: Step rescaling: 162%, Expand (norm0 = 18.8, norm1 = 6.846, norm01 = 11.95) (level 3)
#> 2025-05-20 17:02:28.262503: iinla: Step rescaling: 100%, Overstep (norm0 = 11.74, norm1 = 0.2094, norm01 = 11.95) (level 3)
#> 2025-05-20 17:02:28.265148: iinla: Step rescaling: 101.8%, Approx Optimisation (norm0 = 11.95, norm1 = 0.01917, norm01 = 11.95) (level 3)
#> 2025-05-20 17:02:28.266382: iinla: |lin1-lin0| = 11.95
#> <eta-lin1,delta>/|delta| = -4e-05
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 0.01917 (level 4)
#> 2025-05-20 17:02:28.267547: iinla: Step rescaling: 102% (norm0 = 11.95, norm1 = 0.01917, norm01 = 11.95) (level 2)
#> 2025-05-20 17:02:28.269199: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:28.270332: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:28.271527: Linearise components (level 5)
#> 2025-05-20 17:02:28.272676: Linearise component 'z' (level 5)
#> 2025-05-20 17:02:28.281698: Linearise component 'Intercept' (level 5)
#> 2025-05-20 17:02:28.290421: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:28.292449: Linearise with respect to component 'z' (level 5)
#> 2025-05-20 17:02:28.295805: Linearise with respect to component 'Intercept' (level 5)
#> 2025-05-20 17:02:28.308321: iinla: Max deviation from previous: 555% of SD, and line search is active
#> [stop if: <10% and line search inactive] (level 1)
#> 2025-05-20 17:02:28.310061: iinla: Iteration 4 [max:10] (level 1)
#> 2025-05-20 17:02:28.86514: iinla: Step rescaling: 162%, Expand (norm0 = 0.03103, norm1 = 0.01185, norm01 = 0.01917) (level 3)
#> 2025-05-20 17:02:28.867123: iinla: Step rescaling: 100%, Overstep (norm0 = 0.01917, norm1 = 1.444e-07, norm01 = 0.01917) (level 3)
#> 2025-05-20 17:02:28.86982: iinla: Step rescaling: 100%, Approx Optimisation (norm0 = 0.01917, norm1 = 1.438e-07, norm01 = 0.01917) (level 3)
#> 2025-05-20 17:02:28.87102: iinla: |lin1-lin0| = 0.01917
#> <eta-lin1,delta>/|delta| = 2.759e-10
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 1.438e-07 (level 4)
#> 2025-05-20 17:02:28.872694: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:28.87383: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:28.875011: Linearise components (level 5)
#> 2025-05-20 17:02:28.876128: Linearise component 'z' (level 5)
#> 2025-05-20 17:02:28.885798: Linearise component 'Intercept' (level 5)
#> 2025-05-20 17:02:28.899522: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:28.901507: Linearise with respect to component 'z' (level 5)
#> 2025-05-20 17:02:28.904892: Linearise with respect to component 'Intercept' (level 5)
#> 2025-05-20 17:02:28.917312: iinla: Max deviation from previous: 9.69% of SD, and line search is inactive
#> [stop if: <10% and line search inactive] (level 1)
#> 2025-05-20 17:02:28.918522: iinla: Convergence criterion met.
#> Running final INLA integration step with known theta mode. (level 1)
#> 2025-05-20 17:02:28.920253: iinla: Iteration 5 [max:10] (level 1)
#> 2025-05-20 17:02:30.398266: bru: Preprocessing (level 1)
#> 2025-05-20 17:02:30.403213: Evaluate component inputs for each observation model (level 3)
#> 2025-05-20 17:02:30.404474: input_eval.component_list (level 4)
#> 2025-05-20 17:02:30.405703: input_eval.component(field) (level 4)
#> 2025-05-20 17:02:30.406892: input_eval.bru_input(field) (level 5)
#> 2025-05-20 17:02:30.415253: input_eval.bru_input(field.group) (level 5)
#> 2025-05-20 17:02:30.422039: input_eval.bru_input(field.repl) (level 5)
#> 2025-05-20 17:02:30.450392: iinla: Start (level 3)
#> 2025-05-20 17:02:30.451613: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:30.452853: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:30.454098: Linearise components (level 5)
#> 2025-05-20 17:02:30.455299: Linearise component 'field' (level 5)
#> 2025-05-20 17:02:30.479026: iinla: Evaluate component simplifications (level 3)
#> 2025-05-20 17:02:30.480313: Simplify model components (level 3)
#> 2025-05-20 17:02:30.481566: Simplify component 'field' (level 4)
#> 2025-05-20 17:02:30.492422: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:30.495399: iinla: Construct inla stack (level 3)
#> 2025-05-20 17:02:30.506115: iinla: Model initialisation completed (level 3)
#> 2025-05-20 17:02:30.507348: iinla: Iteration 1 [max:1] (level 1)
#> 2025-05-20 17:02:33.184556: input_eval.component_list (level 4)
#> 2025-05-20 17:02:36.85247: bru: Preprocessing (level 1)
#> 2025-05-20 17:02:36.865775: Evaluate component inputs for each observation model (level 3)
#> 2025-05-20 17:02:36.867008: input_eval.component_list (level 4)
#> 2025-05-20 17:02:36.868182: input_eval.component(x) (level 4)
#> 2025-05-20 17:02:36.869362: input_eval.bru_input(x) (level 5)
#> 2025-05-20 17:02:36.875779: input_eval.bru_input(x.group) (level 5)
#> 2025-05-20 17:02:36.880942: input_eval.bru_input(x.repl) (level 5)
#> 2025-05-20 17:02:36.886088: input_eval.component_list (level 4)
#> 2025-05-20 17:02:36.887257: input_eval.component(x) (level 4)
#> 2025-05-20 17:02:36.888412: input_eval.bru_input(x) (level 5)
#> 2025-05-20 17:02:36.893656: input_eval.bru_input(x.group) (level 5)
#> 2025-05-20 17:02:36.898849: input_eval.bru_input(x.repl) (level 5)
#> 2025-05-20 17:02:36.925966: iinla: Start (level 3)
#> 2025-05-20 17:02:36.927164: iinla: Evaluate component linearisations (level 3)
#> 2025-05-20 17:02:36.92834: Linearise components for each observation model (level 3)
#> 2025-05-20 17:02:36.929574: Linearise components (level 5)
#> 2025-05-20 17:02:36.930785: Linearise component 'x' (level 5)
#> 2025-05-20 17:02:36.942208: Linearise components (level 5)
#> 2025-05-20 17:02:36.943432: Linearise component 'x' (level 5)
#> 2025-05-20 17:02:36.952892: iinla: Evaluate component simplifications (level 3)
#> 2025-05-20 17:02:36.954095: Simplify model components (level 3)
#> 2025-05-20 17:02:36.955339: Simplify component 'x' (level 4)
#> 2025-05-20 17:02:36.964736: Simplify component 'x' (level 4)
#> 2025-05-20 17:02:36.974164: iinla: Evaluate predictor linearisation (level 3)
#> 2025-05-20 17:02:36.981042: iinla: Construct inla stack (level 3)
#> 2025-05-20 17:02:37.002827: iinla: Model initialisation completed (level 3)
#> 2025-05-20 17:02:37.00406: iinla: Iteration 1 [max:1] (level 1)