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)
#> 2025-04-24 16:02:58.288822: inlabru loaded
#> 2025-04-24 16:02:58.289315: Clear override options
#> 2025-04-24 16:03:03.237577: bru: Preprocessing
#> 2025-04-24 16:03:03.499292: iinla: Iteration 1 [max:1]
#> 2025-04-24 16:03:04.066319: bru: Preprocessing
#> 2025-04-24 16:03:04.226424: iinla: Iteration 1 [max:1]
#> 2025-04-24 16:03:04.687358: bru: Preprocessing
#> 2025-04-24 16:03:04.847133: iinla: Iteration 1 [max:10]
#> 2025-04-24 16:03:05.269035: iinla: Step rescaling: 27.5% (norm0 = 404.7, norm1 = 497.5, norm01 = 765.5)
#> 2025-04-24 16:03:05.318985: iinla: Iteration 2 [max:10]
#> 2025-04-24 16:03:06.007688: iinla: Step rescaling: 99.7% (norm0 = 495.7, norm1 = 22.64, norm01 = 497.2)
#> 2025-04-24 16:03:06.048925: iinla: Max deviation from previous: 101000% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:06.050672: iinla: Iteration 3 [max:10]
#> 2025-04-24 16:03:06.476417: iinla: Step rescaling: 102% (norm0 = 22.65, norm1 = 0.02081, norm01 = 22.65)
#> 2025-04-24 16:03:06.517911: iinla: Max deviation from previous: 1050% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:06.519674: iinla: Iteration 4 [max:10]
#> 2025-04-24 16:03:06.978681: iinla: Max deviation from previous: 16.7% of SD, and line search is inactive
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:06.980437: iinla: Iteration 5 [max:10]
#> 2025-04-24 16:03:07.448189: iinla: Max deviation from previous: 0.0918% of SD, and line search is inactive
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:07.449473: iinla: Convergence criterion met.
#> Running final INLA integration step with known theta mode.
#> 2025-04-24 16:03:07.451251: iinla: Iteration 6 [max:10]
#> 2025-04-24 16:03:08.790088: bru: Preprocessing
#> 2025-04-24 16:03:08.885181: iinla: Iteration 1 [max:1]
#> 2025-04-24 16:03:15.275511: bru: Preprocessing
#> 2025-04-24 16:03:15.438039: iinla: Iteration 1 [max:1]
format(bru_log())
#> [1] "2025-04-24 16:02:58.288822: inlabru loaded"
#> [2] "2025-04-24 16:02:58.289315: Clear override options"
#> [3] "2025-04-24 16:03:03.237577: bru: Preprocessing"
#> [4] "2025-04-24 16:03:03.245726: Evaluate component inputs for each observation model"
#> [5] "2025-04-24 16:03:03.247089: input_eval.component_list"
#> [6] "2025-04-24 16:03:03.248392: input_eval.component(x)"
#> [7] "2025-04-24 16:03:03.249893: input_eval.bru_input(x)"
#> [8] "2025-04-24 16:03:03.257263: input_eval.bru_input(x.group)"
#> [9] "2025-04-24 16:03:03.262578: input_eval.bru_input(x.repl)"
#> [10] "2025-04-24 16:03:03.267676: input_eval.component(Intercept)"
#> [11] "2025-04-24 16:03:03.26892: input_eval.bru_input(Intercept)"
#> [12] "2025-04-24 16:03:03.274001: input_eval.bru_input(Intercept.group)"
#> [13] "2025-04-24 16:03:03.279135: input_eval.bru_input(Intercept.repl)"
#> [14] "2025-04-24 16:03:03.403614: iinla: Start"
#> [15] "2025-04-24 16:03:03.404839: iinla: Evaluate component linearisations"
#> [16] "2025-04-24 16:03:03.406129: Linearise components for each observation model"
#> [17] "2025-04-24 16:03:03.407483: Linearise components"
#> [18] "2025-04-24 16:03:03.408727: Linearise component 'x'"
#> [19] "2025-04-24 16:03:03.429179: Linearise component 'Intercept'"
#> [20] "2025-04-24 16:03:03.438501: iinla: Evaluate component simplifications"
#> [21] "2025-04-24 16:03:03.43991: Simplify model components"
#> [22] "2025-04-24 16:03:03.441312: Simplify component 'x'"
#> [23] "2025-04-24 16:03:03.451384: Simplify component 'Intercept'"
#> [24] "2025-04-24 16:03:03.460676: iinla: Evaluate predictor linearisation"
#> [25] "2025-04-24 16:03:03.474296: iinla: Construct inla stack"
#> [26] "2025-04-24 16:03:03.497964: iinla: Model initialisation completed"
#> [27] "2025-04-24 16:03:03.499292: iinla: Iteration 1 [max:1]"
#> [28] "2025-04-24 16:03:04.066319: bru: Preprocessing"
#> [29] "2025-04-24 16:03:04.068973: Evaluate component inputs for each observation model"
#> [30] "2025-04-24 16:03:04.070269: input_eval.component_list"
#> [31] "2025-04-24 16:03:04.071509: input_eval.component(x)"
#> [32] "2025-04-24 16:03:04.07274: input_eval.bru_input(x)"
#> [33] "2025-04-24 16:03:04.079765: input_eval.bru_input(x.group)"
#> [34] "2025-04-24 16:03:04.085236: input_eval.bru_input(x.repl)"
#> [35] "2025-04-24 16:03:04.090434: input_eval.component(Intercept)"
#> [36] "2025-04-24 16:03:04.091659: input_eval.bru_input(Intercept)"
#> [37] "2025-04-24 16:03:04.097027: input_eval.bru_input(Intercept.group)"
#> [38] "2025-04-24 16:03:04.102308: input_eval.bru_input(Intercept.repl)"
#> [39] "2025-04-24 16:03:04.151714: iinla: Start"
#> [40] "2025-04-24 16:03:04.152966: iinla: Evaluate component linearisations"
#> [41] "2025-04-24 16:03:04.161423: Linearise components for each observation model"
#> [42] "2025-04-24 16:03:04.162782: Linearise components"
#> [43] "2025-04-24 16:03:04.16401: Linearise component 'x'"
#> [44] "2025-04-24 16:03:04.174828: Linearise component 'Intercept'"
#> [45] "2025-04-24 16:03:04.183782: iinla: Evaluate component simplifications"
#> [46] "2025-04-24 16:03:04.185042: Simplify model components"
#> [47] "2025-04-24 16:03:04.186331: Simplify component 'x'"
#> [48] "2025-04-24 16:03:04.195887: Simplify component 'Intercept'"
#> [49] "2025-04-24 16:03:04.205116: iinla: Evaluate predictor linearisation"
#> [50] "2025-04-24 16:03:04.211413: iinla: Construct inla stack"
#> [51] "2025-04-24 16:03:04.225133: iinla: Model initialisation completed"
#> [52] "2025-04-24 16:03:04.226424: iinla: Iteration 1 [max:1]"
#> [53] "2025-04-24 16:03:04.687358: bru: Preprocessing"
#> [54] "2025-04-24 16:03:04.690036: Evaluate component inputs for each observation model"
#> [55] "2025-04-24 16:03:04.69136: input_eval.component_list"
#> [56] "2025-04-24 16:03:04.692636: input_eval.component(z)"
#> [57] "2025-04-24 16:03:04.693909: input_eval.bru_input(z)"
#> [58] "2025-04-24 16:03:04.702099: input_eval.bru_input(z.group)"
#> [59] "2025-04-24 16:03:04.708433: input_eval.bru_input(z.repl)"
#> [60] "2025-04-24 16:03:04.713912: input_eval.component(Intercept)"
#> [61] "2025-04-24 16:03:04.715192: input_eval.bru_input(Intercept)"
#> [62] "2025-04-24 16:03:04.720614: input_eval.bru_input(Intercept.group)"
#> [63] "2025-04-24 16:03:04.72578: input_eval.bru_input(Intercept.repl)"
#> [64] "2025-04-24 16:03:04.771877: iinla: Start"
#> [65] "2025-04-24 16:03:04.773108: iinla: Evaluate component linearisations"
#> [66] "2025-04-24 16:03:04.774327: Linearise components for each observation model"
#> [67] "2025-04-24 16:03:04.775613: Linearise components"
#> [68] "2025-04-24 16:03:04.776864: Linearise component 'z'"
#> [69] "2025-04-24 16:03:04.786352: Linearise component 'Intercept'"
#> [70] "2025-04-24 16:03:04.79541: iinla: Evaluate component simplifications"
#> [71] "2025-04-24 16:03:04.796667: Simplify model components"
#> [72] "2025-04-24 16:03:04.797984: Simplify component 'z'"
#> [73] "2025-04-24 16:03:04.807053: Simplify component 'Intercept'"
#> [74] "2025-04-24 16:03:04.81617: iinla: Evaluate predictor linearisation"
#> [75] "2025-04-24 16:03:04.818703: Linearise with respect to component 'z'"
#> [76] "2025-04-24 16:03:04.823483: Linearise with respect to component 'Intercept'"
#> [77] "2025-04-24 16:03:04.826748: iinla: Construct inla stack"
#> [78] "2025-04-24 16:03:04.84573: iinla: Model initialisation completed"
#> [79] "2025-04-24 16:03:04.847133: iinla: Iteration 1 [max:10]"
#> [80] "2025-04-24 16:03:05.261109: iinla: Step rescaling: 61.8%, Contract (norm0 = 4270, norm1 = 3917, norm01 = 765.5)"
#> [81] "2025-04-24 16:03:05.263337: iinla: Step rescaling: 38.2%, Contract (norm0 = 868.3, norm1 = 645.9, norm01 = 765.5)"
#> [82] "2025-04-24 16:03:05.266269: iinla: Step rescaling: 27.49%, Approx Optimisation (norm0 = 404.7, norm1 = 497.5, norm01 = 765.5)"
#> [83] "2025-04-24 16:03:05.267626: iinla: |lin1-lin0| = 765.5\n <eta-lin1,delta>/|delta| = -437.5\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 236.9"
#> [84] "2025-04-24 16:03:05.269035: iinla: Step rescaling: 27.5% (norm0 = 404.7, norm1 = 497.5, norm01 = 765.5)"
#> [85] "2025-04-24 16:03:05.270903: iinla: Evaluate component linearisations"
#> [86] "2025-04-24 16:03:05.272168: Linearise components for each observation model"
#> [87] "2025-04-24 16:03:05.273484: Linearise components"
#> [88] "2025-04-24 16:03:05.274729: Linearise component 'z'"
#> [89] "2025-04-24 16:03:05.284107: Linearise component 'Intercept'"
#> [90] "2025-04-24 16:03:05.293272: iinla: Evaluate predictor linearisation"
#> [91] "2025-04-24 16:03:05.295374: Linearise with respect to component 'z'"
#> [92] "2025-04-24 16:03:05.304948: Linearise with respect to component 'Intercept'"
#> [93] "2025-04-24 16:03:05.318985: iinla: Iteration 2 [max:10]"
#> [94] "2025-04-24 16:03:06.000694: iinla: Step rescaling: 162%, Expand (norm0 = 804.8, norm1 = 311.5, norm01 = 497.2)"
#> [95] "2025-04-24 16:03:06.002769: iinla: Step rescaling: 100%, Overstep (norm0 = 496.9, norm1 = 22.68, norm01 = 497.2)"
#> [96] "2025-04-24 16:03:06.005348: iinla: Step rescaling: 99.75%, Approx Optimisation (norm0 = 495.7, norm1 = 22.64, norm01 = 497.2)"
#> [97] "2025-04-24 16:03:06.00655: iinla: |lin1-lin0| = 497.2\n <eta-lin1,delta>/|delta| = -2.065\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 22.54"
#> [98] "2025-04-24 16:03:06.007688: iinla: Step rescaling: 99.7% (norm0 = 495.7, norm1 = 22.64, norm01 = 497.2)"
#> [99] "2025-04-24 16:03:06.009319: iinla: Evaluate component linearisations"
#> [100] "2025-04-24 16:03:06.010431: Linearise components for each observation model"
#> [101] "2025-04-24 16:03:06.01166: Linearise components"
#> [102] "2025-04-24 16:03:06.012855: Linearise component 'z'"
#> [103] "2025-04-24 16:03:06.021703: Linearise component 'Intercept'"
#> [104] "2025-04-24 16:03:06.030456: iinla: Evaluate predictor linearisation"
#> [105] "2025-04-24 16:03:06.032573: Linearise with respect to component 'z'"
#> [106] "2025-04-24 16:03:06.036028: Linearise with respect to component 'Intercept'"
#> [107] "2025-04-24 16:03:06.048925: iinla: Max deviation from previous: 101000% of SD, and line search is active\n [stop if: <10% and line search inactive]"
#> [108] "2025-04-24 16:03:06.050672: iinla: Iteration 3 [max:10]"
#> [109] "2025-04-24 16:03:06.464121: iinla: Step rescaling: 162%, Expand (norm0 = 35.71, norm1 = 13.06, norm01 = 22.65)"
#> [110] "2025-04-24 16:03:06.466237: iinla: Step rescaling: 100%, Overstep (norm0 = 22.29, norm1 = 0.3609, norm01 = 22.65)"
#> [111] "2025-04-24 16:03:06.474027: iinla: Step rescaling: 101.6%, Approx Optimisation (norm0 = 22.65, norm1 = 0.02081, norm01 = 22.65)"
#> [112] "2025-04-24 16:03:06.47526: iinla: |lin1-lin0| = 22.65\n <eta-lin1,delta>/|delta| = -1.089e-05\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 0.02081"
#> [113] "2025-04-24 16:03:06.476417: iinla: Step rescaling: 102% (norm0 = 22.65, norm1 = 0.02081, norm01 = 22.65)"
#> [114] "2025-04-24 16:03:06.478068: iinla: Evaluate component linearisations"
#> [115] "2025-04-24 16:03:06.479236: Linearise components for each observation model"
#> [116] "2025-04-24 16:03:06.480442: Linearise components"
#> [117] "2025-04-24 16:03:06.481575: Linearise component 'z'"
#> [118] "2025-04-24 16:03:06.490626: Linearise component 'Intercept'"
#> [119] "2025-04-24 16:03:06.499416: iinla: Evaluate predictor linearisation"
#> [120] "2025-04-24 16:03:06.501537: Linearise with respect to component 'z'"
#> [121] "2025-04-24 16:03:06.505: Linearise with respect to component 'Intercept'"
#> [122] "2025-04-24 16:03:06.517911: iinla: Max deviation from previous: 1050% of SD, and line search is active\n [stop if: <10% and line search inactive]"
#> [123] "2025-04-24 16:03:06.519674: iinla: Iteration 4 [max:10]"
#> [124] "2025-04-24 16:03:06.927184: iinla: Step rescaling: 162%, Expand (norm0 = 0.03369, norm1 = 0.01287, norm01 = 0.02082)"
#> [125] "2025-04-24 16:03:06.929191: iinla: Step rescaling: 100%, Overstep (norm0 = 0.02082, norm1 = 8.833e-08, norm01 = 0.02082)"
#> [126] "2025-04-24 16:03:06.931819: iinla: Step rescaling: 100%, Approx Optimisation (norm0 = 0.02082, norm1 = 8.819e-08, norm01 = 0.02082)"
#> [127] "2025-04-24 16:03:06.933051: iinla: |lin1-lin0| = 0.02082\n <eta-lin1,delta>/|delta| = 1.053e-10\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 8.819e-08"
#> [128] "2025-04-24 16:03:06.939495: iinla: Evaluate component linearisations"
#> [129] "2025-04-24 16:03:06.940813: Linearise components for each observation model"
#> [130] "2025-04-24 16:03:06.942036: Linearise components"
#> [131] "2025-04-24 16:03:06.943184: Linearise component 'z'"
#> [132] "2025-04-24 16:03:06.952225: Linearise component 'Intercept'"
#> [133] "2025-04-24 16:03:06.960905: iinla: Evaluate predictor linearisation"
#> [134] "2025-04-24 16:03:06.962963: Linearise with respect to component 'z'"
#> [135] "2025-04-24 16:03:06.966319: Linearise with respect to component 'Intercept'"
#> [136] "2025-04-24 16:03:06.978681: iinla: Max deviation from previous: 16.7% of SD, and line search is inactive\n [stop if: <10% and line search inactive]"
#> [137] "2025-04-24 16:03:06.980437: iinla: Iteration 5 [max:10]"
#> [138] "2025-04-24 16:03:07.39534: iinla: Step rescaling: 162%, Expand (norm0 = 1.85e-07, norm1 = 7.065e-08, norm01 = 1.143e-07)"
#> [139] "2025-04-24 16:03:07.397391: iinla: Step rescaling: 100%, Overstep (norm0 = 1.143e-07, norm1 = 5.038e-13, norm01 = 1.143e-07)"
#> [140] "2025-04-24 16:03:07.400062: iinla: Step rescaling: 100%, Approx Optimisation (norm0 = 1.143e-07, norm1 = 3.571e-13, norm01 = 1.143e-07)"
#> [141] "2025-04-24 16:03:07.401287: iinla: |lin1-lin0| = 1.143e-07\n <eta-lin1,delta>/|delta| = -2.055e-14\n |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 3.565e-13"
#> [142] "2025-04-24 16:03:07.402997: iinla: Evaluate component linearisations"
#> [143] "2025-04-24 16:03:07.404168: Linearise components for each observation model"
#> [144] "2025-04-24 16:03:07.405383: Linearise components"
#> [145] "2025-04-24 16:03:07.406542: Linearise component 'z'"
#> [146] "2025-04-24 16:03:07.420868: Linearise component 'Intercept'"
#> [147] "2025-04-24 16:03:07.429992: iinla: Evaluate predictor linearisation"
#> [148] "2025-04-24 16:03:07.432222: Linearise with respect to component 'z'"
#> [149] "2025-04-24 16:03:07.435566: Linearise with respect to component 'Intercept'"
#> [150] "2025-04-24 16:03:07.448189: iinla: Max deviation from previous: 0.0918% of SD, and line search is inactive\n [stop if: <10% and line search inactive]"
#> [151] "2025-04-24 16:03:07.449473: iinla: Convergence criterion met.\n Running final INLA integration step with known theta mode."
#> [152] "2025-04-24 16:03:07.451251: iinla: Iteration 6 [max:10]"
#> [153] "2025-04-24 16:03:08.790088: bru: Preprocessing"
#> [154] "2025-04-24 16:03:08.794979: Evaluate component inputs for each observation model"
#> [155] "2025-04-24 16:03:08.796247: input_eval.component_list"
#> [156] "2025-04-24 16:03:08.797471: input_eval.component(field)"
#> [157] "2025-04-24 16:03:08.798671: input_eval.bru_input(field)"
#> [158] "2025-04-24 16:03:08.805494: input_eval.bru_input(field.group)"
#> [159] "2025-04-24 16:03:08.810878: input_eval.bru_input(field.repl)"
#> [160] "2025-04-24 16:03:08.838488: iinla: Start"
#> [161] "2025-04-24 16:03:08.839684: iinla: Evaluate component linearisations"
#> [162] "2025-04-24 16:03:08.840926: Linearise components for each observation model"
#> [163] "2025-04-24 16:03:08.842219: Linearise components"
#> [164] "2025-04-24 16:03:08.843414: Linearise component 'field'"
#> [165] "2025-04-24 16:03:08.855998: iinla: Evaluate component simplifications"
#> [166] "2025-04-24 16:03:08.857229: Simplify model components"
#> [167] "2025-04-24 16:03:08.858478: Simplify component 'field'"
#> [168] "2025-04-24 16:03:08.869422: iinla: Evaluate predictor linearisation"
#> [169] "2025-04-24 16:03:08.87252: iinla: Construct inla stack"
#> [170] "2025-04-24 16:03:08.883904: iinla: Model initialisation completed"
#> [171] "2025-04-24 16:03:08.885181: iinla: Iteration 1 [max:1]"
#> [172] "2025-04-24 16:03:11.475895: input_eval.component_list"
#> [173] "2025-04-24 16:03:15.275511: bru: Preprocessing"
#> [174] "2025-04-24 16:03:15.283063: Evaluate component inputs for each observation model"
#> [175] "2025-04-24 16:03:15.284412: input_eval.component_list"
#> [176] "2025-04-24 16:03:15.285671: input_eval.component(x)"
#> [177] "2025-04-24 16:03:15.286929: input_eval.bru_input(x)"
#> [178] "2025-04-24 16:03:15.295333: input_eval.bru_input(x.group)"
#> [179] "2025-04-24 16:03:15.302027: input_eval.bru_input(x.repl)"
#> [180] "2025-04-24 16:03:15.308326: input_eval.component_list"
#> [181] "2025-04-24 16:03:15.31037: input_eval.component(x)"
#> [182] "2025-04-24 16:03:15.312236: input_eval.bru_input(x)"
#> [183] "2025-04-24 16:03:15.319985: input_eval.bru_input(x.group)"
#> [184] "2025-04-24 16:03:15.327062: input_eval.bru_input(x.repl)"
#> [185] "2025-04-24 16:03:15.357233: iinla: Start"
#> [186] "2025-04-24 16:03:15.35848: iinla: Evaluate component linearisations"
#> [187] "2025-04-24 16:03:15.359699: Linearise components for each observation model"
#> [188] "2025-04-24 16:03:15.361009: Linearise components"
#> [189] "2025-04-24 16:03:15.362221: Linearise component 'x'"
#> [190] "2025-04-24 16:03:15.373784: Linearise components"
#> [191] "2025-04-24 16:03:15.375073: Linearise component 'x'"
#> [192] "2025-04-24 16:03:15.384714: iinla: Evaluate component simplifications"
#> [193] "2025-04-24 16:03:15.385965: Simplify model components"
#> [194] "2025-04-24 16:03:15.387223: Simplify component 'x'"
#> [195] "2025-04-24 16:03:15.39738: Simplify component 'x'"
#> [196] "2025-04-24 16:03:15.413742: iinla: Evaluate predictor linearisation"
#> [197] "2025-04-24 16:03:15.420917: iinla: Construct inla stack"
#> [198] "2025-04-24 16:03:15.43661: iinla: Model initialisation completed"
#> [199] "2025-04-24 16:03:15.438039: iinla: Iteration 1 [max:1]"
bru_log(verbosity = 2L)
#> 2025-04-24 16:02:58.288822: inlabru loaded
#> 2025-04-24 16:02:58.289315: Clear override options
#> 2025-04-24 16:03:03.237577: bru: Preprocessing
#> 2025-04-24 16:03:03.499292: iinla: Iteration 1 [max:1]
#> 2025-04-24 16:03:04.066319: bru: Preprocessing
#> 2025-04-24 16:03:04.226424: iinla: Iteration 1 [max:1]
#> 2025-04-24 16:03:04.687358: bru: Preprocessing
#> 2025-04-24 16:03:04.847133: iinla: Iteration 1 [max:10]
#> 2025-04-24 16:03:05.269035: iinla: Step rescaling: 27.5% (norm0 = 404.7, norm1 = 497.5, norm01 = 765.5)
#> 2025-04-24 16:03:05.318985: iinla: Iteration 2 [max:10]
#> 2025-04-24 16:03:06.007688: iinla: Step rescaling: 99.7% (norm0 = 495.7, norm1 = 22.64, norm01 = 497.2)
#> 2025-04-24 16:03:06.048925: iinla: Max deviation from previous: 101000% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:06.050672: iinla: Iteration 3 [max:10]
#> 2025-04-24 16:03:06.476417: iinla: Step rescaling: 102% (norm0 = 22.65, norm1 = 0.02081, norm01 = 22.65)
#> 2025-04-24 16:03:06.517911: iinla: Max deviation from previous: 1050% of SD, and line search is active
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:06.519674: iinla: Iteration 4 [max:10]
#> 2025-04-24 16:03:06.978681: iinla: Max deviation from previous: 16.7% of SD, and line search is inactive
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:06.980437: iinla: Iteration 5 [max:10]
#> 2025-04-24 16:03:07.448189: iinla: Max deviation from previous: 0.0918% of SD, and line search is inactive
#> [stop if: <10% and line search inactive]
#> 2025-04-24 16:03:07.449473: iinla: Convergence criterion met.
#> Running final INLA integration step with known theta mode.
#> 2025-04-24 16:03:07.451251: iinla: Iteration 6 [max:10]
#> 2025-04-24 16:03:08.790088: bru: Preprocessing
#> 2025-04-24 16:03:08.885181: iinla: Iteration 1 [max:1]
#> 2025-04-24 16:03:15.275511: bru: Preprocessing
#> 2025-04-24 16:03:15.438039: iinla: Iteration 1 [max:1]
print(bru_log(), timestamp = TRUE, verbosity = TRUE)
#> 2025-04-24 16:02:58.288822: inlabru loaded (level 1)
#> 2025-04-24 16:02:58.289315: Clear override options (level 1)
#> 2025-04-24 16:03:03.237577: bru: Preprocessing (level 1)
#> 2025-04-24 16:03:03.245726: Evaluate component inputs for each observation model (level 3)
#> 2025-04-24 16:03:03.247089: input_eval.component_list (level 4)
#> 2025-04-24 16:03:03.248392: input_eval.component(x) (level 4)
#> 2025-04-24 16:03:03.249893: input_eval.bru_input(x) (level 5)
#> 2025-04-24 16:03:03.257263: input_eval.bru_input(x.group) (level 5)
#> 2025-04-24 16:03:03.262578: input_eval.bru_input(x.repl) (level 5)
#> 2025-04-24 16:03:03.267676: input_eval.component(Intercept) (level 4)
#> 2025-04-24 16:03:03.26892: input_eval.bru_input(Intercept) (level 5)
#> 2025-04-24 16:03:03.274001: input_eval.bru_input(Intercept.group) (level 5)
#> 2025-04-24 16:03:03.279135: input_eval.bru_input(Intercept.repl) (level 5)
#> 2025-04-24 16:03:03.403614: iinla: Start (level 3)
#> 2025-04-24 16:03:03.404839: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:03.406129: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:03.407483: Linearise components (level 3)
#> 2025-04-24 16:03:03.408727: Linearise component 'x' (level 4)
#> 2025-04-24 16:03:03.429179: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:03.438501: iinla: Evaluate component simplifications (level 3)
#> 2025-04-24 16:03:03.43991: Simplify model components (level 3)
#> 2025-04-24 16:03:03.441312: Simplify component 'x' (level 4)
#> 2025-04-24 16:03:03.451384: Simplify component 'Intercept' (level 4)
#> 2025-04-24 16:03:03.460676: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:03.474296: iinla: Construct inla stack (level 3)
#> 2025-04-24 16:03:03.497964: iinla: Model initialisation completed (level 3)
#> 2025-04-24 16:03:03.499292: iinla: Iteration 1 [max:1] (level 1)
#> 2025-04-24 16:03:04.066319: bru: Preprocessing (level 1)
#> 2025-04-24 16:03:04.068973: Evaluate component inputs for each observation model (level 3)
#> 2025-04-24 16:03:04.070269: input_eval.component_list (level 4)
#> 2025-04-24 16:03:04.071509: input_eval.component(x) (level 4)
#> 2025-04-24 16:03:04.07274: input_eval.bru_input(x) (level 5)
#> 2025-04-24 16:03:04.079765: input_eval.bru_input(x.group) (level 5)
#> 2025-04-24 16:03:04.085236: input_eval.bru_input(x.repl) (level 5)
#> 2025-04-24 16:03:04.090434: input_eval.component(Intercept) (level 4)
#> 2025-04-24 16:03:04.091659: input_eval.bru_input(Intercept) (level 5)
#> 2025-04-24 16:03:04.097027: input_eval.bru_input(Intercept.group) (level 5)
#> 2025-04-24 16:03:04.102308: input_eval.bru_input(Intercept.repl) (level 5)
#> 2025-04-24 16:03:04.151714: iinla: Start (level 3)
#> 2025-04-24 16:03:04.152966: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:04.161423: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:04.162782: Linearise components (level 3)
#> 2025-04-24 16:03:04.16401: Linearise component 'x' (level 4)
#> 2025-04-24 16:03:04.174828: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:04.183782: iinla: Evaluate component simplifications (level 3)
#> 2025-04-24 16:03:04.185042: Simplify model components (level 3)
#> 2025-04-24 16:03:04.186331: Simplify component 'x' (level 4)
#> 2025-04-24 16:03:04.195887: Simplify component 'Intercept' (level 4)
#> 2025-04-24 16:03:04.205116: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:04.211413: iinla: Construct inla stack (level 3)
#> 2025-04-24 16:03:04.225133: iinla: Model initialisation completed (level 3)
#> 2025-04-24 16:03:04.226424: iinla: Iteration 1 [max:1] (level 1)
#> 2025-04-24 16:03:04.687358: bru: Preprocessing (level 1)
#> 2025-04-24 16:03:04.690036: Evaluate component inputs for each observation model (level 3)
#> 2025-04-24 16:03:04.69136: input_eval.component_list (level 4)
#> 2025-04-24 16:03:04.692636: input_eval.component(z) (level 4)
#> 2025-04-24 16:03:04.693909: input_eval.bru_input(z) (level 5)
#> 2025-04-24 16:03:04.702099: input_eval.bru_input(z.group) (level 5)
#> 2025-04-24 16:03:04.708433: input_eval.bru_input(z.repl) (level 5)
#> 2025-04-24 16:03:04.713912: input_eval.component(Intercept) (level 4)
#> 2025-04-24 16:03:04.715192: input_eval.bru_input(Intercept) (level 5)
#> 2025-04-24 16:03:04.720614: input_eval.bru_input(Intercept.group) (level 5)
#> 2025-04-24 16:03:04.72578: input_eval.bru_input(Intercept.repl) (level 5)
#> 2025-04-24 16:03:04.771877: iinla: Start (level 3)
#> 2025-04-24 16:03:04.773108: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:04.774327: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:04.775613: Linearise components (level 3)
#> 2025-04-24 16:03:04.776864: Linearise component 'z' (level 4)
#> 2025-04-24 16:03:04.786352: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:04.79541: iinla: Evaluate component simplifications (level 3)
#> 2025-04-24 16:03:04.796667: Simplify model components (level 3)
#> 2025-04-24 16:03:04.797984: Simplify component 'z' (level 4)
#> 2025-04-24 16:03:04.807053: Simplify component 'Intercept' (level 4)
#> 2025-04-24 16:03:04.81617: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:04.818703: Linearise with respect to component 'z' (level 4)
#> 2025-04-24 16:03:04.823483: Linearise with respect to component 'Intercept' (level 4)
#> 2025-04-24 16:03:04.826748: iinla: Construct inla stack (level 3)
#> 2025-04-24 16:03:04.84573: iinla: Model initialisation completed (level 3)
#> 2025-04-24 16:03:04.847133: iinla: Iteration 1 [max:10] (level 1)
#> 2025-04-24 16:03:05.261109: iinla: Step rescaling: 61.8%, Contract (norm0 = 4270, norm1 = 3917, norm01 = 765.5) (level 3)
#> 2025-04-24 16:03:05.263337: iinla: Step rescaling: 38.2%, Contract (norm0 = 868.3, norm1 = 645.9, norm01 = 765.5) (level 3)
#> 2025-04-24 16:03:05.266269: iinla: Step rescaling: 27.49%, Approx Optimisation (norm0 = 404.7, norm1 = 497.5, norm01 = 765.5) (level 3)
#> 2025-04-24 16:03:05.267626: iinla: |lin1-lin0| = 765.5
#> <eta-lin1,delta>/|delta| = -437.5
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 236.9 (level 4)
#> 2025-04-24 16:03:05.269035: iinla: Step rescaling: 27.5% (norm0 = 404.7, norm1 = 497.5, norm01 = 765.5) (level 2)
#> 2025-04-24 16:03:05.270903: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:05.272168: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:05.273484: Linearise components (level 3)
#> 2025-04-24 16:03:05.274729: Linearise component 'z' (level 4)
#> 2025-04-24 16:03:05.284107: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:05.293272: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:05.295374: Linearise with respect to component 'z' (level 4)
#> 2025-04-24 16:03:05.304948: Linearise with respect to component 'Intercept' (level 4)
#> 2025-04-24 16:03:05.318985: iinla: Iteration 2 [max:10] (level 1)
#> 2025-04-24 16:03:06.000694: iinla: Step rescaling: 162%, Expand (norm0 = 804.8, norm1 = 311.5, norm01 = 497.2) (level 3)
#> 2025-04-24 16:03:06.002769: iinla: Step rescaling: 100%, Overstep (norm0 = 496.9, norm1 = 22.68, norm01 = 497.2) (level 3)
#> 2025-04-24 16:03:06.005348: iinla: Step rescaling: 99.75%, Approx Optimisation (norm0 = 495.7, norm1 = 22.64, norm01 = 497.2) (level 3)
#> 2025-04-24 16:03:06.00655: iinla: |lin1-lin0| = 497.2
#> <eta-lin1,delta>/|delta| = -2.065
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 22.54 (level 4)
#> 2025-04-24 16:03:06.007688: iinla: Step rescaling: 99.7% (norm0 = 495.7, norm1 = 22.64, norm01 = 497.2) (level 2)
#> 2025-04-24 16:03:06.009319: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:06.010431: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:06.01166: Linearise components (level 3)
#> 2025-04-24 16:03:06.012855: Linearise component 'z' (level 4)
#> 2025-04-24 16:03:06.021703: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:06.030456: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:06.032573: Linearise with respect to component 'z' (level 4)
#> 2025-04-24 16:03:06.036028: Linearise with respect to component 'Intercept' (level 4)
#> 2025-04-24 16:03:06.048925: iinla: Max deviation from previous: 101000% of SD, and line search is active
#> [stop if: <10% and line search inactive] (level 1)
#> 2025-04-24 16:03:06.050672: iinla: Iteration 3 [max:10] (level 1)
#> 2025-04-24 16:03:06.464121: iinla: Step rescaling: 162%, Expand (norm0 = 35.71, norm1 = 13.06, norm01 = 22.65) (level 3)
#> 2025-04-24 16:03:06.466237: iinla: Step rescaling: 100%, Overstep (norm0 = 22.29, norm1 = 0.3609, norm01 = 22.65) (level 3)
#> 2025-04-24 16:03:06.474027: iinla: Step rescaling: 101.6%, Approx Optimisation (norm0 = 22.65, norm1 = 0.02081, norm01 = 22.65) (level 3)
#> 2025-04-24 16:03:06.47526: iinla: |lin1-lin0| = 22.65
#> <eta-lin1,delta>/|delta| = -1.089e-05
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 0.02081 (level 4)
#> 2025-04-24 16:03:06.476417: iinla: Step rescaling: 102% (norm0 = 22.65, norm1 = 0.02081, norm01 = 22.65) (level 2)
#> 2025-04-24 16:03:06.478068: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:06.479236: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:06.480442: Linearise components (level 3)
#> 2025-04-24 16:03:06.481575: Linearise component 'z' (level 4)
#> 2025-04-24 16:03:06.490626: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:06.499416: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:06.501537: Linearise with respect to component 'z' (level 4)
#> 2025-04-24 16:03:06.505: Linearise with respect to component 'Intercept' (level 4)
#> 2025-04-24 16:03:06.517911: iinla: Max deviation from previous: 1050% of SD, and line search is active
#> [stop if: <10% and line search inactive] (level 1)
#> 2025-04-24 16:03:06.519674: iinla: Iteration 4 [max:10] (level 1)
#> 2025-04-24 16:03:06.927184: iinla: Step rescaling: 162%, Expand (norm0 = 0.03369, norm1 = 0.01287, norm01 = 0.02082) (level 3)
#> 2025-04-24 16:03:06.929191: iinla: Step rescaling: 100%, Overstep (norm0 = 0.02082, norm1 = 8.833e-08, norm01 = 0.02082) (level 3)
#> 2025-04-24 16:03:06.931819: iinla: Step rescaling: 100%, Approx Optimisation (norm0 = 0.02082, norm1 = 8.819e-08, norm01 = 0.02082) (level 3)
#> 2025-04-24 16:03:06.933051: iinla: |lin1-lin0| = 0.02082
#> <eta-lin1,delta>/|delta| = 1.053e-10
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 8.819e-08 (level 4)
#> 2025-04-24 16:03:06.939495: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:06.940813: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:06.942036: Linearise components (level 3)
#> 2025-04-24 16:03:06.943184: Linearise component 'z' (level 4)
#> 2025-04-24 16:03:06.952225: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:06.960905: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:06.962963: Linearise with respect to component 'z' (level 4)
#> 2025-04-24 16:03:06.966319: Linearise with respect to component 'Intercept' (level 4)
#> 2025-04-24 16:03:06.978681: iinla: Max deviation from previous: 16.7% of SD, and line search is inactive
#> [stop if: <10% and line search inactive] (level 1)
#> 2025-04-24 16:03:06.980437: iinla: Iteration 5 [max:10] (level 1)
#> 2025-04-24 16:03:07.39534: iinla: Step rescaling: 162%, Expand (norm0 = 1.85e-07, norm1 = 7.065e-08, norm01 = 1.143e-07) (level 3)
#> 2025-04-24 16:03:07.397391: iinla: Step rescaling: 100%, Overstep (norm0 = 1.143e-07, norm1 = 5.038e-13, norm01 = 1.143e-07) (level 3)
#> 2025-04-24 16:03:07.400062: iinla: Step rescaling: 100%, Approx Optimisation (norm0 = 1.143e-07, norm1 = 3.571e-13, norm01 = 1.143e-07) (level 3)
#> 2025-04-24 16:03:07.401287: iinla: |lin1-lin0| = 1.143e-07
#> <eta-lin1,delta>/|delta| = -2.055e-14
#> |eta-lin0 - delta <delta,eta-lin0>/<delta,delta>| = 3.565e-13 (level 4)
#> 2025-04-24 16:03:07.402997: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:07.404168: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:07.405383: Linearise components (level 3)
#> 2025-04-24 16:03:07.406542: Linearise component 'z' (level 4)
#> 2025-04-24 16:03:07.420868: Linearise component 'Intercept' (level 4)
#> 2025-04-24 16:03:07.429992: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:07.432222: Linearise with respect to component 'z' (level 4)
#> 2025-04-24 16:03:07.435566: Linearise with respect to component 'Intercept' (level 4)
#> 2025-04-24 16:03:07.448189: iinla: Max deviation from previous: 0.0918% of SD, and line search is inactive
#> [stop if: <10% and line search inactive] (level 1)
#> 2025-04-24 16:03:07.449473: iinla: Convergence criterion met.
#> Running final INLA integration step with known theta mode. (level 1)
#> 2025-04-24 16:03:07.451251: iinla: Iteration 6 [max:10] (level 1)
#> 2025-04-24 16:03:08.790088: bru: Preprocessing (level 1)
#> 2025-04-24 16:03:08.794979: Evaluate component inputs for each observation model (level 3)
#> 2025-04-24 16:03:08.796247: input_eval.component_list (level 4)
#> 2025-04-24 16:03:08.797471: input_eval.component(field) (level 4)
#> 2025-04-24 16:03:08.798671: input_eval.bru_input(field) (level 5)
#> 2025-04-24 16:03:08.805494: input_eval.bru_input(field.group) (level 5)
#> 2025-04-24 16:03:08.810878: input_eval.bru_input(field.repl) (level 5)
#> 2025-04-24 16:03:08.838488: iinla: Start (level 3)
#> 2025-04-24 16:03:08.839684: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:08.840926: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:08.842219: Linearise components (level 3)
#> 2025-04-24 16:03:08.843414: Linearise component 'field' (level 4)
#> 2025-04-24 16:03:08.855998: iinla: Evaluate component simplifications (level 3)
#> 2025-04-24 16:03:08.857229: Simplify model components (level 3)
#> 2025-04-24 16:03:08.858478: Simplify component 'field' (level 4)
#> 2025-04-24 16:03:08.869422: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:08.87252: iinla: Construct inla stack (level 3)
#> 2025-04-24 16:03:08.883904: iinla: Model initialisation completed (level 3)
#> 2025-04-24 16:03:08.885181: iinla: Iteration 1 [max:1] (level 1)
#> 2025-04-24 16:03:11.475895: input_eval.component_list (level 4)
#> 2025-04-24 16:03:15.275511: bru: Preprocessing (level 1)
#> 2025-04-24 16:03:15.283063: Evaluate component inputs for each observation model (level 3)
#> 2025-04-24 16:03:15.284412: input_eval.component_list (level 4)
#> 2025-04-24 16:03:15.285671: input_eval.component(x) (level 4)
#> 2025-04-24 16:03:15.286929: input_eval.bru_input(x) (level 5)
#> 2025-04-24 16:03:15.295333: input_eval.bru_input(x.group) (level 5)
#> 2025-04-24 16:03:15.302027: input_eval.bru_input(x.repl) (level 5)
#> 2025-04-24 16:03:15.308326: input_eval.component_list (level 4)
#> 2025-04-24 16:03:15.31037: input_eval.component(x) (level 4)
#> 2025-04-24 16:03:15.312236: input_eval.bru_input(x) (level 5)
#> 2025-04-24 16:03:15.319985: input_eval.bru_input(x.group) (level 5)
#> 2025-04-24 16:03:15.327062: input_eval.bru_input(x.repl) (level 5)
#> 2025-04-24 16:03:15.357233: iinla: Start (level 3)
#> 2025-04-24 16:03:15.35848: iinla: Evaluate component linearisations (level 3)
#> 2025-04-24 16:03:15.359699: Linearise components for each observation model (level 3)
#> 2025-04-24 16:03:15.361009: Linearise components (level 3)
#> 2025-04-24 16:03:15.362221: Linearise component 'x' (level 4)
#> 2025-04-24 16:03:15.373784: Linearise components (level 3)
#> 2025-04-24 16:03:15.375073: Linearise component 'x' (level 4)
#> 2025-04-24 16:03:15.384714: iinla: Evaluate component simplifications (level 3)
#> 2025-04-24 16:03:15.385965: Simplify model components (level 3)
#> 2025-04-24 16:03:15.387223: Simplify component 'x' (level 4)
#> 2025-04-24 16:03:15.39738: Simplify component 'x' (level 4)
#> 2025-04-24 16:03:15.413742: iinla: Evaluate predictor linearisation (level 3)
#> 2025-04-24 16:03:15.420917: iinla: Construct inla stack (level 3)
#> 2025-04-24 16:03:15.43661: iinla: Model initialisation completed (level 3)
#> 2025-04-24 16:03:15.438039: iinla: Iteration 1 [max:1] (level 1)