Create testing output similar to when running a 'BEAST2' run with nested sampling
See also
Use parse_beast2_output_to_ns to parse this output to a Nested Sampling result. See create_ns_mcmc to see how to do a marginal likelihood estimation using Nested Sampling.
Examples
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
create_test_ns_output()
#> [1] "[/usr/lib/jvm/java-8-oracle/bin/java, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar, beast.app.beastapp.BeastMain, nested_sampling.xml]"
#> [2] ""
#> [3] " BEAST v2.5.0, 2002-2018"
#> [4] " Bayesian Evolutionary Analysis Sampling Trees"
#> [5] " Designed and developed by"
#> [6] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
#> [7] " "
#> [8] " Department of Computer Science"
#> [9] " University of Auckland"
#> [10] " remco@cs.auckland.ac.nz"
#> [11] " alexei@cs.auckland.ac.nz"
#> [12] " "
#> [13] " Institute of Evolutionary Biology"
#> [14] " University of Edinburgh"
#> [15] " a.rambaut@ed.ac.uk"
#> [16] " "
#> [17] " David Geffen School of Medicine"
#> [18] " University of California, Los Angeles"
#> [19] " msuchard@ucla.edu"
#> [20] " "
#> [21] " Downloads, Help & Resources:"
#> [22] " http://beast2.org/"
#> [23] " "
#> [24] " Source code distributed under the GNU Lesser General Public License:"
#> [25] " http://github.com/CompEvol/beast2"
#> [26] " "
#> [27] " BEAST developers:"
#> [28] " Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "
#> [29] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "
#> [30] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "
#> [31] " Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"
#> [32] " "
#> [33] " Thanks to:"
#> [34] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
#> [35] ""
#> [36] "Random number seed: 1539258042094"
#> [37] ""
#> [38] "File: nested_sampling.xml seed: 1539258042094 threads: 1"
#> [39] "61430_aco: 78 4"
#> [40] "626029_aco: 78 4"
#> [41] "630116_aco: 78 4"
#> [42] "630210_aco: 78 4"
#> [43] "B25702_aco: 78 4"
#> [44] "Alignment(anthus_aco_sub)"
#> [45] " 5 taxa"
#> [46] " 78 sites"
#> [47] " 9 patterns"
#> [48] ""
#> [49] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"
#> [50] "TreeLikelihood(treeLikelihood.anthus_aco_sub0) uses BeerLikelihoodCore4"
#> [51] " Alignment(anthus_aco_sub): [taxa, patterns, sites] = [5, 9, 78]"
#> [52] "==============================================================================="
#> [53] "Citations for this model:"
#> [54] ""
#> [55] "Patricio Maturana, Brendon J. Brewer, Steffen Klaere, Remco Bouckaert. Model selection and parameter inference in phylogenetics using Nested Sampling. Systematic Biology, syy050, 2018"
#> [56] ""
#> [57] "==============================================================================="
#> [58] "Counting 19 parameters"
#> [59] "replacing logger tracelog with NSLogger"
#> [60] "Writing file anthus_aco_sub.trees"
#> [61] " Sample posterior ESS(posterior) likelihood prior"
#> [62] "Writing file anthus_aco_sub.log"
#> [63] "Start likelihood 0: -225.2488738545589 "
#> [64] "1 particles initialised"
#> [65] " 0 -140.6759 N -157.4874 16.8115 --"
#> [66] "ML: -158.32601908408833 Information: 0.8385606384288167"
#> [67] " 1 -124.4630 2.0 -143.0242 18.5611 --"
#> [68] "ML: -144.86277038390745 Information: 1.8385386453449868"
#> [69] " 2 -124.6624 3.0 -141.6496 16.9872 --"
#> [70] "ML: -143.96492404000415 Information: 1.7551898946725117"
#> [71] " 3 -124.9536 4.0 -139.0497 14.0961 --"
#> [72] "ML: -142.59510010333074 Information: 2.7422179576086307"
#> [73] " 24 -125.0399 14.8 -137.0128 11.9729 --"
#> [74] "ML: -141.98047696172614 Information: 2.8349216678190885"
#> [75] " 25 -124.7614 15.4 -137.0127 12.2512 --"
#> [76] "ML: -141.98047696086337 Information: 2.8349216687952605"
#> [77] " 26 -124.7070 15.9 -137.0124 12.3054 --"
#> [78] "ML: -141.98047696054587 Information: 2.8349216691561026"
#> [79] " 27 -124.6071 16.2 -137.0106 12.4035 --"
#> [80] "ML: -141.98047696042886 Information: 2.8349216692884056"
#> [81] "28<=10000&& (28<2.0*2.8349216692884056*1||Math.abs(-141.98047696042886 - -141.98047696054587)/Math.abs(-141.98047696042886) > 1.0E-12"
#> [82] "Finished in 28 steps!"
#> [83] "Marginal likelihood: -141.31236790862764 (bootstrap SD=1.4240215445106443)"
#> [84] "Marginal likelihood: -140.98848039195855 (subsample SD=1.8638865000383444)"
#> [85] "Marginal likelihood: -141.1644574217485(1.1601428428211327)"
#> [86] "Information: 2.8349216692884056"
#> [87] "SD: 1.6837225630395305"
#> [88] ""
#> [89] "Operator Tuning #accept #reject Pr(m) Pr(acc|m)"
#> [90] "ScaleOperator(YuleBirthRateScaler.t:anthus_aco_sub) 0.75000 4797 998 0.04000 0.82778 Try setting scaleFactor to about 0.562"
#> [91] "ScaleOperator(YuleModelTreeScaler.t:anthus_aco_sub) 0.50000 1116 4748 0.04000 0.19031 "
#> [92] "ScaleOperator(YuleModelTreeRootScaler.t:anthus_aco_sub) 0.50000 887 4915 0.04000 0.15288 "
#> [93] "Uniform(YuleModelUniformOperator.t:anthus_aco_sub) - 11869 46191 0.40000 0.20443 "
#> [94] "SubtreeSlide(YuleModelSubtreeSlide.t:anthus_aco_sub) 1.00000 128 28742 0.20000 0.00443 Try decreasing size to about 0.5"
#> [95] "Exchange(YuleModelNarrow.t:anthus_aco_sub) - 3007 26046 0.20000 0.10350 "
#> [96] "Exchange(YuleModelWide.t:anthus_aco_sub) - 180 5641 0.04000 0.03092 "
#> [97] "WilsonBalding(YuleModelWilsonBalding.t:anthus_aco_sub) - 92 5643 0.04000 0.01604 "
#> [98] ""
#> [99] " Tuning: The value of the operator's tuning parameter, or '-' if the operator can't be optimized."
#> [100] " #accept: The total number of times a proposal by this operator has been accepted."
#> [101] " #reject: The total number of times a proposal by this operator has been rejected."
#> [102] " Pr(m): The probability this operator is chosen in a step of the MCMC (i.e. the normalized weight)."
#> [103] " Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator)."
#> [104] ""
#> [105] ""
#> [106] "Total calculation time: 0.823 seconds"
#> [107] "End likelihood: 12.388056869575024"
#> [108] "Producing posterior samples"
#> [109] ""
#> [110] "Marginal likelihood: -141.3000915386624 sqrt(H/N)=(NaN)=?=SD=(1.4593051179523482) Information: -0.19242514244311712"
#> [111] "Max ESS: 5.659472090348357"
#> [112] ""
#> [113] ""
#> [114] "Processing 28 trees from file."
#> [115] "Log file written to anthus_aco_sub.posterior.trees"
#> [116] "Done!"
#> [117] ""
#> [118] "Marginal likelihood: -141.31271098696405 sqrt(H/N)=(NaN)=?=SD=(1.462246661656647) Information: -0.1353639346412825"
#> [119] "Max ESS: 5.4945059635784155"
#> [120] ""
#> [121] ""
#> [122] "Log file written to anthus_aco_sub.posterior.log"
#> [123] "Done!"
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()