R/log_lik_occupancy.R
log_lik_flocker.RdCompute unit-wise or series-wise log-likelihood matrix for a flocker_fit object
log_lik_flocker(flocker_fit, draw_ids = NULL)A flocker_fit object
the draw ids to compute log-likelihoods for. Defaults to using the full posterior.
A posterior log-likelihood matrix, where iterations are rows and units, series, or species are columns.
In single-season models, rows are units (e.g. points or species-points; suitable for leave-one-unit-out CV). In multiseason models, rows are series (i.e. points or species-points, suitable for leave-one-series-out CV). In augmented models, rows are species (suitable for leave-one-species-out CV).
log_lik_flocker(example_flocker_model_single)
#> site_1 site_2 site_3 site_4 site_5 site_6
#> draw_1 -0.87891758 -0.5597283 -0.8252117 -1.943163 -2.097238 -0.6440278
#> draw_2 -0.77305511 -0.2623331 -0.4178537 -2.512035 -4.737141 -0.3356766
#> draw_3 -0.21096295 -0.7271022 -0.5800918 -3.179967 -2.170735 -0.6083554
#> draw_4 -0.08673553 -0.7403768 -0.9607153 -3.276819 -3.461628 -0.7544938
#> draw_5 -0.40036394 -0.8696530 -0.8339110 -2.085036 -2.572523 -0.8068541
#> draw_6 -0.66920482 -0.7739873 -0.8001075 -2.430320 -1.956537 -0.7551397
#> draw_7 -0.09215167 -0.5310144 -0.6741906 -3.189182 -1.875427 -0.5679291
#> draw_8 -0.30523172 -0.4757615 -0.4825484 -2.586512 -1.518854 -0.4658906
#> site_7 site_8 site_9 site_10 site_11 site_12 site_13
#> draw_1 -0.9924530 -2.731411 -3.234262 -4.005054 -0.5365798 -0.6254423 -3.079324
#> draw_2 -0.5348009 -4.856002 -3.483731 -3.772242 -0.2869831 -0.3129835 -3.658535
#> draw_3 -0.4723265 -2.674439 -3.130066 -3.650284 -0.6722063 -0.6483157 -3.274728
#> draw_4 -0.7437716 -4.345119 -2.085552 -2.797655 -0.7513833 -0.8004936 -4.192567
#> draw_5 -0.7083146 -3.386394 -2.018494 -3.765140 -0.5697973 -0.8334238 -3.167069
#> draw_6 -0.7873685 -2.385257 -3.328710 -3.812360 -0.7535037 -0.7665819 -2.943182
#> draw_7 -0.6718816 -2.536176 -3.866100 -4.099667 -0.5465667 -0.5694589 -3.632175
#> draw_8 -0.4812510 -1.970520 -4.924409 -5.076458 -0.4679467 -0.4716973 -3.284056
#> site_14 site_15 site_16 site_17 site_18 site_19
#> draw_1 -0.5018729 -0.3389531 -0.8653871 -0.7992531 -0.23002184 -0.3123688
#> draw_2 -0.4751614 -0.4718973 -0.5843060 -0.4764098 -0.60669447 -0.1133998
#> draw_3 -0.4045043 -0.3583822 -0.3596700 -0.4620661 -0.20943290 -1.3211313
#> draw_4 -0.3279614 -0.2510413 -0.2795428 -0.4855568 -0.07883871 -0.0509454
#> draw_5 -0.4449195 -0.2742904 -0.5889667 -0.6967435 -0.23761697 -1.5600575
#> draw_6 -0.6651154 -0.5918989 -0.7150666 -0.7430469 -0.49745291 -0.8819645
#> draw_7 -0.3410051 -0.2619090 -0.3136435 -0.4829660 -0.07847817 -0.2714011
#> draw_8 -0.3647182 -0.2892029 -0.4107507 -0.4483865 -0.15151707 -0.4835975
#> site_20 site_21 site_22 site_23 site_24 site_25 site_26
#> draw_1 -0.3755507 -7.851043 -3.768770 -0.6126683 -6.215604 -2.836559 -2.994910
#> draw_2 -0.2003850 -5.102267 -3.997444 -1.0911630 -3.163826 -3.313834 -3.034481
#> draw_3 -0.7647025 -1.702316 -4.999056 -0.6084213 -3.327844 -3.679849 -3.174248
#> draw_4 -0.4338517 -2.569300 -2.946781 -0.6610667 -4.183526 -4.292509 -3.873074
#> draw_5 -0.2852839 -4.565646 -4.382289 -0.6981140 -3.386514 -3.498286 -3.182267
#> draw_6 -0.7125152 -4.189913 -4.148620 -0.7676379 -3.504605 -3.064089 -3.406331
#> draw_7 -0.4490793 -2.429049 -4.581673 -0.8652063 -3.262614 -3.094173 -3.077116
#> draw_8 -0.4644687 -3.433147 -4.672091 -0.5855575 -3.302310 -3.843564 -3.099333
#> site_27 site_28 site_29 site_30 site_31 site_32
#> draw_1 -0.2252793 -1.8443219 -2.267364 -2.582375 -1.3612906 -1.1567991
#> draw_2 -1.1043927 -1.0661440 -2.375431 -2.817362 -1.0144854 -1.0226241
#> draw_3 -0.6569741 -0.5238500 -2.844846 -3.099807 -0.5195898 -0.5439364
#> draw_4 -0.8219116 -0.4330563 -4.079735 -4.802280 -0.5055839 -0.5477811
#> draw_5 -0.6599413 -0.7646075 -2.479718 -2.979901 -0.7103488 -0.7033877
#> draw_6 -0.6622283 -0.9455785 -3.062325 -2.864636 -0.8195013 -0.8030414
#> draw_7 -0.7810296 -0.9776631 -2.718527 -2.690042 -0.8654679 -0.8738753
#> draw_8 -0.5803299 -0.5937159 -2.358490 -3.197589 -0.5744877 -0.5758734
#> site_33 site_34 site_35 site_36 site_37 site_38
#> draw_1 -0.3726850 -0.2066755 -0.1674808 -5.521951 -0.2692863 -0.01603136
#> draw_2 -0.9957654 -0.9305708 -0.8628720 -2.895637 -1.0115490 -0.70924907
#> draw_3 -0.6178370 -0.6377410 -0.6321649 -4.886695 -0.6390489 -0.74462679
#> draw_4 -0.7693034 -0.8759418 -0.9145038 -4.144671 -0.8233709 -1.37105365
#> draw_5 -0.6379256 -0.5900853 -0.5522466 -3.535806 -0.6336565 -0.44427829
#> draw_6 -0.6609828 -0.5855939 -0.5427447 -3.579156 -0.6413767 -0.38207936
#> draw_7 -0.7887396 -0.7308034 -0.6916432 -4.347835 -0.7753726 -0.57163944
#> draw_8 -0.5648382 -0.5487696 -0.5297860 -4.081815 -0.5673963 -0.49766270
#> site_39 site_40 site_41 site_42 site_43 site_44
#> draw_1 -2.505388 -3.062977 -2.588723 -0.16371531 -2.880414 -2.802050
#> draw_2 -2.882697 -3.378901 -2.124933 -0.10077460 -2.617515 -2.659242
#> draw_3 -3.885600 -4.171268 -1.801393 -0.16355201 -1.586281 -2.212497
#> draw_4 -5.541089 -4.435989 -1.261960 -0.02657529 -2.315110 -1.923592
#> draw_5 -3.003995 -3.596557 -1.650537 -0.01072913 -2.576427 -2.222495
#> draw_6 -2.910039 -3.518018 -1.346116 -0.12459328 -1.955039 -2.077377
#> draw_7 -3.181297 -3.743519 -3.461980 -0.03782123 -1.938655 -3.079759
#> draw_8 -3.299295 -3.818085 -1.359286 -0.15982784 -1.956094 -2.176377
#> site_45 site_46 site_47 site_48 site_49 site_50
#> draw_1 -0.076075057 -0.31103251 -2.705061 -0.143615449 -0.145803053 -0.16633358
#> draw_2 -0.045445904 -0.16589019 -3.092403 -0.077642761 -0.077325080 -0.09697319
#> draw_3 -0.035230259 -0.32401055 -2.631790 -0.084972526 -0.088839246 -0.13880464
#> draw_4 -0.001281782 -0.10710424 -2.760883 -0.008549257 -0.009238782 -0.01909699
#> draw_5 -0.000781172 -0.07303318 -2.380217 -0.005502942 -0.005757812 -0.01004680
#> draw_6 -0.031426303 -0.27143768 -2.547609 -0.079257888 -0.080415296 -0.11509565
#> draw_7 -0.006045436 -0.17137842 -2.451071 -0.025329233 -0.026519184 -0.03810974
#> draw_8 -0.030581864 -0.25092676 -2.740338 -0.064578587 -0.065956234 -0.11390121
#> site_51 site_52 site_53 site_54 site_55 site_56
#> draw_1 -0.20774931 -0.25626289 -0.5991579 -2.776743 -0.8769837 -1.1372157
#> draw_2 -0.11750367 -0.14143077 -0.2879000 -3.174318 -0.4394834 -0.5082383
#> draw_3 -0.18746954 -0.26214743 -0.6346159 -2.274036 -1.0394361 -0.8853790
#> draw_4 -0.03575411 -0.07235454 -0.3843646 -2.173254 -0.9156003 -1.0235502
#> draw_5 -0.02026179 -0.04038359 -0.4712743 -2.298511 -1.1540075 -1.3370805
#> draw_6 -0.15701565 -0.21259485 -0.6082220 -2.743963 -1.0335972 -1.2640885
#> draw_7 -0.06449825 -0.10865594 -0.6471338 -2.199059 -1.1387671 -0.7782948
#> draw_8 -0.15011440 -0.21590360 -0.4579260 -2.271001 -0.8071308 -0.7782043
#> site_57 site_58 site_59 site_60 site_61 site_62
#> draw_1 -0.7040048 -2.993500 -1.343771e-02 -0.089061011 -3.076350 -0.3734605
#> draw_2 -0.3176978 -4.162081 -1.248792e-02 -0.064922554 -2.438216 -0.3697498
#> draw_3 -0.6182911 -4.609549 -5.308854e-03 -0.085570033 -2.438884 -0.2366897
#> draw_4 -0.4018544 -4.244773 -1.159029e-05 -0.006156103 -2.367145 -1.0042482
#> draw_5 -0.6309109 -3.569854 -5.990316e-06 -0.001961713 -2.782414 -0.3588091
#> draw_6 -0.7023399 -4.162157 -3.343681e-03 -0.062214085 -3.137486 -0.5915801
#> draw_7 -0.6963371 -4.703440 -1.616892e-04 -0.008953396 -2.509339 -0.5574330
#> draw_8 -0.4384940 -4.202516 -7.034980e-03 -0.117013691 -2.197424 -0.8408139
#> site_63 site_64 site_65 site_66 site_67 site_68
#> draw_1 -0.6592435 -1.3441938 -3.410962 -0.5165405 -3.529440 -0.3716090
#> draw_2 -0.4985821 -0.5265267 -4.574796 -0.4298433 -4.164472 -0.3708889
#> draw_3 -0.4385336 -0.9705245 -4.246387 -0.3512846 -3.495157 -0.2208957
#> draw_4 -1.1056869 -1.2562112 -2.339772 -1.0552163 -3.267660 -1.0099060
#> draw_5 -0.4888874 -0.7595208 -3.329619 -0.4270844 -3.679656 -0.3574416
#> draw_6 -0.5906132 -0.3510018 -2.795904 -0.5459721 -4.541115 -0.6656161
#> draw_7 -0.6929439 -0.7785639 -3.684710 -0.6159270 -3.850159 -0.5688892
#> draw_8 -1.0376709 -0.9119395 -2.707158 -0.9222736 -3.521014 -0.8705235
#> site_69 site_70 site_71 site_72 site_73 site_74 site_75
#> draw_1 -4.241889 -3.852462 -0.4210623 -0.4700972 -3.252844 -3.424920 -2.903192
#> draw_2 -3.304476 -3.763361 -0.3907962 -0.4126679 -3.465016 -4.019245 -2.963614
#> draw_3 -4.945558 -4.301389 -0.2742255 -0.3119250 -3.695222 -3.484480 -2.853292
#> draw_4 -4.373917 -3.377272 -1.0228693 -1.0402146 -3.258875 -3.272841 -2.351949
#> draw_5 -4.604050 -3.968156 -0.3826392 -0.4056405 -3.620066 -3.669402 -2.960054
#> draw_6 -3.264712 -3.399621 -0.5654067 -0.5656401 -3.482091 -4.330618 -3.027726
#> draw_7 -3.162873 -3.435744 -0.5774960 -0.5998781 -3.234529 -3.678348 -2.886115
#> draw_8 -3.782905 -3.309234 -0.8729138 -0.9042583 -3.277025 -3.561173 -2.353170
#> site_76 site_77 site_78 site_79 site_80 site_81
#> draw_1 -2.874999 -0.8130038 -1.3938292 -0.12837585 -4.412647 -2.258352
#> draw_2 -3.207441 -0.5240656 -0.4708502 -0.20400301 -4.211876 -2.457934
#> draw_3 -3.479064 -0.5853811 -1.0293908 -0.05336183 -4.593276 -1.741401
#> draw_4 -3.164827 -1.1407627 -1.2628384 -0.88319622 -3.466592 -1.920207
#> draw_5 -3.362048 -0.5527914 -0.7802040 -0.20707341 -4.235363 -1.409522
#> draw_6 -3.233532 -0.4918153 -0.3058177 -0.99205482 -3.979088 -1.517008
#> draw_7 -2.957819 -0.7160213 -0.7358648 -0.40233500 -3.789103 -2.002276
#> draw_8 -3.221517 -1.0048302 -0.8460237 -0.51335025 -3.550238 -2.153234
#> site_82 site_83 site_84 site_85 site_86 site_87 site_88
#> draw_1 -3.266105 -0.3942287 -3.043158 -0.2244774 -3.516885 -3.759867 -0.2830539
#> draw_2 -2.784376 -0.7174877 -2.975304 -0.6257611 -3.045959 -3.499992 -0.6795961
#> draw_3 -3.013702 -0.3622389 -2.765293 -0.1095776 -3.528535 -4.895282 -0.1751916
#> draw_4 -1.992498 -0.7238079 -2.667207 -0.3875317 -3.223443 -4.419191 -0.5197989
#> draw_5 -2.981529 -0.4116809 -2.730660 -0.1614889 -3.327863 -4.539812 -0.2335002
#> draw_6 -2.345676 -0.3402927 -2.896581 -0.1002847 -3.644684 -5.406092 -0.1595821
#> draw_7 -3.618281 -0.5767602 -2.654560 -0.1561684 -3.376414 -3.195903 -0.2561739
#> draw_8 -2.592336 -0.9105561 -2.709176 -0.5622250 -2.969400 -3.248759 -0.6937769
#> site_89 site_90 site_91 site_92 site_93 site_94
#> draw_1 -0.2770110 -3.596252 -0.3477487 -0.3723918 -0.4838838 -3.568473
#> draw_2 -0.6606507 -3.016598 -0.7608306 -0.7741518 -0.8163780 -3.139153
#> draw_3 -0.1771753 -3.597125 -0.2893264 -0.3441917 -0.5404334 -3.412956
#> draw_4 -0.4980348 -3.404741 -0.7681999 -0.8463057 -1.0430856 -2.601902
#> draw_5 -0.2408483 -3.100311 -0.3700574 -0.4203008 -0.5560921 -3.888582
#> draw_6 -0.1693596 -3.767625 -0.3223468 -0.4045755 -0.4965654 -3.689492
#> draw_7 -0.2557357 -3.680486 -0.3529767 -0.4143333 -0.7759275 -3.244410
#> draw_8 -0.6754796 -3.043434 -0.8396955 -0.8894552 -1.1067953 -2.930878
#> site_95 site_96 site_97 site_98 site_99 site_100
#> draw_1 -3.369413 -2.929728 -0.4984285 -2.766637 -4.419232 -0.2907612
#> draw_2 -3.098964 -2.657628 -0.8022316 -2.470054 -3.271457 -0.7596424
#> draw_3 -3.095683 -2.399502 -0.5302864 -1.757681 -6.199384 -0.2138548
#> draw_4 -2.901815 -2.116047 -0.9945519 -1.883444 -3.750963 -0.7883172
#> draw_5 -3.157848 -2.659354 -0.5406105 -2.354512 -5.980767 -0.3215979
#> draw_6 -3.213288 -2.692500 -0.4474061 -2.657996 -6.242662 -0.3826895
#> draw_7 -2.995837 -2.569147 -0.8555885 -2.364995 -5.650015 -0.1903686
#> draw_8 -2.895333 -2.507089 -1.1244276 -2.456556 -3.417929 -0.7211745