Get posterior distribution of the Z matrix
get_Z(
flocker_fit,
draw_ids = NULL,
history_condition = TRUE,
sample = FALSE,
new_data = NULL,
allow_new_levels = FALSE,
sample_new_levels = "uncertainty"
)A flocker_fit object
Vector of indices of the posterior draws to be used. If `NULL` (the default) all draws are used in their native order.
Should the posterior distribution for Z directly condition on the observed detection history (`TRUE`) or not (`FALSE`)? For example, at sites with at least one detection, the true occupancy state conditioned on the history is one with absolute certainty. Without directly conditioning on the history, the occupancy state is controlled by the posterior distribution for the occupancy probability psi.
Should the return be posterior probabilities of occupancy (FALSE), or bernoulli samples from those probabilities (TRUE)
Optional new data at which to predict the Z matrix. Can be the output of `make_flocker_data` or the `unit_covs` input to `make_flocker_data` provided that `history_condition` is `FALSE` and the occupancy model is a single-season, non-augmented model.
allow new levels for random effect terms in `new_data`? Will error if set to `FALSE` and new levels are provided in `new_data`.
If `new_data` is provided and contains random effect levels not present in the original data, how should predictions be handled? Passed directly to `brms::prepare_predictions`, which see.
The posterior Z matrix in the shape of the first visit in `obs` as passed to make_flocker_data, with posterior iterations stacked along the final dimension
# \donttest{
get_Z(example_flocker_model_single)
#> draw_1 draw_2 draw_3 draw_4 draw_5
#> site_1 5.337827e-01 0.449233056 0.025043658 9.996248e-01 2.826521e-03
#> site_2 5.317473e-02 0.053380948 0.072717107 3.593804e-01 1.683079e-01
#> site_3 1.031352e-02 0.081116769 0.014904487 8.444902e-01 1.087789e-03
#> site_4 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_5 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_6 9.310078e-02 0.081056383 0.062366134 7.435026e-01 1.057937e-01
#> site_7 1.278793e-02 0.120712743 0.009850924 9.632986e-01 2.629333e-04
#> site_8 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_9 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_10 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_11 1.148864e-01 0.062754540 0.078284661 5.255761e-01 3.519847e-01
#> site_12 7.229651e-02 0.070139228 0.061067665 6.338181e-01 1.183807e-01
#> site_13 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_14 3.981870e-01 0.175193158 0.072443387 9.765077e-01 2.295337e-01
#> site_15 5.038291e-01 0.202261492 0.099094632 9.823302e-01 3.375285e-01
#> site_16 2.642255e-01 0.221734012 0.036002139 9.924761e-01 1.842546e-02
#> site_17 1.576762e-01 0.142001070 0.039884911 9.638860e-01 3.470729e-02
#> site_18 6.999086e-01 0.404322376 0.082702950 9.987726e-01 2.169190e-01
#> site_19 8.464525e-07 0.005136408 0.003078839 2.732189e-05 4.864312e-05
#> site_20 1.292691e-01 0.042333504 0.154543112 1.408870e-01 5.932121e-01
#> site_21 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_22 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_23 2.053512e-02 0.075528958 0.004613601 3.285588e-02 2.285311e-02
#> site_24 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_25 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_26 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_27 4.905990e-03 0.091766773 0.001902879 5.648307e-02 2.088242e-02
#> site_28 1.831769e-01 0.051901022 0.018373399 1.772930e-02 2.623098e-02
#> site_29 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_30 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_31 1.922527e-01 0.112038045 0.040968165 5.349022e-03 5.911154e-02
#> site_32 1.283623e-01 0.112891258 0.029713595 5.488522e-03 5.359308e-02
#> site_33 2.589624e-02 0.171995573 0.016774414 1.059365e-02 6.182188e-02
#> site_34 1.730880e-02 0.237256069 0.022034042 8.935150e-03 8.607185e-02
#> site_35 1.870761e-02 0.290869955 0.035080371 4.130492e-03 1.142544e-01
#> site_36 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_37 1.475688e-02 0.167273263 0.010679703 1.819031e-02 5.358507e-02
#> site_38 1.952623e-03 0.428669468 0.021306039 3.992046e-03 1.437956e-01
#> site_39 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_40 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_41 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_42 6.158190e-02 0.011874309 0.039349936 2.813879e-01 1.118227e-02
#> site_43 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_44 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_45 3.981889e-02 0.019115532 0.051553190 9.731014e-02 2.618023e-03
#> site_46 1.030941e-01 0.025599710 0.106950019 5.814868e-01 5.782159e-02
#> site_47 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_48 6.216458e-02 0.026512907 0.092505730 2.558282e-01 1.144439e-02
#> site_49 6.536899e-02 0.029126804 0.094610767 2.663688e-01 1.251798e-02
#> site_50 6.455646e-02 0.018010288 0.068930905 2.982751e-01 1.348111e-02
#> site_51 7.500849e-02 0.019310362 0.080352425 3.906011e-01 2.207898e-02
#> site_52 8.880124e-02 0.021390028 0.082482200 4.859509e-01 3.577271e-02
#> site_53 1.797602e-01 0.058936784 0.266247657 8.415706e-01 2.974885e-01
#> site_54 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_55 2.301096e-01 0.059316587 0.313843617 8.983533e-01 5.029780e-01
#> site_56 3.315599e-01 0.171318134 0.660687477 9.586289e-01 8.356313e-01
#> site_57 2.139135e-01 0.090751475 0.411181734 8.959749e-01 4.587520e-01
#> site_58 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_59 1.139922e-02 0.006046394 0.007404212 5.345272e-03 4.917308e-05
#> site_60 3.608054e-02 0.003937266 0.011253260 1.072077e-01 2.217754e-03
#> site_61 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_62 1.074555e-01 0.027438335 0.046631524 7.345825e-01 1.197290e-01
#> site_63 1.092457e-01 0.045060721 0.122796142 7.278299e-01 1.327102e-01
#> site_64 1.999318e-01 0.329052805 0.449535003 7.264760e-01 2.000121e-01
#> site_65 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_66 1.236723e-01 0.050461848 0.081744122 7.332053e-01 1.332133e-01
#> site_67 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_68 9.128194e-02 0.015842873 0.045382396 7.313719e-01 1.113201e-01
#> site_69 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_70 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_71 1.136541e-01 0.035141522 0.057464930 7.340399e-01 1.244344e-01
#> site_72 1.172896e-01 0.040681437 0.069135425 7.334156e-01 1.283657e-01
#> site_73 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_74 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_75 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_76 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_77 1.415145e-01 0.107144246 0.183840438 7.293084e-01 1.533896e-01
#> site_78 2.337155e-01 0.393241979 0.485598010 7.286061e-01 2.153355e-01
#> site_79 4.196964e-02 0.000415023 0.008036245 7.277113e-01 7.044907e-02
#> site_80 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_81 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_82 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_83 1.127026e-01 0.221232476 0.204454124 7.800565e-01 1.496068e-01
#> site_84 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_85 8.416035e-02 0.187518023 0.107043635 7.183022e-01 1.512609e-01
#> site_86 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_87 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_88 8.258801e-02 0.178135619 0.127555745 7.324408e-01 1.485379e-01
#> site_89 9.075084e-02 0.195202499 0.130077156 7.405151e-01 1.452859e-01
#> site_90 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_91 5.631314e-02 0.130578257 0.082503069 6.923750e-01 6.665473e-02
#> site_92 5.695607e-02 0.133366902 0.075410432 6.905287e-01 4.881544e-02
#> site_93 7.613342e-02 0.163740815 0.147326506 7.316128e-01 7.667284e-02
#> site_94 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_95 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_96 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_97 9.516955e-02 0.191023003 0.221831836 7.645533e-01 1.306798e-01
#> site_98 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_99 1.000000e+00 1.000000000 1.000000000 1.000000e+00 1.000000e+00
#> site_100 2.805775e-02 0.076071170 0.018709179 5.890240e-01 1.201351e-02
#> draw_6 draw_7 draw_8
#> site_1 0.0796146168 7.806933e-01 1.653971e-01
#> site_2 0.0600471381 2.955640e-02 8.637652e-03
#> site_3 0.0124513551 1.012656e-01 2.317418e-03
#> site_4 1.0000000000 1.000000e+00 1.000000e+00
#> site_5 1.0000000000 1.000000e+00 1.000000e+00
#> site_6 0.0645560261 1.123125e-01 1.862982e-02
#> site_7 0.0101952676 2.447794e-01 3.893002e-03
#> site_8 1.0000000000 1.000000e+00 1.000000e+00
#> site_9 1.0000000000 1.000000e+00 1.000000e+00
#> site_10 1.0000000000 1.000000e+00 1.000000e+00
#> site_11 0.0743886559 5.637821e-02 1.644721e-02
#> site_12 0.0578829035 7.371881e-02 1.283536e-02
#> site_13 1.0000000000 1.000000e+00 1.000000e+00
#> site_14 0.1237800503 4.599295e-01 1.134699e-01
#> site_15 0.1836216298 5.160686e-01 1.779899e-01
#> site_16 0.0669694080 5.549405e-01 7.193482e-02
#> site_17 0.0558537398 3.524934e-01 3.604440e-02
#> site_18 0.2353119260 7.313837e-01 2.841234e-01
#> site_19 0.0004258146 2.697361e-07 1.004984e-07
#> site_20 0.1272994613 1.390182e-02 1.954108e-02
#> site_21 1.0000000000 1.000000e+00 1.000000e+00
#> site_22 1.0000000000 1.000000e+00 1.000000e+00
#> site_23 0.0497736454 1.529706e-02 7.580856e-03
#> site_24 1.0000000000 1.000000e+00 1.000000e+00
#> site_25 1.0000000000 1.000000e+00 1.000000e+00
#> site_26 1.0000000000 1.000000e+00 1.000000e+00
#> site_27 0.0308089009 5.742018e-03 6.291301e-03
#> site_28 0.1042160245 7.014538e-02 1.030896e-02
#> site_29 1.0000000000 1.000000e+00 1.000000e+00
#> site_30 1.0000000000 1.000000e+00 1.000000e+00
#> site_31 0.1534112266 1.270572e-01 2.618967e-02
#> site_32 0.1298428772 9.173015e-02 2.290143e-02
#> site_33 0.0914305938 4.494871e-02 2.487481e-02
#> site_34 0.0997305206 5.236926e-02 3.701136e-02
#> site_35 0.1206036894 7.507887e-02 5.409985e-02
#> site_36 1.0000000000 1.000000e+00 1.000000e+00
#> site_37 0.0726107370 2.870061e-02 2.030011e-02
#> site_38 0.0842474538 3.493214e-02 7.229211e-02
#> site_39 1.0000000000 1.000000e+00 1.000000e+00
#> site_40 1.0000000000 1.000000e+00 1.000000e+00
#> site_41 1.0000000000 1.000000e+00 1.000000e+00
#> site_42 0.0279549197 2.663699e-03 5.615826e-01
#> site_43 1.0000000000 1.000000e+00 1.000000e+00
#> site_44 1.0000000000 1.000000e+00 1.000000e+00
#> site_45 0.0347494257 1.517362e-03 5.431688e-01
#> site_46 0.0572476830 2.757165e-02 6.018646e-01
#> site_47 1.0000000000 1.000000e+00 1.000000e+00
#> site_48 0.0558703059 6.838584e-03 5.914617e-01
#> site_49 0.0591387535 7.907767e-03 5.938620e-01
#> site_50 0.0418404139 5.069157e-03 5.841989e-01
#> site_51 0.0456192191 8.570859e-03 5.934981e-01
#> site_52 0.0483272119 1.458327e-02 5.917846e-01
#> site_53 0.1210304618 2.686739e-01 6.166656e-01
#> site_54 1.0000000000 1.000000e+00 1.000000e+00
#> site_55 0.1007299844 5.472575e-01 5.420045e-01
#> site_56 0.3071233365 9.019224e-01 6.271185e-01
#> site_57 0.1862978233 4.882866e-01 6.520596e-01
#> site_58 1.0000000000 1.000000e+00 1.000000e+00
#> site_59 0.0067206348 2.107485e-05 3.960029e-01
#> site_60 0.0110180754 1.563149e-04 5.107111e-01
#> site_61 1.0000000000 1.000000e+00 1.000000e+00
#> site_62 0.1875321630 6.605609e-02 3.714846e-01
#> site_63 0.0866747138 6.958699e-02 5.310582e-01
#> site_64 0.1325245476 2.601093e-01 8.561403e-01
#> site_65 1.0000000000 1.000000e+00 1.000000e+00
#> site_66 0.1654432699 8.719778e-02 4.880334e-01
#> site_67 1.0000000000 1.000000e+00 1.000000e+00
#> site_68 0.1342019146 4.504595e-02 3.275554e-01
#> site_69 1.0000000000 1.000000e+00 1.000000e+00
#> site_70 1.0000000000 1.000000e+00 1.000000e+00
#> site_71 0.1870277686 7.409118e-02 4.133029e-01
#> site_72 0.1673483107 7.809762e-02 4.490110e-01
#> site_73 1.0000000000 1.000000e+00 1.000000e+00
#> site_74 1.0000000000 1.000000e+00 1.000000e+00
#> site_75 1.0000000000 1.000000e+00 1.000000e+00
#> site_76 1.0000000000 1.000000e+00 1.000000e+00
#> site_77 0.1239385873 1.222359e-01 6.576442e-01
#> site_78 0.1573530607 3.150871e-01 8.793135e-01
#> site_79 0.0698311578 6.980748e-03 7.085657e-02
#> site_80 1.0000000000 1.000000e+00 1.000000e+00
#> site_81 1.0000000000 1.000000e+00 1.000000e+00
#> site_82 1.0000000000 1.000000e+00 1.000000e+00
#> site_83 0.2529422293 1.330377e-01 3.365642e-01
#> site_84 1.0000000000 1.000000e+00 1.000000e+00
#> site_85 0.3465024255 3.188888e-02 2.432458e-01
#> site_86 1.0000000000 1.000000e+00 1.000000e+00
#> site_87 1.0000000000 1.000000e+00 1.000000e+00
#> site_88 0.3291123358 4.468551e-02 2.518304e-01
#> site_89 0.3236054446 5.138330e-02 2.706003e-01
#> site_90 1.0000000000 1.000000e+00 1.000000e+00
#> site_91 0.2259326798 3.701520e-02 2.075471e-01
#> site_92 0.1705564035 4.410574e-02 2.156195e-01
#> site_93 0.1459925023 1.123415e-01 2.747995e-01
#> site_94 1.0000000000 1.000000e+00 1.000000e+00
#> site_95 1.0000000000 1.000000e+00 1.000000e+00
#> site_96 1.0000000000 1.000000e+00 1.000000e+00
#> site_97 0.1995138863 1.584555e-01 3.151450e-01
#> site_98 1.0000000000 1.000000e+00 1.000000e+00
#> site_99 1.0000000000 1.000000e+00 1.000000e+00
#> site_100 0.1368356576 1.012123e-02 1.282667e-01
#> attr(,"class")
#> [1] "postZ" "matrix" "array"
# }