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  "Title": "Bayesian Occupancy, Abundance and Detection Models via 'tulpa'",
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  "Authors@R": "person(\"Gilles\", \"Colling\", email = \"gilles.colling051@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-3070-6066\"))",
  "Description": "Fits Bayesian models for species observed with imperfect\ndetection: single-season and dynamic site occupancy (MacKenzie\net al. (2002)\n<doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2>),\nN-mixture abundance from replicated counts (Royle (2004)\n<doi:10.1111/j.0006-341X.2004.00142.x>), distance sampling,\nremoval and double-observer counts, false-positive and\ntime-to-detection occupancy, integrated models combining\nseveral data sources, multi-species and joint species\ndistribution models, and a hurdle model for vegetation cover.\nLinear predictors take fixed, random, spatial and temporal\neffects. Each model supplies its observation likelihood to the\n'tulpa' engine, which fits it by Laplace approximation, by\nnested Laplace integration over the hyperparameters, or by\nHamiltonian Monte Carlo with the No-U-Turn Sampler (NUTS) using\nautomatic differentiation. Simulation, prediction and\ndiagnostic functions (posterior predictive checks,\nleave-one-out cross-validation, simulation-based calibration)\naccompany each model.",
  "URL": "https://gillescolling.com/tulpaObs/,\nhttps://github.com/gcol33/tulpaObs",
  "BugReports": "https://github.com/gcol33/tulpaObs/issues",
  "SystemRequirements": "C++17",
  "Roxygen": "list(markdown = TRUE)",
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  "Repository": "https://gcol33.r-universe.dev",
  "Date/Publication": "2026-10-12 11:08:11 UTC",
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  "Author": "Gilles Colling [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-3070-6066>)",
  "Maintainer": "Gilles Colling <gilles.colling051@gmail.com>",
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  "_created": "2026-10-12T17:25:26.000Z",
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    "message": "fix(count-spatial): weight the K.max boundary check by grid weight (#416)\n\n.count_spatial_warn_boundary() warned when any outer-grid node put mass on\nN = K.max, including nodes the posterior gives ~zero weight. Every reported\nsummary is a grid-weighted mixture, so the truncation error it carries is\nsum(weights * boundary_max); warn on that, and name the node contributing\nmost. Applies to all seven areal count fitters (ICAR / proper-CAR / BYM2 /\nSPDE N-mixture, three areal removal fits).\n\nThe #416 BYM2 repro now fits without a warning (weighted mass 1.7e-11);\nper-node boundary_max is still returned unchanged. Smoke manifest row for\ntest-count-spatial-prep.R re-measured (85 asserts, 1 gated skip).\n\nCo-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01AH7H1XETVYkapuS7iyUk7F\n",
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    {
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      "title": "Weakly-informative priors for cover-hurdle Laplace fits",
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      "topics": [
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    },
    {
      "page": "distance_laplace",
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    },
    {
      "page": "double_observer",
      "title": "Double-observer abundance family",
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    {
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    {
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      "title": "Multi-season integrated occupancy family",
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    },
    {
      "page": "dyn_occu",
      "title": "Dynamic (multi-season) occupancy family",
      "topics": [
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    {
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    {
      "page": "foray_counts",
      "title": "Repeated point-count abundance survey (synthetic)",
      "topics": [
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    {
      "page": "fp_occu_laplace",
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      "topics": [
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    {
      "page": "gdistremoval",
      "title": "Joint distance + removal sampling family",
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    {
      "page": "jsdm",
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    },
    {
      "page": "logLik.tobs_fit",
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    {
      "page": "meadow_cover",
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    {
      "page": "ms_abun",
      "title": "Multispecies N-mixture family",
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      "page": "ms_count",
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    },
    {
      "page": "ms_distance",
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      "topics": [
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    },
    {
      "page": "ms_dyn_occu",
      "title": "Community (multispecies) dynamic occupancy family",
      "topics": [
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    },
    {
      "page": "ms_int_occu",
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    },
    {
      "page": "ms_occu",
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      "topics": [
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    {
      "page": "ms_occu_cover",
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      "topics": [
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    },
    {
      "page": "nmix_laplace",
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      "topics": [
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    },
    {
      "page": "nmix_laplace_bym2",
      "title": "BYM2 Royle (2004) N-mixture model via nested Laplace",
      "topics": [
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      ]
    },
    {
      "page": "nmix_laplace_car_proper",
      "title": "Proper CAR Royle (2004) N-mixture model via nested Laplace",
      "topics": [
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    },
    {
      "page": "nmix_laplace_icar",
      "title": "Spatial Royle (2004) N-mixture model via nested Laplace",
      "topics": [
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      ]
    },
    {
      "page": "nmix_laplace_re",
      "title": "Community / multispecies N-mixture by Laplace",
      "topics": [
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    },
    {
      "page": "nmix_site_marginal",
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      "topics": [
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    },
    {
      "page": "nobs.tobs_fit",
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      "topics": [
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      ]
    },
    {
      "page": "occu",
      "title": "Single-season occupancy family",
      "topics": [
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    {
      "page": "occu_aggregation_scan",
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      "topics": [
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    },
    {
      "page": "occu_categorical",
      "title": "Presence + nominal class hurdle family",
      "topics": [
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    },
    {
      "page": "occu_cover",
      "title": "Joint occupancy-detection + cover hurdle family",
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    },
    {
      "page": "occu_cover_inputs",
      "title": "Build occu_cover() model inputs from a long, plot-level frame",
      "topics": [
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    },
    {
      "page": "occu_multi",
      "title": "Multi-species co-occurrence occupancy family",
      "topics": [
        "occu_multi"
      ]
    },
    {
      "page": "occu_multiscale_cover",
      "title": "Three-level (multiscale) occupancy + cover hurdle family",
      "topics": [
        "occu_multiscale_cover"
      ]
    },
    {
      "page": "occu_priors",
      "title": "Weakly-informative priors for occupancy Laplace fits",
      "topics": [
        "occu_priors"
      ]
    },
    {
      "page": "occu_ttd",
      "title": "Time-to-detection occupancy family",
      "topics": [
        "occu_ttd"
      ]
    },
    {
      "page": "peatland_occu",
      "title": "Peatland occupancy survey (synthetic)",
      "topics": [
        "peatland_occu"
      ]
    },
    {
      "page": "pit_residuals.tobs_fit",
      "title": "PIT residuals for a tobs fit",
      "topics": [
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    },
    {
      "page": "plot.tobs_aggregation_scan",
      "title": "Plot an occupancy aggregation scan",
      "topics": [
        "plot.tobs_aggregation_scan"
      ]
    },
    {
      "page": "plot.tobs_data",
      "title": "Plot detection history patterns",
      "topics": [
        "plot.tobs_data"
      ]
    },
    {
      "page": "ppc",
      "title": "Posterior predictive check",
      "topics": [
        "ppc",
        "ppc.tobs_fit"
      ]
    },
    {
      "page": "predict.cover_fit",
      "title": "Predict cover from a cover_fit",
      "topics": [
        "predict.cover_fit"
      ]
    },
    {
      "page": "predict.occu_categorical_fit",
      "title": "Predict from an occu_categorical fit",
      "topics": [
        "predict.occu_categorical_fit"
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    },
    {
      "page": "predict.tobs_fit",
      "title": "Predict from occupancy model",
      "topics": [
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    },
    {
      "page": "print.tobs_batch",
      "title": "Print a batched multi-response occu_cover fit.",
      "topics": [
        "print.tobs_batch"
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    },
    {
      "page": "print.tobs_family",
      "title": "Print method for tobs_family",
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    {
      "page": "print.tobs_fit",
      "title": "Print method for tobs_fit",
      "topics": [
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    },
    {
      "page": "ranef.tobs_fit",
      "title": "Random-effect estimates (BLUPs) for a tobs_fit",
      "topics": [
        "ranef.tobs_fit"
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    },
    {
      "page": "removal",
      "title": "Removal-sampling family",
      "topics": [
        "removal"
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    },
    {
      "page": "removal_laplace",
      "title": "Laplace fit of the removal-sampling abundance model",
      "topics": [
        "removal_laplace"
      ]
    },
    {
      "page": "residuals.tobs_fit",
      "title": "Residuals from occupancy model",
      "topics": [
        "residuals.tobs_fit"
      ]
    },
    {
      "page": "royle_nichols",
      "title": "Royle-Nichols occupancy family",
      "topics": [
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    },
    {
      "page": "sbc.tobs_fit",
      "title": "Simulation-based calibration for a fitted tobs model",
      "topics": [
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    },
    {
      "page": "simulate_abun",
      "title": "Simulate Royle (2004) N-mixture abundance data",
      "topics": [
        "simulate_abun"
      ]
    },
    {
      "page": "simulate_count",
      "title": "Simulate count / relative-abundance GLMM data",
      "topics": [
        "simulate_count"
      ]
    },
    {
      "page": "simulate_cover",
      "title": "Simulate cover-hurdle data (lognormal positive part)",
      "topics": [
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      ]
    },
    {
      "page": "simulate_cover_joint",
      "title": "Simulate cover-hurdle data with a shared BYM2 spatial field",
      "topics": [
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      ]
    },
    {
      "page": "simulate_distance",
      "title": "Simulate binned distance-sampling abundance data",
      "topics": [
        "simulate_distance"
      ]
    },
    {
      "page": "simulate_distsamp_open",
      "title": "Simulate an open-population distance-sampling data set",
      "topics": [
        "simulate_distsamp_open"
      ]
    },
    {
      "page": "simulate_double_observer",
      "title": "Simulate a double-observer abundance data set",
      "topics": [
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      ]
    },
    {
      "page": "simulate_dyn_abun",
      "title": "Simulate Dail-Madsen open N-mixture data",
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