{
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  "Package": "birp",
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  "Title": "Testing for Population Trends Using Low-Cost Ecological Count\nData",
  "Version": "0.9.0",
  "Date": "2026-09-01",
  "Authors@R": "c(person(\"Madleina\", \"Caduff\", role = c(\"aut\"),\nemail = \"madleina.caduff@unifr.ch\"),\nperson(\"Andreas\", \"Füglistaler\", role = c(\"aut\", \"cre\"),\nemail = \"andreas.fueglistaler@unifr.ch\"),\nperson(\"Daniel\", \"Wegmann\", role = c(\"aut\"),\nemail = \"daniel.wegmann@unifr.ch\"),\nperson(\"Liam\", \"Singer\", role = c(\"aut\")),\nperson(\"Raphael\", \"Eckel\", role = c(\"ctb\")),\nperson(\"Conrad\", \"Sanderson\", role = c(\"cph\"),\ncomment = \"Author of Armadillo\"),\nperson(\"Ryan\", \"Curtin\", role = c(\"cph\"),\ncomment = \"Author of Armadillo\"),\nperson(\"Daniel\", \"Lemire\", role = c(\"cph\"),\ncomment = \"Author of fast_float\"),\nperson(\"João Paulo\", \"Magalhaes\", role = c(\"cph\"),\ncomment = \"Author of fast_float\"),\nperson(\"Victor\", \"Zverovich\", role = c(\"cph\"),\ncomment = \"Author of {fmt}\"),\nperson(\"Rene\", \"Brun\", role = c(\"cph\"),\ncomment = \"Author of FindR.cmake (CERN ROOT)\"),\nperson(\"Fons\", \"Rademakers\", role = c(\"cph\"),\ncomment = \"Author of FindR.cmake (CERN ROOT)\"))",
  "Description": "A Bayesian tool to test for population trends and changes\nin trends under arbitrary designs, including before-after (BA),\ncontrol-intervention (CI) and before-after-control-intervention\n(BACI) designs commonly used to assess conservation impact. It\ninfers changes in trends jointly from data obtained with\nmultiple survey methods, as well as from limited and noisy data\nnot necessarily collected in standardized ecological surveys.\nObserved counts can be modeled as following either a Poisson or\na negative binomial model, and both deterministic and\nstochastic trend models are available. For more details on the\nmodel see Singer et al. (2025) <doi:10.1101/2025.01.08.631844>,\nand the file 'AUTHORS' for a list of copyright holders and\ncontributors.",
  "URL": "https://bitbucket.org/wegmannlab/birpr",
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  "Author": "Madleina Caduff [aut], Andreas Füglistaler [aut, cre], Daniel\nWegmann [aut], Liam Singer [aut], Raphael Eckel [ctb], Conrad\nSanderson [cph] (Author of Armadillo), Ryan Curtin [cph]\n(Author of Armadillo), Daniel Lemire [cph] (Author of\nfast_float), João Paulo Magalhaes [cph] (Author of fast_float),\nVictor Zverovich [cph] (Author of {fmt}), Rene Brun [cph]\n(Author of FindR.cmake (CERN ROOT)), Fons Rademakers [cph]\n(Author of FindR.cmake (CERN ROOT))",
  "Maintainer": "Andreas Füglistaler <andreas.fueglistaler@unifr.ch>",
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  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-09-25 22:30:02 UTC",
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  "_devurl": "https://bitbucket.org/wegmannlab/birpr",
  "_topics": [
    "zlib",
    "openblas",
    "arpack",
    "cpp"
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
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      "date": "2025-05-16"
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    },
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      "date": "2025-07-12"
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      "date": "2026-08-21"
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  "_exports": [
    "assess_NB",
    "birp",
    "birp_data",
    "birp_data_from_data_frame",
    "birp_data_from_file",
    "birp_from_command_line",
    "plot_epoch_pair",
    "plot_mcmc",
    "plot_trend",
    "plot.birp",
    "plot.birp_data",
    "print.birp",
    "print.birp_data",
    "prob_step",
    "prob_trend",
    "prob_trend_diff",
    "simulate_birp",
    "simulate_birp_from_results",
    "summary.birp",
    "summary.birp_data"
  ],
  "_help": [
    {
      "page": "birp-package",
      "title": "Testing for Population Trends Using Low-Cost Ecological Count Data",
      "topics": [
        "birp-package"
      ]
    },
    {
      "page": "assess_NB",
      "title": "Assess whether a Poisson model can replace the Negative Binomial model",
      "topics": [
        "assess_NB"
      ]
    },
    {
      "page": "birp",
      "title": "Create a 'birp' Object",
      "topics": [
        "birp"
      ]
    },
    {
      "page": "birp_data",
      "title": "Create a birp_data Object from Count and Effort Matrices",
      "topics": [
        "birp_data"
      ]
    },
    {
      "page": "birp_data_from_data_frame",
      "title": "Create a 'birp_data' Object from a Data Frame or List of Data Frames",
      "topics": [
        "birp_data_from_data_frame"
      ]
    },
    {
      "page": "birp_data_from_file",
      "title": "Create a birp_data Object from File(s)",
      "topics": [
        "birp_data_from_file"
      ]
    },
    {
      "page": "birp_from_command_line",
      "title": "Create a birp Object from Command-Line Output Files",
      "topics": [
        "birp_from_command_line"
      ]
    },
    {
      "page": "plot_epoch_pair",
      "title": "Plot joint posterior of two gamma parameters",
      "topics": [
        "plot_epoch_pair"
      ]
    },
    {
      "page": "plot_mcmc",
      "title": "Plot MCMC Traces and Posterior Densities",
      "topics": [
        "plot_mcmc"
      ]
    },
    {
      "page": "plot_trend",
      "title": "Plot Posterior Trend Estimates",
      "topics": [
        "plot_trend"
      ]
    },
    {
      "page": "plot.birp",
      "title": "Plot posterior distributions of rate and/or step change parameters",
      "topics": [
        "plot.birp"
      ]
    },
    {
      "page": "plot.birp_data",
      "title": "Plot a birp_data Object",
      "topics": [
        "plot.birp_data"
      ]
    },
    {
      "page": "print.birp",
      "title": "Print a birp object",
      "topics": [
        "print.birp"
      ]
    },
    {
      "page": "print.birp_data",
      "title": "Print a birp_data object Prints a summary of a 'birp_data' object, including the number of methods, locations, control-intervention (CI) groups, and timepoints, as well as the names or identifiers for each.",
      "topics": [
        "print.birp_data"
      ]
    },
    {
      "page": "prob_step",
      "title": "Posterior probability of a step change",
      "topics": [
        "prob_step"
      ]
    },
    {
      "page": "prob_trend",
      "title": "Posterior probability of a population trend",
      "topics": [
        "prob_trend"
      ]
    },
    {
      "page": "prob_trend_diff",
      "title": "Pairwise posterior comparisons of population trends",
      "topics": [
        "prob_trend_diff"
      ]
    },
    {
      "page": "simulate_birp",
      "title": "Simulate Data for BIRP Models Generates simulated count data using the BIRP model framework with user-defined parameters.",
      "topics": [
        "simulate_birp"
      ]
    },
    {
      "page": "simulate_birp_from_results",
      "title": "This function simulates a birp_data object using all parameter estimates, dimensionality (methods, locations, timepoints) and the total number of counts nu_ij of a birp object",
      "topics": [
        "simulate_birp_from_results"
      ]
    },
    {
      "page": "summary.birp",
      "title": "Summary method for birp objects",
      "topics": [
        "summary.birp"
      ]
    },
    {
      "page": "summary.birp_data",
      "title": "Summarize a birp_data object",
      "topics": [
        "summary.birp_data"
      ]
    }
  ],
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    "Rcpp"
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      "filename": "birp-introduction.html",
      "title": "birp",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting Started with birp",
        "Input Data Format",
        "Preparing your data",
        "Estimating a Population Trend",
        "Visualizing the result",
        "Testing for Changes in Trends Using Sampling Designs",
        "Before-After (BA) Design: Detecting a Change in Trend Over Time",
        "Before-After (BA) Design with or without Step Changes",
        "Control-Intervention (CI) and Before-After-Control-Intervention (BACI) Designs: Comparing Groups",
        "Control-Intervention (CI) Design",
        "Before-After-Control-Intervention (BACI) Design",
        "Summary",
        "Visualizing the Model Output",
        "Combining multiple survey methods",
        "Running a Negative-Binomial Model",
        "Deciding between Poisson or Negative-binomial",
        "Fitting a Stochastic Trend Model",
        "Using additional covariates",
        "Example: Adding a Detection Covariate",
        "Additional covariates vs stratifying your data",
        "Simulating Example Data",
        "Overview of the birp modeling framework",
        "1. Population Trend Models",
        "Deterministic Model",
        "Stochastic Model",
        "2. Observation Model"
      ],
      "created": "2025-07-06 23:20:05",
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