{
  "_id": "6a1edc9ab401979e7340fdb5",
  "Package": "rbioacc",
  "Title": "Inference and Prediction of ToxicoKinetic (TK) Models",
  "Version": "1.1-2",
  "Authors@R": "c(\nperson(\"Virgile\", \"Baudrot\", role = c(\"aut\", \"cre\"), email = \"virgile.baudrot@posteo.net\"),\nperson(\"Sandrine\", \"Charles\", role = \"aut\"),\nperson(\"Ophélia\", \"Gestin\", role = \"ctb\"),\nperson(\"Miléna\", \"Kaag\", role = \"aut\"),\nperson(\"Christelle\", \"Lopes\", role = \"ctb\"),\nperson(\"Gauthier\", \"Multari\", role = \"ctb\"),\nperson(\"Alain\", \"Pavé\", role = \"ctb\"),\nperson(\"Aude\", \"Ratier\", role = \"aut\"),\nperson(\"Aurélie\", \"Siberchicot\", role = \"ctb\", email = \"aurelie.siberchicot@univ-lyon1.fr\")\n)",
  "Description": "The MOSAICbioacc application is a turnkey package\nproviding bioaccumulation factors (BCF/BMF/BSAF) from a\ntoxicokinetic (TK) model fitted to accumulation-depuration\ndata. It is designed to fulfil the requirements of regulators\nwhen examining applications for market authorization of active\nsubstances. See Ratier et al. (2021)\n<doi:10.1101/2021.09.08.459421>.",
  "URL": "https://github.com/lbbe-software/rbioacc",
  "BugReports": "https://github.com/lbbe-software/rbioacc/issues",
  "License": "MIT + file LICENSE",
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  "Repository": "https://lbbe-software.r-universe.dev",
  "Date/Publication": "2023-10-02 11:30:32 UTC",
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  "Author": "Virgile Baudrot [aut, cre],\nSandrine Charles [aut],\nOphélia Gestin [ctb],\nMiléna Kaag [aut],\nChristelle Lopes [ctb],\nGauthier Multari [ctb],\nAlain Pavé [ctb],\nAude Ratier [aut],\nAurélie Siberchicot [ctb]",
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  "_created": "2026-05-20T08:23:55.000Z",
  "_published": "2026-06-02T13:37:30.179Z",
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    "replace_",
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      "title": "Data on Chironomus with several exposure routes.",
      "object": "Chiro_Creuzot",
      "class": [
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      "title": "Data on Sialis lutaria exposure time series",
      "object": "Exposure_Sialis_lutaria",
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      "table": true,
      "tojson": true
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      "title": "Data on Gammarus exposed to azoxistrobine",
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      "table": true,
      "tojson": true
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      "class": [
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        "Cinternal"
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      "rows": 39,
      "table": true,
      "tojson": true
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    {
      "name": "Male_Gammarus_Merged",
      "title": "Male 'Gammarus fossarum' exposed to Hg spiked water. Three exposure concentrations were tested in triplicates. The duration of the accumulation phase is 4 days for 0.0000708021 and 0.000283208 mu g.m L^{-1} exposure concentrations, and 7 days for 0.000141604 mu g.m L^{-1} exposure concentration.",
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Male 'Gammarus pulex' exposed to seanine spiked water. A single exposure concentration was tested. The duration of the accumulation phase is 1.417 days. Three metabolites were quantified. The growth of organism was included.",
      "object": "Male_Gammarus_seanine_growth",
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      "table": true,
      "tojson": true
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      "title": "Bio-accumulation data set for _Gammarus fossarum_ exposed to Hg spiked water.",
      "object": "Male_Gammarus_Single",
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        "tbl",
        "data.frame"
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        "conc"
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      "table": true,
      "tojson": true
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      "class": [
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        "expw",
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      "table": true,
      "tojson": true
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    {
      "page": "rbioacc-package",
      "title": "The 'rbioacc' package.",
      "topics": [
        "rbioacc-package",
        "rbioacc"
      ]
    },
    {
      "page": "dot-fonte",
      "title": "A simple implementation of to pivot_longer of tidyr",
      "topics": [
        ".fonte"
      ]
    },
    {
      "page": "dot-index_col_exposure",
      "title": "Return column matching \"expw\", \"exps\", \"expf\", \"exppw\" of a 'data.frame'",
      "topics": [
        ".index_col_exposure"
      ]
    },
    {
      "page": "dot-index_col_metabolite",
      "title": "Return column matching \"concX\" of a 'data.frame' where X is metabolite",
      "topics": [
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      ]
    },
    {
      "page": "dot-is_equal_rmInf",
      "title": "Check if two vectors 'x' and y are equal after remove 'Inf'",
      "topics": [
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      "page": "bioacc_metric",
      "title": "Biaccumulation metrics",
      "topics": [
        "bioacc_metric",
        "bioacc_metric.fitTK"
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    },
    {
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      "title": "Data on Chironomus with several exposure routes.",
      "topics": [
        "Chiro_Creuzot"
      ]
    },
    {
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      "title": "Data on Chironomus exposed to benzoapyrene",
      "topics": [
        "Chironomus_benzoapyrene"
      ]
    },
    {
      "page": "corrMatrix",
      "title": "Correlations between parameters: colored matrix",
      "topics": [
        "corrMatrix"
      ]
    },
    {
      "page": "corrPlot",
      "title": "Correlations between parameters: pairs plot",
      "topics": [
        "corrPlot"
      ]
    },
    {
      "page": "ppc",
      "title": "PPC data.frame",
      "topics": [
        "df_ppc",
        "df_ppc.fitTK",
        "ppc",
        "ppc.fitTK"
      ]
    },
    {
      "page": "df_PP",
      "title": "Data frame of Posterior over Prior",
      "topics": [
        "df_PriorPost",
        "df_PriorPost.fitTK"
      ]
    },
    {
      "page": "equations",
      "title": "Equations of the mathematical model used for the fit",
      "topics": [
        "equations"
      ]
    },
    {
      "page": "exposure_names",
      "title": "Retrieve exposure routes names from object",
      "topics": [
        "exposure_names"
      ]
    },
    {
      "page": "Exposure_Sialis_lutaria",
      "title": "Data on Sialis lutaria exposure time series",
      "topics": [
        "Exposure_Sialis_lutaria"
      ]
    },
    {
      "page": "fitTK",
      "title": "Posterior predictive check",
      "topics": [
        "fitTK",
        "fitTK.stanTKdataCST",
        "fitTK.stanTKdataVAR"
      ]
    },
    {
      "page": "Gammarus_azoxistrobine_1d_Rosch2017",
      "title": "Data on Gammarus exposed to azoxistrobine",
      "topics": [
        "Gammarus_azoxistrobine_1d_Rosch2017"
      ]
    },
    {
      "page": "Internal_Sialis_lutaria",
      "title": "Data on Sialis lutaria internal time series",
      "topics": [
        "Internal_Sialis_lutaria"
      ]
    },
    {
      "page": "Male_Gammarus_Merged",
      "title": "Male 'Gammarus fossarum' exposed to Hg spiked water. Three exposure concentrations were tested in triplicates. The duration of the accumulation phase is 4 days for 0.0000708021 and 0.000283208 mu g.m L^{-1} exposure concentrations, and 7 days for 0.000141604 mu g.m L^{-1} exposure concentration.",
      "topics": [
        "Male_Gammarus_Merged"
      ]
    },
    {
      "page": "Male_Gammarus_seanine_growth",
      "title": "Male 'Gammarus pulex' exposed to seanine spiked water. A single exposure concentration was tested. The duration of the accumulation phase is 1.417 days. Three metabolites were quantified. The growth of organism was included.",
      "topics": [
        "Male_Gammarus_seanine_growth"
      ]
    },
    {
      "page": "Male_Gammarus_Single",
      "title": "Bio-accumulation data set for _Gammarus fossarum_ exposed to Hg spiked water.",
      "topics": [
        "Male_Gammarus_Single"
      ]
    },
    {
      "page": "mcmcTraces",
      "title": "Traces of MCMC iterations",
      "topics": [
        "mcmcTraces"
      ]
    },
    {
      "page": "modelData",
      "title": "Create a list giving data and parameters to use in the model inference.",
      "topics": [
        "modelData",
        "modelData.data.frame"
      ]
    },
    {
      "page": "modelData_ode",
      "title": "Create a list giving data and parameters to use in the model inference.",
      "topics": [
        "modelData_ode"
      ]
    },
    {
      "page": "Oncorhynchus_two",
      "title": "Data on Oncorhynchus exposition",
      "topics": [
        "Oncorhynchus_two"
      ]
    },
    {
      "page": "plot_exposure",
      "title": "Plot exposure profile",
      "topics": [
        "plot_exposure"
      ]
    },
    {
      "page": "plot_PP",
      "title": "Plot Posterior over Prior",
      "topics": [
        "plot_PriorPost",
        "plot_PriorPost.df_PP",
        "plot_PriorPost.fitTK"
      ]
    },
    {
      "page": "plot.bioaccMetric",
      "title": "Plot function for object of class 'bioaccMetric'",
      "topics": [
        "plot.bioaccMetric"
      ]
    },
    {
      "page": "plot.fitTK",
      "title": "Plotting method for 'fitTK' objects",
      "topics": [
        "plot.fitTK"
      ]
    },
    {
      "page": "plot_predict",
      "title": "Plotting method for 'predictTK' objects",
      "topics": [
        "plot.predictTK",
        "plot.predictTKstan"
      ]
    },
    {
      "page": "predict",
      "title": "Prediction function using 'fitTK' object",
      "topics": [
        "predict.fitTK",
        "predict_manual",
        "predict_stan"
      ]
    },
    {
      "page": "psrf",
      "title": "Potential Scale Reduction Factors (PSRF) of the parameters",
      "topics": [
        "psrf"
      ]
    },
    {
      "page": "quantile_table",
      "title": "Quantiles of parameters",
      "topics": [
        "quantile_table"
      ]
    },
    {
      "page": "replace_",
      "title": "Replace element of a vector",
      "topics": [
        "replace_"
      ]
    },
    {
      "page": "t95",
      "title": "Return the time at 95% depuration of the parent component",
      "topics": [
        "t95"
      ]
    },
    {
      "page": "waic",
      "title": "Widely Applicable Information Criterion (WAIC)",
      "topics": [
        "waic"
      ]
    }
  ],
  "_readme": "https://github.com/lbbe-software/rbioacc/raw/HEAD/README.md",
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