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  "Package": "Infusion",
  "Type": "Package",
  "Title": "Inference Using Simulation",
  "Description": "Implements functions for simulation-based inference. In\nparticular, implements functions to perform likelihood\ninference from data summaries whose distributions are\nsimulated, as described in Rousset et al. (2026)\n<doi:10.24072/pcjournal.721>.",
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  "Maintainer": "François Rousset <francois.rousset@umontpellier.fr>",
  "License": "CeCILL-2",
  "ByteCompile": "true",
  "URL": "https://gitlab.mbb.univ-montp2.fr/francois/Infusion",
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  "Packaged": {
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  "Author": "François Rousset [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-4670-0371>)",
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  "_exports": [
    "add_reftable",
    "add_simulation",
    "allCIs",
    "C2ST",
    "calc.lrthreshold",
    "calc.lrthreshold.default",
    "calc.lrthreshold.SLik",
    "calc.lrthreshold.SLikp",
    "check_raw_stats",
    "config_mafR",
    "confint.SLik",
    "confint.SLik_j",
    "confint.SLikp",
    "declare_latent",
    "def_projectors",
    "deforest_projectors",
    "focal_refine",
    "get_from",
    "get_from.default",
    "get_from.SLik",
    "get_from.SLik_j",
    "get_LRboot",
    "get_nbCluster_range",
    "get_projection",
    "get_projector",
    "get_trypoints",
    "get_workflow_design",
    "goftest",
    "infer_logL_by_GLMM",
    "infer_logL_by_Hlscv.diag",
    "infer_logL_by_mclust",
    "infer_logL_by_Rmixmod",
    "infer_logLs",
    "infer_SLik_joint",
    "infer_surface",
    "infer_surface.logLs",
    "infer_surface.tailp",
    "infer_tailp",
    "Infusion.getOption",
    "Infusion.options",
    "init_grid",
    "init_reftable",
    "isPointInCHull",
    "latint",
    "load_MAFs",
    "logLik.SLik",
    "logLik.SLik_j",
    "MAF.options",
    "mapMM",
    "MSL",
    "multi_binning",
    "neuralNet",
    "plot_importance",
    "plot_proj",
    "plot.dMixmod",
    "plot.MixmodResults",
    "plot.SLik",
    "plot.SLik_j",
    "plot.SLikp",
    "plot1Dprof",
    "plot2Dprof",
    "pplatent",
    "predict.dMclust",
    "predict.dMixmod",
    "predict.MixmodResults",
    "predict.SLik",
    "predict.SLik_j",
    "predict.SLikp",
    "print.goftest",
    "print.logLs",
    "print.SLik",
    "print.SLik_j",
    "print.SLikp",
    "profile.SLik",
    "profile.SLik_j",
    "project",
    "project.character",
    "project.default",
    "projpath",
    "recluster",
    "refine",
    "refine_nbCluster",
    "refine.default",
    "refine.SLik",
    "refine.SLik_j",
    "refine.SLikp",
    "reparam_fit",
    "reparam_reftable",
    "reproject",
    "resetCHull",
    "rparam",
    "sample_volume",
    "save_MAFs",
    "seq_nbCluster",
    "simulate.SLik_j",
    "SLRT",
    "str.MAF",
    "summary.goftest",
    "summary.logLs",
    "summary.SLik",
    "summary.SLik_j",
    "summary.SLikp",
    "summLik",
    "summLik.default",
    "summLik.SLik_j"
  ],
  "_datasets": [
    {
      "name": "densb",
      "title": "Saved computations of inferred log-likelihoods",
      "object": "densb",
      "file": "densb.RData",
      "class": [
        "logLs",
        "data.frame"
      ],
      "fields": [
        "mu",
        "s2",
        "sample.size",
        "logL",
        "isValid"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    },
    {
      "name": "densv",
      "title": "Saved computations of inferred log-likelihoods",
      "object": "densv",
      "file": "densv.RData",
      "class": [
        "logLs",
        "data.frame"
      ],
      "fields": [
        "mu",
        "s2",
        "sample.size",
        "logL",
        "isValid"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    },
    {
      "name": "myrnorm",
      "title": "Internal Infusion Functions",
      "object": "myrnorm",
      "file": "myrnorm.RData",
      "class": [
        "function"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "saved_seed",
      "title": "Saved computations of inferred log-likelihoods",
      "object": "densb",
      "file": "densb.RData",
      "class": [
        "integer"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "saved_seed",
      "title": "Saved computations of inferred log-likelihoods",
      "object": "densv",
      "file": "densv.RData",
      "class": [
        "integer"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "update_obs",
      "title": "Updating an 'SLik_j' object for new data",
      "topics": [
        ".update_obs"
      ]
    },
    {
      "page": "add.reftable",
      "title": "Create or augment a list of simulated distributions of summary statistics",
      "topics": [
        "add_reftable"
      ]
    },
    {
      "page": "add.simulation",
      "title": "Create or augment a list of simulated distributions of summary statistics",
      "topics": [
        "add_simulation"
      ]
    },
    {
      "page": "C2ST",
      "title": "Diagnostics of the fit",
      "topics": [
        "C2ST"
      ]
    },
    {
      "page": "check_raw_stats",
      "title": "Check linear dependencies among raw summary statistics",
      "topics": [
        "check_raw_stats"
      ]
    },
    {
      "page": "confint.SLik",
      "title": "Compute confidence intervals by (profile) summary likelihood",
      "topics": [
        "allCIs",
        "confint",
        "confint.SLik",
        "confint.SLikp",
        "confint.SLik_j"
      ]
    },
    {
      "page": "constr_crits",
      "title": "Specificying arbitrary constraints on parameters",
      "topics": [
        "constraints",
        "constr_crits"
      ]
    },
    {
      "page": "def_projectors",
      "title": "Wrapper to generate projection functions for all parameters",
      "topics": [
        "def_projectors"
      ]
    },
    {
      "page": "densv",
      "title": "Saved computations of inferred log-likelihoods",
      "topics": [
        "densb",
        "densv",
        "saved_seed"
      ]
    },
    {
      "page": "dMixmod",
      "title": "Internal S4 classes.",
      "topics": [
        "class:dMixmod",
        "class:NULLorChar",
        "class:NULLorNum",
        "dMixmod",
        "dMixmod-class",
        "NULLorChar",
        "NULLorChar-class",
        "NULLorNum",
        "NULLorNum-class",
        "plot.dMixmod"
      ]
    },
    {
      "page": "example_raw",
      "title": "Workflow for primitive method, without projections",
      "topics": [
        "example_raw"
      ]
    },
    {
      "page": "example_raw_proj",
      "title": "Workflow for primitive method, and with projections",
      "topics": [
        "example_raw_proj"
      ]
    },
    {
      "page": "example_reftable",
      "title": "Workflow for method with reference table",
      "topics": [
        "example_reftable"
      ]
    },
    {
      "page": "extractors",
      "title": "Summary, print and logLik methods for Infusion results.",
      "topics": [
        "extractors",
        "logLik",
        "logLik.SLik",
        "logLik.SLik_j",
        "print",
        "print.logLs",
        "print.SLik",
        "print.SLikp",
        "print.SLik_j",
        "summary",
        "summary.logLs",
        "summary.SLik",
        "summary.SLikp",
        "summary.SLik_j"
      ]
    },
    {
      "page": "focal_refine",
      "title": "Refine summary likelihood profile in focal parameter values",
      "topics": [
        "focal_refine"
      ]
    },
    {
      "page": "get_from",
      "title": "Backward-compatible extractor from summary-likelihood objects",
      "topics": [
        "get_from",
        "get_from.default",
        "get_from.SLik",
        "get_from.SLik_j"
      ]
    },
    {
      "page": "SLRT",
      "title": "Summary likelihood ratio tests",
      "topics": [
        "get_LRboot",
        "SLRT"
      ]
    },
    {
      "page": "get_nbCluster_range",
      "title": "Control of number of components in Gaussian mixture modelling",
      "topics": [
        "get_nbCluster_range",
        "refine_nbCluster",
        "seq_nbCluster"
      ]
    },
    {
      "page": "get_workflow_design",
      "title": "Workflow design",
      "topics": [
        "get_workflow_design"
      ]
    },
    {
      "page": "goftest",
      "title": "Assessing goodness of fit of inference using simulation",
      "topics": [
        "goftest",
        "print.goftest",
        "summary.goftest"
      ]
    },
    {
      "page": "handling_NAs",
      "title": "Discrete probability masses and NA/NaN/Inf in distributions of summary statistics.",
      "topics": [
        "boundaries-attribute",
        "handling_NAs",
        "NA_handling"
      ]
    },
    {
      "page": "infer_logLs",
      "title": "Infer log Likelihoods using simulated distributions of summary statistics",
      "topics": [
        "infer_logLs",
        "infer_logL_by_GLMM",
        "infer_logL_by_Hlscv.diag",
        "infer_logL_by_mclust",
        "infer_logL_by_Rmixmod",
        "infer_tailp"
      ]
    },
    {
      "page": "infer_SLik_joint",
      "title": "Infer a (summary) likelihood surface from a simulation table",
      "topics": [
        "infer_SLik_joint"
      ]
    },
    {
      "page": "infer_surface",
      "title": "Infer a (summary) likelihood or tail probability surface from inferred likelihoods",
      "topics": [
        "infer_surface",
        "infer_surface.logLs",
        "infer_surface.tailp"
      ]
    },
    {
      "page": "Infusion",
      "title": "Inference using simulation",
      "topics": [
        "Infusion-package",
        "Infusion"
      ]
    },
    {
      "page": "init_grid",
      "title": "Define starting points in parameter space.",
      "topics": [
        "init_grid",
        "init_reftable"
      ]
    },
    {
      "page": "latent",
      "title": "Modeling and predicting latent variables",
      "topics": [
        "declare_latent",
        "latint",
        "pplatent"
      ]
    },
    {
      "page": "MAF.options",
      "title": "Control of MAF design and training",
      "topics": [
        "config_mafR",
        "MAF.options"
      ]
    },
    {
      "page": "MSL",
      "title": "Maximum likelihood from an inferred likelihood surface",
      "topics": [
        "MSL"
      ]
    },
    {
      "page": "magic.binning",
      "title": "Multivariate histogram",
      "topics": [
        "multi_binning"
      ]
    },
    {
      "page": "options",
      "title": "Infusion options settings",
      "topics": [
        "Infusion.getOption",
        "Infusion.options",
        "parallel"
      ]
    },
    {
      "page": "plot_proj",
      "title": "Diagnostic plots for projections",
      "topics": [
        "plot_importance",
        "plot_proj"
      ]
    },
    {
      "page": "plot.SLik",
      "title": "Plot fit objects",
      "topics": [
        "plot.SLik",
        "plot.SLikp",
        "plot.SLik_j"
      ]
    },
    {
      "page": "plot1Dprof",
      "title": "Plot likelihood profiles",
      "topics": [
        "plot1Dprof",
        "plot2Dprof"
      ]
    },
    {
      "page": "predict.SLik_j",
      "title": "Evaluate log-likelihood for given parameters",
      "topics": [
        "predict.SLik_j"
      ]
    },
    {
      "page": "profile.SLik",
      "title": "Compute profile summary likelihood",
      "topics": [
        "profile",
        "profile.SLik",
        "profile.SLik_j"
      ]
    },
    {
      "page": "project",
      "title": "Learn a projection method for statistics and apply it",
      "topics": [
        "deforest_projectors",
        "get_projection",
        "get_projector",
        "neuralNet",
        "project",
        "project.character",
        "project.default"
      ]
    },
    {
      "page": "refine.SLik",
      "title": "Refine estimates iteratively",
      "topics": [
        "get_trypoints",
        "recluster",
        "refine",
        "refine.default",
        "refine.SLik",
        "refine.SLikp",
        "refine.SLik_j",
        "reproject"
      ]
    },
    {
      "page": "reparam",
      "title": "Conversion to new parameter spaces",
      "topics": [
        "reparam_fit",
        "reparam_reftable"
      ]
    },
    {
      "page": "sample_volume",
      "title": "Sample the parameter space",
      "topics": [
        "rparam",
        "sample_volume"
      ]
    },
    {
      "page": "save_MAFs",
      "title": "Save or load MAF Python objects",
      "topics": [
        "load_MAFs",
        "save_MAFs"
      ]
    },
    {
      "page": "simulate.SLik_j",
      "title": "Simulate method for an 'SLik_j' object.",
      "topics": [
        "simulate",
        "simulate.SLik_j"
      ]
    },
    {
      "page": "summLik",
      "title": "Model density evaluation for given data and parameters",
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