{
  "_id": "6a1014f7acfb0bcc41c83dd3",
  "Package": "multimedia",
  "Title": "Multimodal Mediation Analysis",
  "Version": "0.2.1",
  "Authors@R": "c(person(\"Kris\", \"Sankaran\", , \"ksankaran@wisc.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9415-1971\")),\nperson(\"Hanying\", \"Jiang\", , \"hjiang252@wisc.edu\", role = \"aut\"))",
  "Description": "Multimodal mediation analysis is an emerging problem in\nmicrobiome data analysis. Multimedia make advanced mediation\nanalysis techniques easy to use, ensuring that all statistical\ncomponents are transparent and adaptable to specific problem\ncontexts. The package provides a uniform interface to direct\nand indirect effect estimation, synthetic null hypothesis\ntesting, bootstrap confidence interval construction, and\nsensitivity analysis. More details are available in Jiang et\nal. (2024) \"multimedia: Multimodal Mediation Analysis of\nMicrobiome Data\" <doi:10.1101/2024.03.27.587024>.",
  "License": "CC0",
  "Encoding": "UTF-8",
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  "biocViews": "Coverage, Microbiome, Regression, Sequencing, Software,\nStatisticalMethod, StructuralEquationModels",
  "BugReports": "https://github.com/krisrs1128/multimedia/issues/",
  "URL": "https://krisrs1128.github.io/multimedia/,\nhttps://github.com/krisrs1128/multimedia/",
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  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev zlib1g-dev",
  "Repository": "https://krisrs1128.r-universe.dev",
  "Date/Publication": "2025-04-21 23:51:12 UTC",
  "RemoteUrl": "https://github.com/krisrs1128/multimedia",
  "RemoteRef": "HEAD",
  "RemoteSha": "fdd612976a576b2975d8fb50c4795924fb86adbc",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-14 09:57:38 UTC",
    "User": "root"
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  "Author": "Kris Sankaran [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9415-1971>),\nHanying Jiang [aut]",
  "Maintainer": "Kris Sankaran <ksankaran@wisc.edu>",
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  "_user": "krisrs1128",
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  "_created": "2026-05-14T09:57:38.000Z",
  "_published": "2026-05-22T08:33:59.515Z",
  "_distro": "noble",
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    "author": "Kris Sankaran <sankaran.kris@gmail.com>",
    "committer": "Kris Sankaran <sankaran.kris@gmail.com>",
    "message": "Merge branch 'issue-2'\n",
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      "package": "ranger",
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  "_updates": [],
  "_tags": [],
  "_topics": [
    "coverage",
    "microbiome",
    "regression",
    "sequencing",
    "software",
    "statisticalmethod",
    "structuralequationmodels",
    "causal-inference",
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    "mediation-analysis"
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/multimedia"
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    "extra/citation.json",
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      "date": "2024-09-18"
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  "_exports": [
    "ansi_aware_handler",
    "bind_mediation",
    "bootstrap",
    "brms_model",
    "brms_sampler",
    "contrast_predictions",
    "contrast_samples",
    "demo_joy",
    "demo_spline",
    "direct_effect",
    "edges",
    "effect_summary",
    "estimate",
    "estimator",
    "exper_df",
    "fdr_summary",
    "glmnet_model",
    "glmnet_sampler",
    "indirect_overall",
    "indirect_pathwise",
    "lm_model",
    "lm_sampler",
    "lnm_model",
    "lnm_sampler",
    "mediation_data",
    "mediation_models",
    "mediators",
    "mediators<-",
    "multimedia",
    "n_mediators",
    "n_outcomes",
    "nrow",
    "null_contrast",
    "nullify",
    "outcome_model",
    "outcome_models",
    "outcomes",
    "outcomes<-",
    "parallelize",
    "plot_mediators",
    "plot_sensitivity",
    "predict",
    "predict_across",
    "pretreatments",
    "pretreatments<-",
    "retrieve_names",
    "rf_model",
    "rf_sampler",
    "sample",
    "sensitivity",
    "sensitivity_pathwise",
    "sensitivity_perturb",
    "setup_profile",
    "treatments",
    "treatments<-"
  ],
  "_datasets": [
    {
      "name": "mindfulness",
      "title": "Mindfulness Dataset",
      "object": "mindfulness",
      "file": "mindfulness.rda",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "sub-mediation_data-ANY-ANY-ANY-method",
      "title": "Subset a mediation dataset",
      "topics": [
        "[,mediation_data,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "ansi_aware_handler",
      "title": "Pretty Printing",
      "topics": [
        "ansi_aware_handler"
      ]
    },
    {
      "page": "bind_mediation",
      "title": "Convert 'mediation_data' to a single data.frame",
      "topics": [
        "bind_mediation"
      ]
    },
    {
      "page": "bootstrap",
      "title": "Bootstrap Distribution for Estimators",
      "topics": [
        "bootstrap"
      ]
    },
    {
      "page": "brms_model",
      "title": "Bayesian Regression Model across Responses",
      "topics": [
        "brms_model"
      ]
    },
    {
      "page": "brms_sampler",
      "title": "Sample from a Bayesian Regression Model",
      "topics": [
        "brms_sampler"
      ]
    },
    {
      "page": "contrast_predictions",
      "title": "Estimate the Difference between Profiles",
      "topics": [
        "contrast_predictions"
      ]
    },
    {
      "page": "contrast_samples",
      "title": "Difference between Samples at Contrasting Profiles",
      "topics": [
        "contrast_samples"
      ]
    },
    {
      "page": "demo_joy",
      "title": "A Demo Dataset (Random)",
      "topics": [
        "demo_joy"
      ]
    },
    {
      "page": "demo_spline",
      "title": "A Demo Dataset (Spline)",
      "topics": [
        "demo_spline"
      ]
    },
    {
      "page": "direct_effect",
      "title": "Direct Effects from Estimated Model",
      "topics": [
        "direct_effect"
      ]
    },
    {
      "page": "edges",
      "title": "Graphical Structure for Mediation Objects",
      "topics": [
        "edges"
      ]
    },
    {
      "page": "edges-multimedia-method",
      "title": "Access Mediation Model DAG",
      "topics": [
        "edges,multimedia-method"
      ]
    },
    {
      "page": "effect_summary",
      "title": "Average Effects across j",
      "topics": [
        "effect_summary"
      ]
    },
    {
      "page": "estimate",
      "title": "Estimate a Mediation Model",
      "topics": [
        "estimate"
      ]
    },
    {
      "page": "estimator",
      "title": "Accessor for Model Estimators",
      "topics": [
        "estimator"
      ]
    },
    {
      "page": "estimator-model-method",
      "title": "Accessor for Estimators",
      "topics": [
        "estimator,model-method"
      ]
    },
    {
      "page": "exper_df",
      "title": "Convert a Summarized Experiment to a data.frame",
      "topics": [
        "exper_df"
      ]
    },
    {
      "page": "fdr_summary",
      "title": "Calibration using Synthetic Nulls",
      "topics": [
        "fdr_summary"
      ]
    },
    {
      "page": "glmnet_model",
      "title": "Regularized 'Glmnet' Model across Responses",
      "topics": [
        "glmnet_model"
      ]
    },
    {
      "page": "glmnet_sampler",
      "title": "Sample from a 'Glmnet' Package Model",
      "topics": [
        "glmnet_sampler"
      ]
    },
    {
      "page": "indirect_overall",
      "title": "Overall Indirect Effect",
      "topics": [
        "indirect_overall"
      ]
    },
    {
      "page": "indirect_pathwise",
      "title": "Indirect Effects via Single Mediation Paths",
      "topics": [
        "indirect_pathwise"
      ]
    },
    {
      "page": "lm_model",
      "title": "Linear Model across Responses",
      "topics": [
        "lm_model"
      ]
    },
    {
      "page": "lm_sampler",
      "title": "Sample a Linear Model",
      "topics": [
        "lm_sampler"
      ]
    },
    {
      "page": "lnm_model",
      "title": "Logistic Normal Multinomial Model",
      "topics": [
        "lnm_model"
      ]
    },
    {
      "page": "lnm_sampler",
      "title": "Sample from the Logistic Normal Multinomial",
      "topics": [
        "lnm_sampler"
      ]
    },
    {
      "page": "mediation_data",
      "title": "'mediation_data' Constructor",
      "topics": [
        "mediation_data"
      ]
    },
    {
      "page": "mediation_models",
      "title": "Accessor for Outcome Models",
      "topics": [
        "mediation_models"
      ]
    },
    {
      "page": "mediators",
      "title": "Access Class-Specific Mediators",
      "topics": [
        "mediators"
      ]
    },
    {
      "page": "mediators-mediation_data-method",
      "title": "Access to @mediators in Mediation Data",
      "topics": [
        "mediators,mediation_data-method"
      ]
    },
    {
      "page": "mediators-multimedia-method",
      "title": "Names of Mediators in a Multimedia Object",
      "topics": [
        "mediators,multimedia-method"
      ]
    },
    {
      "page": "mediators-set",
      "title": "Set Mediators",
      "topics": [
        "mediators<-"
      ]
    },
    {
      "page": "mediators-set-mediation_data-method",
      "title": "Set the Mediators in a Mediation Data Object",
      "topics": [
        "mediators<-,mediation_data-method"
      ]
    },
    {
      "page": "mindfulness",
      "title": "Mindfulness Dataset",
      "topics": [
        "mindfulness"
      ]
    },
    {
      "page": "model-class",
      "title": "Representation of an Outcome or Mediation Model",
      "topics": [
        "model-class"
      ]
    },
    {
      "page": "multimedia",
      "title": "'multimedia' Constructor",
      "topics": [
        "multimedia"
      ]
    },
    {
      "page": "n_mediators",
      "title": "Number of Mediators in a Multimedia Object",
      "topics": [
        "n_mediators"
      ]
    },
    {
      "page": "n_outcomes",
      "title": "Number of Outcomes in a Multimedia Object",
      "topics": [
        "n_outcomes"
      ]
    },
    {
      "page": "nrow-mediation_data-method",
      "title": "How many samples in the mediation dataset?",
      "topics": [
        "nrow,mediation_data-method"
      ]
    },
    {
      "page": "null_contrast",
      "title": "Compare Effects from Experimental vs. Null Mediation Data",
      "topics": [
        "null_contrast"
      ]
    },
    {
      "page": "nullify",
      "title": "Nullify Active Edges",
      "topics": [
        "nullify"
      ]
    },
    {
      "page": "outcome_model",
      "title": "Access the Outcome Model in a Multimedia Object",
      "topics": [
        "outcome_model"
      ]
    },
    {
      "page": "outcome_models",
      "title": "Accessor for Outcome Models",
      "topics": [
        "outcome_models"
      ]
    },
    {
      "page": "outcomes",
      "title": "Access Outcomes",
      "topics": [
        "outcomes"
      ]
    },
    {
      "page": "outcomes-mediation_data-method",
      "title": "Outcomes Data in a Mediation Data Object",
      "topics": [
        "outcomes,mediation_data-method"
      ]
    },
    {
      "page": "outcomes-multimedia-method",
      "title": "Names of Outcomes in a Multimedia Object",
      "topics": [
        "outcomes,multimedia-method"
      ]
    },
    {
      "page": "outcomes-set",
      "title": "Set Outcomes This is an setter method for outcomes in an S4 object, usually of class mediation_data.",
      "topics": [
        "outcomes<-"
      ]
    },
    {
      "page": "outcomes-set-mediation_data-method",
      "title": "Set the Outcomes in a Mediation Data Object",
      "topics": [
        "outcomes<-,mediation_data-method"
      ]
    },
    {
      "page": "parallelize",
      "title": "Parallelize Estimation across Responses",
      "topics": [
        "parallelize"
      ]
    },
    {
      "page": "plot_mediators",
      "title": "Visualize Indirect Effects",
      "topics": [
        "plot_mediators"
      ]
    },
    {
      "page": "plot_sensitivity",
      "title": "Generic Sensitivity Plot",
      "topics": [
        "plot_sensitivity"
      ]
    },
    {
      "page": "predict_across",
      "title": "Predict a Subset of Responses",
      "topics": [
        "predict_across"
      ]
    },
    {
      "page": "predict-multimedia-method",
      "title": "Predictions from a Multimedia Class",
      "topics": [
        "predict,multimedia-method"
      ]
    },
    {
      "page": "pretreatments",
      "title": "Access Pretreatments",
      "topics": [
        "pretreatments"
      ]
    },
    {
      "page": "pretreatments-mediation_data-method",
      "title": "Pretreatments in a Mediation Data Object",
      "topics": [
        "pretreatments,mediation_data-method"
      ]
    },
    {
      "page": "pretreatments-set",
      "title": "Set Pretreatments This is an setter method for pretreatments in an S4 object, usually of class mediation_data.",
      "topics": [
        "pretreatments<-"
      ]
    },
    {
      "page": "pretreatments-set-mediation_data-method",
      "title": "Set the Pretreatments in a Mediation Data Object",
      "topics": [
        "pretreatments<-,mediation_data-method"
      ]
    },
    {
      "page": "retrieve_names",
      "title": "Variables in a Multimedia Object",
      "topics": [
        "retrieve_names"
      ]
    },
    {
      "page": "rf_model",
      "title": "Random Forest Model",
      "topics": [
        "rf_model"
      ]
    },
    {
      "page": "rf_sampler",
      "title": "Sample from a Random Forest Model",
      "topics": [
        "rf_sampler"
      ]
    },
    {
      "page": "sample-multimedia-method",
      "title": "Sample New Mediator/Outcome Data",
      "topics": [
        "sample,multimedia-method"
      ]
    },
    {
      "page": "sensitivity",
      "title": "Sensitivity Analysis for Overall Indirect Effect",
      "topics": [
        "sensitivity"
      ]
    },
    {
      "page": "sensitivity_pathwise",
      "title": "Sensitivity Analysis for Pathwise Indirect Effects",
      "topics": [
        "sensitivity_pathwise"
      ]
    },
    {
      "page": "sensitivity_perturb",
      "title": "Sensitivity to User-Specified Perturbations",
      "topics": [
        "sensitivity_perturb"
      ]
    },
    {
      "page": "setup_profile",
      "title": "Define a 'treatment_profile' object",
      "topics": [
        "setup_profile"
      ]
    },
    {
      "page": "spline_fun",
      "title": "Generate Random Spline",
      "topics": [
        "spline_fun"
      ]
    },
    {
      "page": "sub_formula",
      "title": "Helper to Modify Formulas",
      "topics": [
        "sub_formula"
      ]
    },
    {
      "page": "treatment_profile-class",
      "title": "Define a Treatment Profile",
      "topics": [
        "treatment_profile-class"
      ]
    },
    {
      "page": "treatments",
      "title": "Access Treatments",
      "topics": [
        "treatments"
      ]
    },
    {
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