{
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  "Package": "rCISSVAE",
  "Title": "Clustering-Informed Shared-Structure VAE for Imputation",
  "Version": "1.0.1",
  "Authors@R": "c(  person(given = \"Yasin\", family = \"Khadem Charvadeh\", email = \"khademy@mskcc.org\", role = c(\"aut\")),\nperson(given = \"Kenneth\", family = \"Seier\", role = c(\"aut\")),\nperson( given = c(\"Katherine\", \"S.\"), family = \"Panageas\", role = c(\"aut\")),\nperson(given = \"Danielle\", family = \"Vaithilingam\", email = \"vaithid1@mskcc.org\", role = c(\"aut\", \"cre\")),\nperson(given = \"Mithat\", family = \"Gönen\", role = c(\"aut\")),\nperson(given = \"Yuan\", family = \"Chen\", email = \"cheny19@mskcc.org\", role = c(\"aut\"))\n)",
  "Maintainer": "Danielle Vaithilingam <vaithid1@mskcc.org>",
  "Description": "Implements the Clustering-Informed Shared-Structure\nVariational Autoencoder ('CISS-VAE'), a deep learning framework\nfor missing data imputation introduced in Khadem Charvadeh et\nal. (2025) <doi:10.1002/sim.70335>. The model accommodates all\nthree types of missing data mechanisms: Missing Completely At\nRandom (MCAR), Missing At Random (MAR), and Missing Not At\nRandom (MNAR). While it is particularly well-suited to MNAR\nscenarios, where missingness patterns carry informative\nsignals, 'CISS-VAE' also functions effectively under MAR\nassumptions.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://ciss-vae.github.io/rCISS-VAE/",
  "BugReports": "https://github.com/CISS-VAE/rCISS-VAE/issues",
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  "Date/Publication": "2026-05-14 13:12:39 UTC",
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  "Author": "Yasin Khadem Charvadeh [aut],\nKenneth Seier [aut],\nKatherine S. Panageas [aut],\nDanielle Vaithilingam [aut, cre],\nMithat Gönen [aut],\nYuan Chen [aut]",
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    "plot_vae_architecture",
    "run_cissvae",
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      "title": "Cluster assignments based on missingness patterns",
      "object": "clusters",
      "class": [
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        "tbl",
        "data.frame"
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      "fields": [
        "index",
        "clusters"
      ],
      "rows": 8000,
      "table": true,
      "tojson": true
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      "name": "df_missing",
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      "object": "df_missing",
      "class": [
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        "tbl_df",
        "tbl",
        "data.frame"
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      "fields": [
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        "Age",
        "Salary",
        "ZipCode10001",
        "ZipCode20002",
        "ZipCode30003",
        "Y11",
        "Y12",
        "Y13",
        "Y14",
        "Y15",
        "Y21",
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        "Y55"
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      "rows": 8000,
      "table": true,
      "tojson": true
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      "title": "Example dni matrix for demo of imputable_matrix",
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        "data.frame"
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      "fields": [
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      "table": true,
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      "page": "autotune_cissvae",
      "title": "Autotune CISS-VAE hyperparameters with Optuna",
      "topics": [
        "autotune_cissvae"
      ]
    },
    {
      "page": "check_devices",
      "title": "Check PyTorch device availability",
      "topics": [
        "check_devices"
      ]
    },
    {
      "page": "cluster_heatmap",
      "title": "Cluster-wise Heatmap of Missing Data Patterns",
      "topics": [
        "cluster_heatmap"
      ]
    },
    {
      "page": "cluster_on_missing",
      "title": "Cluster on Missingness Patterns",
      "topics": [
        "cluster_on_missing"
      ]
    },
    {
      "page": "cluster_on_missing_prop",
      "title": "Cluster Samples Based on Missingness Proportions",
      "topics": [
        "cluster_on_missing_prop"
      ]
    },
    {
      "page": "cluster_summary",
      "title": "Cluster-wise summary table using a separate cluster vector (gtsummary + gt)",
      "topics": [
        "cluster_summary"
      ]
    },
    {
      "page": "clusters",
      "title": "Cluster assignments based on missingness patterns",
      "topics": [
        "clusters"
      ]
    },
    {
      "page": "create_cissvae_env",
      "title": "Create or reuse a CISSVAE Python virtual environment",
      "topics": [
        "create_cissvae_env"
      ]
    },
    {
      "page": "create_missingness_prop_matrix",
      "title": "Create Missingness Proportion Matrix",
      "topics": [
        "create_missingness_prop_matrix"
      ]
    },
    {
      "page": "df_missing",
      "title": "Sample dataset with missing values",
      "topics": [
        "df_missing"
      ]
    },
    {
      "page": "dni",
      "title": "Example dni matrix for demo of imputable_matrix",
      "topics": [
        "dni"
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    },
    {
      "page": "impute_result",
      "title": "CISS-VAE imputation result object",
      "topics": [
        "impute_result"
      ]
    },
    {
      "page": "impute_with_cissvae",
      "title": "Impute new data with a loaded Python CISS-VAE model",
      "topics": [
        "impute_with_cissvae"
      ]
    },
    {
      "page": "load_cissvae_model",
      "title": "Load a saved CISS-VAE model",
      "topics": [
        "load_cissvae_model"
      ]
    },
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      "page": "load_impute_result",
      "title": "Load an 'impute_result' object from disk",
      "topics": [
        "load_impute_result"
      ]
    },
    {
      "page": "mock_surv",
      "title": "Example survival data for demo of imputable_matrix",
      "topics": [
        "mock_surv"
      ]
    },
    {
      "page": "performance_by_cluster",
      "title": "Compute per-cluster and per-group performance metrics (MSE, BCE)",
      "topics": [
        "performance_by_cluster"
      ]
    },
    {
      "page": "plot_vae_architecture",
      "title": "Plot VAE Architecture Diagram",
      "topics": [
        "plot_vae_architecture"
      ]
    },
    {
      "page": "print.impute_result",
      "title": "Print an 'impute_result' object",
      "topics": [
        "print.impute_result"
      ]
    },
    {
      "page": "run_cissvae",
      "title": "Run the CISS-VAE pipeline for missing data imputation",
      "topics": [
        "run_cissvae"
      ]
    },
    {
      "page": "save_cissvae_model",
      "title": "Save a trained CISS-VAE model to disk",
      "topics": [
        "save_cissvae_model"
      ]
    },
    {
      "page": "save_impute_result",
      "title": "Save an 'impute_result' object to disk",
      "topics": [
        "save_impute_result"
      ]
    },
    {
      "page": "update_cissvae_env",
      "title": "Update (pip install -upgrade) CISSVAE inside the CISSVAE virtualenv",
      "topics": [
        "update_cissvae_env"
      ]
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        "Alternative: Using Conda Environment",
        "Command Line Approach:",
        "R Approach:",
        "Troubleshooting Common Issues",
        "Issue 1: \"Python not found\"",
        "Issue 2: \"Permission denied\" errors",
        "Issue 3: Package installation fails",
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      "headings": [
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