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  "Package": "lineagefreq",
  "Title": "Lineage Frequency Dynamics from Genomic Surveillance Counts",
  "Version": "0.6.0",
  "Authors@R": "person(\"Cuiwei\", \"Gao\", , \"48gaocuiwei@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"))",
  "Description": "Models pathogen lineage frequency dynamics from genomic\nsurveillance count data. Provides a unified interface for\nmultinomial logistic regression, hierarchical partial-pooling\nmodels, and the Piantham approximation for relative\nreproduction number estimation. Features include rolling-origin\nbacktesting, standardized forecast scoring, Compositional\nAdaptive Prediction Sets (CAPS) for horizon-aware calibrated\nforecasting, lineage collapsing, emergence detection, and\nsequencing power analysis. Designed for real-time public health\nsurveillance of any variant-resolved pathogen. Methods\ndescribed in Abousamra, Figgins, and Bedford (2024)\n<doi:10.1371/journal.pcbi.1012443>.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/CuiweiG/lineagefreq,\nhttps://cuiweig.github.io/lineagefreq",
  "BugReports": "https://github.com/CuiweiG/lineagefreq/issues",
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  "Repository": "https://cuiweig.r-universe.dev",
  "Date/Publication": "2026-04-19 04:22:42 UTC",
  "RemoteUrl": "https://github.com/cuiweig/lineagefreq",
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  "Author": "Cuiwei Gao [aut, cre, cph]",
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  "_published": "2026-06-02T15:33:36.158Z",
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    "augment.lfq_fit",
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    "calibrate",
    "calibrate_joint",
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    "collapse_lineages",
    "compare_models",
    "conformal_forecast",
    "conformal_forecast_joint",
    "detection_horizon",
    "evaluate_caps",
    "evaluate_prospective",
    "filter_sparse",
    "fit_dms_prior",
    "fit_model",
    "fitness_decomposition",
    "forecast",
    "glance.lfq_fit",
    "growth_advantage",
    "immune_landscape",
    "is_lfq_data",
    "lfq_advantage",
    "lfq_data",
    "lfq_engines",
    "lfq_fit",
    "lfq_forecast",
    "lfq_score",
    "lfq_stan_available",
    "lfq_summary",
    "lfq_version",
    "plot_backtest",
    "read_lineage_counts",
    "recalibrate",
    "register_engine",
    "score_forecasts",
    "selective_pressure",
    "sequencing_power",
    "simulate_dynamics",
    "summarize_emerging",
    "surveillance_dashboard",
    "surveillance_value",
    "tidy.fitness_decomposition",
    "tidy.lfq_fit",
    "unregister_engine"
  ],
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      "name": "cdc_ba2_transition",
      "title": "CDC SARS-CoV-2 variant proportions: BA.1 to BA.2 transition (US, 2022)",
      "object": "cdc_ba2_transition",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "lineage",
        "count",
        "proportion"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "cdc_sarscov2_jn1",
      "title": "CDC SARS-CoV-2 variant proportions: JN.1 emergence (US, 2023-2024)",
      "object": "cdc_sarscov2_jn1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "date",
        "lineage",
        "count",
        "proportion"
      ],
      "rows": 171,
      "table": true,
      "tojson": true
    },
    {
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      "title": "Simulated influenza A/H3N2 clade frequency data",
      "object": "influenza_h3n2",
      "class": [
        "data.frame"
      ],
      "fields": [
        "date",
        "clade",
        "count",
        "total"
      ],
      "rows": 96,
      "table": true,
      "tojson": true
    },
    {
      "name": "sarscov2_us_2022",
      "title": "Simulated SARS-CoV-2 variant frequency data (US, 2022)",
      "object": "sarscov2_us_2022",
      "class": [
        "data.frame"
      ],
      "fields": [
        "date",
        "variant",
        "count",
        "total"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "adaptive_design",
      "title": "Adaptive sequencing allocation via Thompson sampling",
      "topics": [
        "adaptive_design"
      ]
    },
    {
      "page": "alert_threshold",
      "title": "Sequential detection of emerging variants",
      "topics": [
        "alert_threshold"
      ]
    },
    {
      "page": "as_lfq_data",
      "title": "Coerce to lfq_data",
      "topics": [
        "as_lfq_data",
        "as_lfq_data.data.frame",
        "as_lfq_data.lfq_data"
      ]
    },
    {
      "page": "as.data.frame.lfq_data",
      "title": "Convert lfq_data to long-format tibble",
      "topics": [
        "as.data.frame.lfq_data"
      ]
    },
    {
      "page": "augment.lfq_fit",
      "title": "Augment data with fitted values from an lfq_fit object",
      "topics": [
        "augment.lfq_fit"
      ]
    },
    {
      "page": "autoplot.lfq_fit",
      "title": "Plot lineage frequency model results",
      "topics": [
        "autoplot.lfq_fit"
      ]
    },
    {
      "page": "autoplot.lfq_forecast",
      "title": "Plot a lineage frequency forecast",
      "topics": [
        "autoplot.lfq_forecast"
      ]
    },
    {
      "page": "backtest",
      "title": "Rolling-origin backtesting of lineage frequency models",
      "topics": [
        "backtest"
      ]
    },
    {
      "page": "calibrate",
      "title": "Calibration diagnostics for lineage frequency forecasts",
      "topics": [
        "calibrate",
        "calibrate.lfq_backtest",
        "calibrate.lfq_forecast"
      ]
    },
    {
      "page": "calibrate_joint",
      "title": "Joint Calibration Diagnostics",
      "topics": [
        "calibrate_joint"
      ]
    },
    {
      "page": "cdc_ba2_transition",
      "title": "CDC SARS-CoV-2 variant proportions: BA.1 to BA.2 transition (US, 2022)",
      "topics": [
        "cdc_ba2_transition"
      ]
    },
    {
      "page": "cdc_sarscov2_jn1",
      "title": "CDC SARS-CoV-2 variant proportions: JN.1 emergence (US, 2023-2024)",
      "topics": [
        "cdc_sarscov2_jn1"
      ]
    },
    {
      "page": "coef.lfq_fit",
      "title": "Extract coefficients from a lineage frequency model",
      "topics": [
        "coef.lfq_fit"
      ]
    },
    {
      "page": "collapse_lineages",
      "title": "Collapse rare lineages into an aggregate group",
      "topics": [
        "collapse_lineages"
      ]
    },
    {
      "page": "compare_models",
      "title": "Compare model engines from backtest scores",
      "topics": [
        "compare_models"
      ]
    },
    {
      "page": "conformal_forecast",
      "title": "Conformal prediction intervals for lineage frequencies",
      "topics": [
        "conformal_forecast"
      ]
    },
    {
      "page": "conformal_forecast_joint",
      "title": "Joint Conformal Prediction on the Simplex",
      "topics": [
        "conformal_forecast_joint"
      ]
    },
    {
      "page": "detection_horizon",
      "title": "Detection horizon for an emerging variant",
      "topics": [
        "detection_horizon"
      ]
    },
    {
      "page": "evaluate_prospective",
      "title": "Pseudo-Prospective Evaluation of Conformal Prediction",
      "topics": [
        "evaluate_prospective"
      ]
    },
    {
      "page": "filter_sparse",
      "title": "Filter sparse time points and lineages",
      "topics": [
        "filter_sparse"
      ]
    },
    {
      "page": "fit_dms_prior",
      "title": "Fit model with Deep Mutational Scanning priors",
      "topics": [
        "fit_dms_prior"
      ]
    },
    {
      "page": "fit_model",
      "title": "Fit a lineage frequency model",
      "topics": [
        "fit_model"
      ]
    },
    {
      "page": "fitness_decomposition",
      "title": "Decompose variant fitness into transmissibility and immune escape",
      "topics": [
        "fitness_decomposition"
      ]
    },
    {
      "page": "forecast",
      "title": "Forecast lineage frequencies (generic)",
      "topics": [
        "forecast"
      ]
    },
    {
      "page": "forecast.lfq_fit",
      "title": "Forecast lineage frequencies",
      "topics": [
        "forecast.lfq_fit"
      ]
    },
    {
      "page": "glance.lfq_fit",
      "title": "Glance at an lfq_fit object",
      "topics": [
        "glance.lfq_fit"
      ]
    },
    {
      "page": "growth_advantage",
      "title": "Extract growth advantage estimates",
      "topics": [
        "growth_advantage"
      ]
    },
    {
      "page": "immune_landscape",
      "title": "Construct a population immunity landscape",
      "topics": [
        "immune_landscape"
      ]
    },
    {
      "page": "influenza_h3n2",
      "title": "Simulated influenza A/H3N2 clade frequency data",
      "topics": [
        "influenza_h3n2"
      ]
    },
    {
      "page": "is_lfq_data",
      "title": "Test if an object is an lfq_data object",
      "topics": [
        "is_lfq_data"
      ]
    },
    {
      "page": "lfq_advantage",
      "title": "Pipe-friendly growth advantage extraction",
      "topics": [
        "lfq_advantage"
      ]
    },
    {
      "page": "lfq_data",
      "title": "Create a lineage frequency data object",
      "topics": [
        "lfq_data"
      ]
    },
    {
      "page": "lfq_engines",
      "title": "List available modeling engines",
      "topics": [
        "lfq_engines"
      ]
    },
    {
      "page": "lfq_fit",
      "title": "Pipe-friendly model fitting",
      "topics": [
        "lfq_fit"
      ]
    },
    {
      "page": "lfq_forecast",
      "title": "Pipe-friendly forecasting",
      "topics": [
        "lfq_forecast"
      ]
    },
    {
      "page": "lfq_score",
      "title": "Pipe-friendly backtesting + scoring",
      "topics": [
        "lfq_score"
      ]
    },
    {
      "page": "lfq_stan_available",
      "title": "Check if 'CmdStan' backend is available",
      "topics": [
        "lfq_stan_available"
      ]
    },
    {
      "page": "lfq_summary",
      "title": "Convert lfq_fit results to a summary tibble",
      "topics": [
        "lfq_summary"
      ]
    },
    {
      "page": "lfq_version",
      "title": "Package version and system information",
      "topics": [
        "lfq_version"
      ]
    },
    {
      "page": "plot_backtest",
      "title": "Plot backtest scores",
      "topics": [
        "plot_backtest"
      ]
    },
    {
      "page": "plot.adaptive_allocation",
      "title": "Plot adaptive allocation",
      "topics": [
        "plot.adaptive_allocation"
      ]
    },
    {
      "page": "plot.calibration_report",
      "title": "Plot calibration diagnostics",
      "topics": [
        "plot.calibration_report"
      ]
    },
    {
      "page": "plot.evoi",
      "title": "Plot EVOI curve",
      "topics": [
        "plot.evoi"
      ]
    },
    {
      "page": "plot.fitness_decomposition",
      "title": "Plot fitness decomposition",
      "topics": [
        "plot.fitness_decomposition"
      ]
    },
    {
      "page": "plot.immune_landscape",
      "title": "Plot population immunity landscape",
      "topics": [
        "plot.immune_landscape"
      ]
    },
    {
      "page": "plot.lfq_prospective",
      "title": "Plot Prospective Evaluation Results",
      "topics": [
        "plot.lfq_prospective"
      ]
    },
    {
      "page": "print.lfq_fit",
      "title": "Print a lineage frequency model",
      "topics": [
        "print.lfq_fit"
      ]
    },
    {
      "page": "read_lineage_counts",
      "title": "Read lineage count data from a CSV file",
      "topics": [
        "read_lineage_counts"
      ]
    },
    {
      "page": "recalibrate",
      "title": "Recalibrate prediction intervals",
      "topics": [
        "recalibrate"
      ]
    },
    {
      "page": "register_engine",
      "title": "Register a custom modeling engine",
      "topics": [
        "register_engine"
      ]
    },
    {
      "page": "sarscov2_us_2022",
      "title": "Simulated SARS-CoV-2 variant frequency data (US, 2022)",
      "topics": [
        "sarscov2_us_2022"
      ]
    },
    {
      "page": "score_forecasts",
      "title": "Score backtest forecast accuracy",
      "topics": [
        "score_forecasts"
      ]
    },
    {
      "page": "selective_pressure",
      "title": "Population-level selective pressure from variant dynamics",
      "topics": [
        "selective_pressure"
      ]
    },
    {
      "page": "sequencing_power",
      "title": "Sequencing power analysis",
      "topics": [
        "sequencing_power"
      ]
    },
    {
      "page": "simulate_dynamics",
      "title": "Simulate lineage frequency dynamics",
      "topics": [
        "simulate_dynamics"
      ]
    },
    {
      "page": "summarize_emerging",
      "title": "Summarize emerging lineages",
      "topics": [
        "summarize_emerging"
      ]
    },
    {
      "page": "summary.lfq_fit",
      "title": "Summarise a lineage frequency model",
      "topics": [
        "summary.lfq_fit"
      ]
    },
    {
      "page": "surveillance_dashboard",
      "title": "Comprehensive surveillance quality dashboard",
      "topics": [
        "surveillance_dashboard"
      ]
    },
    {
      "page": "surveillance_value",
      "title": "Expected Value of Information for genomic surveillance",
      "topics": [
        "surveillance_value"
      ]
    },
    {
      "page": "tidy.fitness_decomposition",
      "title": "Tidy a fitness decomposition",
      "topics": [
        "tidy.fitness_decomposition"
      ]
    },
    {
      "page": "tidy.lfq_fit",
      "title": "Tidy an lfq_fit object",
      "topics": [
        "tidy.lfq_fit"
      ]
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