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  "Title": "Microbiome Time-Series Data Analysis",
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  "Authors@R": "person(\"Shijia\", \"Li\", email = \"s.li2@uva.nl\", role = c(\"aut\", \"cre\"),comment = c(ORCID = \"0009-0006-6827-5344\"))",
  "Description": "Provides tools specifically designed for analyzing\nlongitudinal microbiome data. This tool integrates seven\nfunctional modules, providing a systematic framework for\nmicrobiome time-series analysis. For more details on inferences\ninvolving interspecies interactions see Fisher (2014)\n<doi:10.1371/journal.pone.0102451>. Details on this package are\nalso described in an unpublished manuscript.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://lishijiagg.r-universe.dev",
  "Date/Publication": "2025-09-29 16:36:59 UTC",
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      "title": "Visualize Microbial Feature Classification Results Using NMDS",
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      "title": "Create Design Matrix for Regression Analysis",
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      "page": "fujita.data",
      "title": "Example dataset 2 - The in vitro aquatic microbiota dataset.",
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      "title": "Example dataset 2 - sample metadata.",
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      "title": "Example dataset 1 - The OSLO term infant gut microbiota dataset.",
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    {
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      "title": "Example dataset 1 - sample metadata.",
      "topics": [
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      "page": "OSLO.infant.taxa",
      "title": "Example dataset 1 - taxonomic information.",
      "topics": [
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      "page": "plot.DataOppCorVis",
      "title": "Plot Method for DataOppCorVis Objects",
      "topics": [
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      "page": "plot.DataRFClassifier",
      "title": "Plot Method for DataRFClassifier Objects",
      "topics": [
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    },
    {
      "page": "plot.microbTiSDA_dynamic_vis",
      "title": "Plot Method for microbTiSDA Dynamic Visualization Objects",
      "topics": [
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    },
    {
      "page": "plot.MicrobTiSDA.cluster",
      "title": "Plot Method for MicrobTiSDA Cluster Objects",
      "topics": [
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    },
    {
      "page": "plot.MicrobTiSDA.clusterCut",
      "title": "Plot Method for MicrobTiSDA Cluster Cut Objects",
      "topics": [
        "plot.MicrobTiSDA.clusterCut"
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    },
    {
      "page": "plot.MicrobTiSDA.MSERvisual",
      "title": "Plot Method for MicrobTiSDA MSER Visualization Objects",
      "topics": [
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    {
      "page": "plot.MicrobTiSDA.visual",
      "title": "Plot Method for MicrobTiSDA Visual Objects",
      "topics": [
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    {
      "page": "plot.RfBiomarker",
      "title": "Plot Method for RfBiomarker Objects",
      "topics": [
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    {
      "page": "Pred.data",
      "title": "Predict Time-Series Data from Fitted Spline Models",
      "topics": [
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    },
    {
      "page": "Pred.data.MESR",
      "title": "Predict Time-Series Data from Fitted Mixed-Effect Spline regression Models",
      "topics": [
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    {
      "page": "preterm.data",
      "title": "Example dataset 3 - The preterm infant gut microbiota dataset.",
      "topics": [
        "preterm.data"
      ]
    },
    {
      "page": "preterm.meta",
      "title": "Example dataset 3 - sample metadata.",
      "topics": [
        "preterm.meta"
      ]
    },
    {
      "page": "preterm.taxa",
      "title": "Example dataset 3 - taxonomic information.",
      "topics": [
        "preterm.taxa"
      ]
    },
    {
      "page": "print.DataOppCorVis",
      "title": "Information of Microbial features with opposite temporal shapes to users selected feature",
      "topics": [
        "print.DataOppCorVis"
      ]
    },
    {
      "page": "print.DataRFClassifier",
      "title": "Information of the constructed Random Forest classification model",
      "topics": [
        "print.DataRFClassifier"
      ]
    },
    {
      "page": "print.Design",
      "title": "Print information of the Design matrix",
      "topics": [
        "print.Design"
      ]
    },
    {
      "page": "print.FilteredData",
      "title": "Print Method for FilteredData Object",
      "topics": [
        "print.FilteredData"
      ]
    },
    {
      "page": "print.microbTiSDA",
      "title": "Print MicrobTiSDA objects",
      "topics": [
        "print.microbTiSDA"
      ]
    },
    {
      "page": "print.microbTiSDA_dynamic_vis",
      "title": "Print information of species interaction dynamic visualizations",
      "topics": [
        "print.microbTiSDA_dynamic_vis"
      ]
    },
    {
      "page": "print.MicrobTiSDA_spline_regression",
      "title": "Print information of fitted natural spline regression models",
      "topics": [
        "print.MicrobTiSDA_spline_regression"
      ]
    },
    {
      "page": "print.MicrobTiSDA.cluster",
      "title": "Print the information of fitted temporal profile clusters",
      "topics": [
        "print.MicrobTiSDA.cluster"
      ]
    },
    {
      "page": "print.MicrobTiSDA.clusterCut",
      "title": "Print the plot information of user selected feature clustering figures",
      "topics": [
        "print.MicrobTiSDA.clusterCut"
      ]
    },
    {
      "page": "print.MicrobTiSDA.interpolate",
      "title": "Print MicrobTiSDA.interpolate object",
      "topics": [
        "print.MicrobTiSDA.interpolate"
      ]
    },
    {
      "page": "print.MicrobTiSDA.MSERvisual",
      "title": "Information of visualizations of feature temporal patterns fitted with mixed-effect spline regression models",
      "topics": [
        "print.MicrobTiSDA.MSERvisual"
      ]
    },
    {
      "page": "print.MicrobTiSDA.visual",
      "title": "Print the information of those clustered microbial features' temporal patterns",
      "topics": [
        "print.MicrobTiSDA.visual"
      ]
    },
    {
      "page": "print.PredictedData",
      "title": "Print the information of fitted regression model predicted data",
      "topics": [
        "print.PredictedData"
      ]
    },
    {
      "page": "print.PredictedDataMESR",
      "title": "Print method for PredictedDataMESR objects",
      "topics": [
        "print.PredictedDataMESR"
      ]
    },
    {
      "page": "print.RegMESR",
      "title": "Information of the fitted mixed-effect spline regression models",
      "topics": [
        "print.RegMESR"
      ]
    },
    {
      "page": "print.TransformedData",
      "title": "Print Method for TransformedData Object",
      "topics": [
        "print.TransformedData"
      ]
    },
    {
      "page": "Reg.MESR",
      "title": "Fit Mixed-Effects Spline Regression Models with GAM for Microbial Features on Group-Level",
      "topics": [
        "Reg.MESR"
      ]
    },
    {
      "page": "Reg.SPLR",
      "title": "Fit Spline Regression Models with Knot Selection",
      "topics": [
        "Reg.SPLR"
      ]
    },
    {
      "page": "Rf.biomarkers",
      "title": "Select Biomarkers Based on Random Forest Cross-Validation Results",
      "topics": [
        "Rf.biomarkers"
      ]
    },
    {
      "page": "Spec.interact",
      "title": "Species Interaction Inferrences",
      "topics": [
        "Spec.interact"
      ]
    },
    {
      "page": "summary.Design",
      "title": "Summary Method for Design Objects",
      "topics": [
        "summary.Design"
      ]
    },
    {
      "page": "summary.FilteredData",
      "title": "Summary Method for FilteredData Object",
      "topics": [
        "summary.FilteredData"
      ]
    },
    {
      "page": "summary.microbTiSDA",
      "title": "Summary method for MicrobTiSDA objects Provides a structure summary of a 'microbTiSDA' object, including its parameters and results. It prints object class, parameters settings, number of result groups/items, and previews of tabular of list-based result elements.",
      "topics": [
        "summary.microbTiSDA"
      ]
    },
    {
      "page": "summary.microbTiSDA_dynamic_vis",
      "title": "Summary Method for MicrobTiSDA Dynamic Interaction Visualization Objects",
      "topics": [
        "summary.microbTiSDA_dynamic_vis"
      ]
    },
    {
      "page": "summary.MicrobTiSDA_spline_regression",
      "title": "Summary Method for MicrobTiSDA Spline Regression Objects",
      "topics": [
        "summary.MicrobTiSDA_spline_regression"
      ]
    },
    {
      "page": "summary.MicrobTiSDA.cluster",
      "title": "Summary Method for MicrobTiSDA Cluster Objects",
      "topics": [
        "summary.MicrobTiSDA.cluster"
      ]
    },
    {
      "page": "summary.MicrobTiSDA.clusterCut",
      "title": "Summary Method for MicrobTiSDA ClusterCut OBjects",
      "topics": [
        "summary.MicrobTiSDA.clusterCut"
      ]
    },
    {
      "page": "summary.MicrobTiSDA.interpolate",
      "title": "Summary method for MicrobTiSDA.interpolate objects",
      "topics": [
        "summary.MicrobTiSDA.interpolate"
      ]
    },
    {
      "page": "summary.MicrobTiSDA.visual",
      "title": "Summary Method for MicrobTiSDA Visual Objects",
      "topics": [
        "summary.MicrobTiSDA.visual"
      ]
    },
    {
      "page": "summary.PredictedData",
      "title": "Summary Method for PredictedData Objects",
      "topics": [
        "summary.PredictedData"
      ]
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    {
      "page": "summary.PredictedDataMESR",
      "title": "Summary method for PredictedDataMESR objects",
      "topics": [
        "summary.PredictedDataMESR"
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    },
    {
      "page": "summary.RegMESR",
      "title": "Summary method for RegMESR objects",
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        "summary.RegMESR"
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      "title": "Summary method for RfBiomarker objects",
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    {
      "page": "summary.TransformedData",
      "title": "Summary Method for TransformedData Objects",
      "topics": [
        "summary.TransformedData"
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        "Case study 1: Infant gut microbiome dataset",
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      "created": "2025-08-27 19:14:52",
      "modified": "2025-08-30 17:40:04",
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