Classify.vis            Visualize Microbial Feature Classification
                        Results Using NMDS
Data.cluster            Cluster OTU Time-Series Data Based on
                        Regression Model prediction and Generate
                        Dendrogram Plots
Data.cluster.cut        Cut and Annotate Dendrogram Based on a
                        Specified Cut-Off Height
Data.filter             Filtering for Microbial Features of Low
                        Abundance and Low Prevalence.
Data.interpolate        Interpolate Time-Series Data Based on Sample
                        Time
Data.opp.cor.vis        Visualize Opposing Temporal profiles among
                        Microbial features.
Data.rf.classifier      Random Forest classification for OTU/ASV Data
Data.trans              Transform Microbial Composition Data.
Data.visual             Visualize Temporal OTU Profiles from Clustered
                        Predicted Data
Data.visual.MESR        Visualize Group-Level OTU Temporal Profiles
                        from Clustered Predicted Data
Design                  Create Design Matrix for Regression Analysis
Interact.dyvis          Dynamic Visualization of Microbial Interaction
                        Networks
OSLO.infant.data        Example dataset 1 - The OSLO term infant gut
                        microbiota dataset.
OSLO.infant.meta        Example dataset 1 - sample metadata.
OSLO.infant.taxa        Example dataset 1 - taxonomic information.
Pred.data               Predict Time-Series Data from Fitted Spline
                        Models
Pred.data.MESR          Predict Time-Series Data from Fitted
                        Mixed-Effect Spline regression Models
Reg.MESR                Fit Mixed-Effects Spline Regression Models with
                        GAM for Microbial Features on Group-Level
Reg.SPLR                Fit Spline Regression Models with Knot
                        Selection
Rf.biomarkers           Select Biomarkers Based on Random Forest
                        Cross-Validation Results
Spec.interact           Species Interaction Inferrences
fujita.data             Example dataset 2 - The in vitro aquatic
                        microbiota dataset.
fujita.meta             Example dataset 2 - sample metadata.
fujita.taxa             Example dataset 2 - taxonomic information.
mclr.transform          Modified Centered Log-Ratio (MCLR)
                        Transformation
plot.DataOppCorVis      Plot Method for DataOppCorVis Objects
plot.DataRFClassifier   Plot Method for DataRFClassifier Objects
plot.MicrobTiSDA.MSERvisual
                        Plot Method for MicrobTiSDA MSER Visualization
                        Objects
plot.MicrobTiSDA.cluster
                        Plot Method for MicrobTiSDA Cluster Objects
plot.MicrobTiSDA.clusterCut
                        Plot Method for MicrobTiSDA Cluster Cut Objects
plot.MicrobTiSDA.visual
                        Plot Method for MicrobTiSDA Visual Objects
plot.RfBiomarker        Plot Method for RfBiomarker Objects
plot.microbTiSDA_dynamic_vis
                        Plot Method for microbTiSDA Dynamic
                        Visualization Objects
preterm.data            Example dataset 3 - The preterm infant gut
                        microbiota dataset.
preterm.meta            Example dataset 3 - sample metadata.
preterm.taxa            Example dataset 3 - taxonomic information.
print.DataOppCorVis     Information of Microbial features with opposite
                        temporal shapes to users selected feature
print.DataRFClassifier
                        Information of the constructed Random Forest
                        classification model
print.Design            Print information of the Design matrix
print.FilteredData      Print Method for FilteredData Object
print.MicrobTiSDA.MSERvisual
                        Information of visualizations of feature
                        temporal patterns fitted with mixed-effect
                        spline regression models
print.MicrobTiSDA.cluster
                        Print the information of fitted temporal
                        profile clusters
print.MicrobTiSDA.clusterCut
                        Print the plot information of user selected
                        feature clustering figures
print.MicrobTiSDA.interpolate
                        Print MicrobTiSDA.interpolate object
print.MicrobTiSDA.visual
                        Print the information of those clustered
                        microbial features' temporal patterns
print.MicrobTiSDA_spline_regression
                        Print information of fitted natural spline
                        regression models
print.PredictedData     Print the information of fitted regression
                        model predicted data
print.PredictedDataMESR
                        Print method for PredictedDataMESR objects
print.RegMESR           Information of the fitted mixed-effect spline
                        regression models
print.TransformedData   Print Method for TransformedData Object
print.microbTiSDA       Print MicrobTiSDA objects
print.microbTiSDA_dynamic_vis
                        Print information of species interaction
                        dynamic visualizations
summary.Design          Summary Method for Design Objects
summary.FilteredData    Summary Method for FilteredData Object
summary.MicrobTiSDA.cluster
                        Summary Method for MicrobTiSDA Cluster Objects
summary.MicrobTiSDA.clusterCut
                        Summary Method for MicrobTiSDA ClusterCut
                        OBjects
summary.MicrobTiSDA.interpolate
                        Summary method for MicrobTiSDA.interpolate
                        objects
summary.MicrobTiSDA.visual
                        Summary Method for MicrobTiSDA Visual Objects
summary.MicrobTiSDA_spline_regression
                        Summary Method for MicrobTiSDA Spline
                        Regression Objects
summary.PredictedData   Summary Method for PredictedData Objects
summary.PredictedDataMESR
                        Summary method for PredictedDataMESR objects
summary.RegMESR         Summary method for RegMESR objects
summary.RfBiomarker     Summary method for RfBiomarker objects
summary.TransformedData
                        Summary Method for TransformedData Objects
summary.microbTiSDA     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.
summary.microbTiSDA_dynamic_vis
                        Summary Method for MicrobTiSDA Dynamic
                        Interaction Visualization Objects
