Microbiome Time-Series Data Analysis
Visualize Microbial Feature Classification Results Using NMDS
Cut and Annotate Dendrogram Based on a Specified Cut-Off Height
Cluster OTU Time-Series Data Based on Regression Model prediction and ...
Filtering for Microbial Features of Low Abundance and Low Prevalence.
Interpolate Time-Series Data Based on Sample Time
Visualize Opposing Temporal profiles among Microbial features.
Random Forest classification for OTU/ASV Data
Transform Microbial Composition Data.
Visualize Group-Level OTU Temporal Profiles from Clustered Predicted D...
Visualize Temporal OTU Profiles from Clustered Predicted Data
Create Design Matrix for Regression Analysis
Dynamic Visualization of Microbial Interaction Networks
Modified Centered Log-Ratio (MCLR) Transformation
Plot Method for DataOppCorVis Objects
Plot Method for DataRFClassifier Objects
Plot Method for microbTiSDA Dynamic Visualization Objects
Plot Method for MicrobTiSDA Cluster Objects
Plot Method for MicrobTiSDA Cluster Cut Objects
Plot Method for MicrobTiSDA MSER Visualization Objects
Plot Method for MicrobTiSDA Visual Objects
Plot Method for RfBiomarker Objects
Predict Time-Series Data from Fitted Mixed-Effect Spline regression Mo...
Predict Time-Series Data from Fitted Spline Models
Information of Microbial features with opposite temporal shapes to use...
Information of the constructed Random Forest classification model
Print information of the Design matrix
Print Method for FilteredData Object
Print information of species interaction dynamic visualizations
Print information of fitted natural spline regression models
Print the information of fitted temporal profile clusters
Print the plot information of user selected feature clustering figures
Print MicrobTiSDA.interpolate object
Information of visualizations of feature temporal patterns fitted with...
Print MicrobTiSDA objects
Print the information of those clustered microbial features' temporal ...
Print the information of fitted regression model predicted data
Print method for PredictedDataMESR objects
Information of the fitted mixed-effect spline regression models
Print Method for TransformedData Object
Fit Mixed-Effects Spline Regression Models with GAM for Microbial Feat...
Fit Spline Regression Models with Knot Selection
Select Biomarkers Based on Random Forest Cross-Validation Results
Species Interaction Inferrences
Summary Method for Design Objects
Summary Method for FilteredData Object
Summary Method for MicrobTiSDA Dynamic Interaction Visualization Objec...
Summary Method for MicrobTiSDA Spline Regression Objects
Summary Method for MicrobTiSDA Cluster Objects
Summary Method for MicrobTiSDA ClusterCut OBjects
Summary method for MicrobTiSDA.interpolate objects
Summary method for MicrobTiSDA objects Provides a structure summary of...
Summary Method for MicrobTiSDA Visual Objects
Summary Method for PredictedData Objects
Summary method for PredictedDataMESR objects
Summary method for RegMESR objects
Summary method for RfBiomarker objects
Summary Method for TransformedData Objects
Provides tools specifically designed for analyzing longitudinal microbiome data. This tool integrates seven functional modules, providing a systematic framework for microbiome time-series analysis. For more details on inferences involving interspecies interactions see Fisher (2014) <doi:10.1371/journal.pone.0102451>. Details on this package are also described in an unpublished manuscript.
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