| 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 |
| 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. |
| Interact.dyvis | Dynamic Visualization of Microbial Interaction Networks |
| mclr.transform | Modified Centered Log-Ratio (MCLR) Transformation |
| 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. |
| plot.DataOppCorVis | Plot Method for DataOppCorVis Objects |
| plot.DataRFClassifier | Plot Method for DataRFClassifier Objects |
| plot.MicrobTiSDA.cluster | Plot Method for MicrobTiSDA Cluster Objects |
| plot.MicrobTiSDA.clusterCut | Plot Method for MicrobTiSDA Cluster Cut Objects |
| plot.MicrobTiSDA.MSERvisual | Plot Method for MicrobTiSDA MSER Visualization Objects |
| plot.MicrobTiSDA.visual | Plot Method for MicrobTiSDA Visual Objects |
| plot.microbTiSDA_dynamic_vis | Plot Method for microbTiSDA Dynamic Visualization Objects |
| plot.RfBiomarker | Plot Method for RfBiomarker Objects |
| Pred.data | Predict Time-Series Data from Fitted Spline Models |
| Pred.data.MESR | Predict Time-Series Data from Fitted Mixed-Effect Spline regression Models |
| 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 | Print MicrobTiSDA objects |
| 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.MSERvisual | Information of visualizations of feature temporal patterns fitted with mixed-effect spline regression models |
| print.MicrobTiSDA.visual | Print the information of those clustered microbial features' temporal patterns |
| print.microbTiSDA_dynamic_vis | Print information of species interaction dynamic visualizations |
| 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 |
| 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 |
| summary.Design | Summary Method for Design Objects |
| summary.FilteredData | Summary Method for FilteredData Object |
| 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.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_dynamic_vis | Summary Method for MicrobTiSDA Dynamic Interaction Visualization 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 |