# Microbiome Time-Series Data Analysis

## Documentation for package ‘MicrobTiSDA’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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