Microbiome Time-Series Data Analysis


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Documentation for package ‘MicrobTiSDA’ version 0.1.0

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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